Lysm Receptor-like Kinases To Improve Plant Defense Response Against Fungal Pathogens

  *US08097771B2*
  US008097771B2                                 
(12)United States Patent(10)Patent No.: US 8,097,771 B2
 Wan et al. (45) Date of Patent:Jan.  17, 2012

(54)LysM receptor-like kinases to improve plant defense response against fungal pathogens 
    
(75)Inventors: Jinrong Wan,  Columbia, MO (US); 
  Gary Stacey,  Columbia, MO (US); 
  Minviluz Stacey,  Columbia, MO (US); 
  Xuecheng Zhang,  Columbia, MO (US) 
(73)Assignee:The Curators Of The University Of Missouri,  Columbia, MO (US), Type: US Company 
(*)Notice: Subject to any disclaimer, the term of this patent is extended or adjusted under 35 U.S.C. 154(b) by 313 days. 
(21)Appl. No.: 11/835,328 
(22)Filed: Aug.  7, 2007 
(65)Prior Publication Data 
 US 2008/0057093 A1 Mar.  6, 2008 
 Related U.S. Patent Documents 
(60)Provisional application No. 60/836,084, filed on Aug.  7, 2006.
 
(51)Int. Cl. A01H 005/00 (20060101); A01H 001/00 (20060101); C12N 015/09 (20060101); C12N 015/82 (20060101)
(52)U.S. Cl. 800/279; 800/278; 800/298; 800/312; 800/306; 435/468
(58)Field of Search  None

 
(56)References Cited
 
 U.S. PATENT DOCUMENTS
 2006//0150283  A1*7/2006    Alexandrov et al. 800/288
 2007//0275464  A1*11/2007    Kaku et al. 435/410

 
 FOREIGN PATENT DOCUMENTS 
 
       WO       WO 20/05003338                         1/2005      

 OTHER PUBLICATIONS
  
  Arrighi, JB et al “The Medicago truncatula Lysine Motif-Receptor-Like Kinase Gene Family Includes NFP and New nodule-Expressed Genes” Plant Physiol 142, Sep. 2006 pp. 265-279.
  Bulawa, C.E., et al “Attenuated virulence of chitin-deficient mutants of Candida albicans” Proc. Natl. Acad. Sci. U.S.A. 92 (Nov. 1995) pp. 10570-10574.
  Chisholm, S. T., et al. “Host-Microbe Interactions: Shaping the Evolution of the Plant Immune Response” Cell 124 (Feb. 2006) pp. 803-814.
  Clamp M., et al. “The Jalview Java alignment editor” (2004) Bioinformatics 20(3): 426-427.
  Day, R.B. et al. “Binding Site For Chitin Oligosaccharides in the Soybean Plasma Membrane” Plant Physiol. (Jul. 2001) 126, pp. 1162-1173.
  Eddy, S.R. “Profile hidden Markov models” Bioinformatics (1998) vol. 14, No. 9: pp. 755-763.
  Felsenstein, J. “PHYLIP (Phylogeny Inference Package)”, Ed 3.6. (2000) University of Washington, Seattle; http://evolution.genetics.washington.edu/phylip/general.html; 1 page.
  Gomez-Gomez, L. & Boller, T; “FLS2: An LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis”; T. Mol. Cell (2000) 5, pp. 1003-1011.
  Goring, D. R., Walker, J. C. “Self-Rejection—A New Kinase Connection” Plant Science 303, pp. 1474-1475 (Mar. 2004).
  Ito, Y., Kaku, H., Shibuya, N. “Identification of a high-affinity binding protein for N-acetylchitooligosaccharide elicgtor in the plasma membrane of suspension-cultured rice cells by affinity labeling” Plant J. 12, pp. 347-356 (1997).
  Joris, B. “Modular design of the Enterococcus hirae muramidase-2 and Streptococcus faecalis autolysin” FEMS Microbiol. Lett. 91, pp. 257-264 (1992).
  Schmidt, H.A. et al. “Tree-Puzzle: maximum likelihood phylogenetic analysis using quartets and parallel computing” Bioinformatics 18: 502-504 (2002).
  Kaku, H. et al. “Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor” Proc. Natl. Acad. Sci. U.S.A. vol. 103, pp. 11086-11091 (Jul. 2006).
  Limpens, E. et al. “LysM Domain Receptor Kinases Regulating Rhizobial Nod Factor-Induced Infection” Science 302, 630-633 (Oct. 2003).
  Libault, M., et al. “Identification of 118 Arabidopsis Transcription Factor and 30 Ubiquitin-Ligase Genes Responding to Chitin, a Plant-Defense Elicitor. Molecular Plant-Microbe Interactions”, vol. 20, No. 8, 2007, pp. 900-911.
  Madsen, EB; et al. “A receptor kinase gene of the LysM type is involved in legume perception of rhizobial signals” Nature 425 (Oct. 2003) 637-640.
  Nürnberger, T. & Kemmerling. B. “Receptor protein kinases—pattern recognition receptors in plant immunity” Trends Plant Sci. vol. 11 No. 11, 519-522 (2006).
  Okada, M.,et al. “High-Affinity Binding Proteins for N-Acetylchitooligosaccharide Elicitor in the Plasma Membranes from Wheat, Barley and Carrot Cells: Conserved Presence and Correlation with the Responsiveness to the Elicitor” Plant Cell Physiol. 43, 505-512 (2002).
  Passarinho, P. et al. “Arabidopsis Chitinases: A Genomic Survey” The Arabidopsis Book, American Society of Plant Biologists (2002) pp. 1-25.
  Radutoiu, S. et al. “Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases” (Oct. 2003) Nature 425: pp. 585-592.
  Ramonell, K., et al. “Microarray analysis of chitin elicitation in Arabidopsis thaliana” Mol. Plant Pathol. (2002) 3 (1): 301-311.
  Ramonell K., et al “Loss-of-function mutations in chitin responsive genes show increased susceptibility to the powdery mildew pathogen, Erysiphe cichoracearum” )2005) Plant Physiol. 138: 1027-1036.
  Shibuya, N., Minami, E. “Oligosaccharide signaling for defence responses in plant” Physiol. Mol. Plant Pathol. 59, 223-233 (2001).
  Soulie, M. C. et al., Botrytis cineria virulence is drastically reduced after disruption of chitin synthase class III gene (Bcchs3a) Cellular Microbiol. 8(8), 1310-1321 (2006).
  Stacey, G, & Shibuya, N. “Chitin recognition in rice and legumes” (1997) Plant and Soil 194: 161-169.
  Stacey, G et al., “Genetics and functional genomics of legume nodulation” Curr. Opin. in Plant. Biol. 9, 110-121 (2006).
  Tanabe, S., et al., “Induction of Resistance Against Rice Blast Fungus in Rice Plants Treated with a Potent Elicitor, N-Acetylchitooligosaccharide” Biosci. Biotechnol. Biochem. (2006) 70, pp. 1599-1605.
  Thompson, J.D., et al. “The Clustal-X windows interface—flexible strategies for multiple sequence alignment aided by quality analysis tools” (1997) Nucleic Acids Research 25: 4876-4882.
  Wan, J., et al. “Activation of a mitogen-activated protein kinase pathway in Arabidopsis by chitin” (2004) Mol. Plant Pathol. 5(1): 125-135.
  Yang, Z. Paml: a program package for phylogenetic analysis by maximum likelihood. (1997) Comput Appl Biosci 13: 555-556.
  Zhang, B. et al. “Characterization of Early, Chitin-Induced Gene Expression in Arabidopsis” Mol. Plant-Microbe Int. vol. 15, No. 9 (2002) pp. 963-970.
  Zhang, X.-C. et al., Molecular Evolution of Lysin Motif-Type Receptor-Like Kinases in Plants; Plant Physiol. 144, 623-636 (Jun. 2007).
  Zmasek, C.M. & Eddy, S.R. (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17: 383-384.
  PCTUS/2007/075398 Invitation to Pay Additional Fees and Partial Search Report mailed Sep. 25, 2008.
  Database Geneseq “Lotus Japonicus NFR1 gene derived 2187bp region”, Apr. 7, 2005, 2 pages.
  Rosso, M.G. et al., “An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics” Plant Molecular Biol., Sep. 2003, pp. 247-259.
 
 
     * cited by examiner
 
     Primary Examiner —Medina A Ibrahim
     Art Unit — 1638
     Exemplary claim number — 1
 
(74)Attorney, Agent, or Firm — Lathrop & Gage LLP

(57)

Abstract

Perception of chitin fragments (chitooligosaccharides) is an important first step in plant defense response against fungal pathogen. LysM receptor-like kinases (LysM RLKs) are instrumental in this perception process. LysM RLKs also play a role in activating transcription of chitin-responsive genes (CRGs) in plants. Mutations in the LysM kinase receptor genes or the downstream CRGs may affect the fungal susceptibility of a plant. Mutations in LysM RLKs or transgenes carrying the same may be beneficial in imparting resistance against fungal pathogens.
17 Claims, 22 Drawing Sheets, and 43 Figures


[0001] This application claims priority to U.S. provisional patent application Ser. No. 60/836,084 filed on Aug. 7, 2006.

GOVERNMENT INTERESTS

[0002] This work was funded in part by a grant from the United States Department of Energy, Energy Biosciences Program, Office of Basic Energy Sciences (grant number DE-FG02-02ER15309). The United States government may have certain rights in the invention disclosed herein.

SEQUENCE LISTING

[0003] This application is accompanied by a sequence listing that accurately reproduces the sequences described herein.

BACKGROUND

[0004] This disclosure relates to the use of molecular genetic technology involving LysM receptor kinase family genes and the expression or nonexpression thereof to modulate plant defense responses, especially against fungal pathogens.
[0005] Fungal disease causes significant agricultural losses in the United States and other parts of the world. Control of these pathogens is particularly difficult, often requiring treatment of entire fields with biocidal compounds. Although effective, increasing concern about the environmental and economic costs of such treatments require the need for alternative control methods.
[0006] Phakopsora pachyrhizi is a fungus that causes a rust disease of soybean (Glycine max), also known as Asian Soybean Rust. The pathogen has spread from Asia to all other soybean production regions in the world, and is reported to have arrived in the United States in the fall of 2004. At present, there is no known durable resistance available in any soybean varieties. Uromyces appendiculatus is a fungus that causes rust on bean (Phaseolus vulgaris). Breeders are working to identify genes in bean that can be manipulated for rust resistance. United States soybean producers have anticipated the arrival of P. pachyrhizi, the fungus that causes soybean rust, since its reported occurrence in Brazil. The arrival of P. pachyrhizi in the U.S. in late 2004 ended the anticipation, and farmers must now respond to the potential annual occurrence of this new disease. Farmer concerns have been based on reports of losses ranging from 10 to 80% in other regions of the world when control measures were not successfully implemented.
[0007] As rust-inducing fungi, U. appendiculatus and P. pachyrhizi belong to the order Uredinales, within the class Basidiomycetes. U. appendiculatus produces five spore stages on a single host plant. P. pachyrhizi reproduces predominantly by uredospores on a single host plant. Uredospores are responsible for rapid spread of the fungus. P. pachyrhizi can infect dozens of legume species, in addition to soybean.
[0008] Uredospores of U. appendiculatus penetrate through foliar stomatal openings. P. pachyrhizi differs in that germinated uredospores penetrate directly through the leaf epidermal cell layer. Typically, a uredospore that lands on a leaf surface germinates to produce an infection pad (appressorium) that adheres to the surface. In both species, the appressorium produces a hyphal peg that penetrates the plant. After penetration, each fungus develops thread-like structures (hyphae) that grow inter-cellularly through leaf tissues. The hyphae enter host cells without killing them. There, they produce spherical structures (haustoria) that extract nutrients from the living leaf cells. Soon after infection each fungus forms uredia that produce additional spores.
[0009] Soybean producers are particularly concerned because no durable, natural resistance to rust has been discovered after testing more than 18,000 soybean varieties. The pathogen, P. pachyrhizi can potentially infect any cultivar produced. In anticipation of the arrival of the rust pathogen, a great deal of research has been conducted to identify effective fungicides, and emergency governmental clearance for application to soybean has been obtained. Traditional screening and breeding methods have identified no major resistance genes to the aforementioned pathogens, and particularly in the case of U. appendiculatus and P. pachyrhizi.
[0010] Fungicides will likely be the front-line of defense against these and other fungal pathogens for many years until new resistance genes or other forms of resistance are identified. Fungicides have not traditionally been used in most soybean production. Consequently, there is limited information concerning the costs of this disease management practice and its likely economic viability. Widespread use of fungicides may also raise environmental concerns. These concerns have led to variable estimates of the acreage in Missouri and other states that may be shifted from soybean to alternative crops.
[0011] To protect soybean farmers and to ensure that soybean production meets increasing market demand, it is imperative that alternatives to fungicides be developed as rapidly as possible. Biotechnology-based approaches for defense against plant diseases are more preferable due to the minimal use of chemicals and the relative ease of deployment.
[0012] Chitin is a polymer of N-acetyl-D-glucosamine, found in fungal cell walls, insect exoskeletons, and crustacean shells. It has been hypothesized that plant chitinases can degrade chitin in the fungal cell walls to directly affect the viability of the invading fungal pathogen and to release short fragments (chitooligosaccharides) that can act as a general elicitor of plant innate immunity pathways. See e.g., Shibuya et al., 2001 and Stacey et al., 1997. In support of the above hypothesis, purified chitooligosaccharides have been shown to induce various defense responses in plants or cultured cells, such as induction of defense related genes and synthesis of phytoalexin. Shibuya et al., 2001 and Ramonell et al., 2005.
[0013] More particularly, chitooligosaccharides have been shown to induce a large number of genes (including many defense-related genes), and mutations in selected chitooligosaccharide-responsive genes or chitin-responsive genes (CRGs) have been shown to increase the susceptibility of a plant to certain fungal pathogens. See Ramonell et al., 2002; and Ramonell et al., 2005. Taken together, these studies suggest that plants possess a specific system to recognize chitooligosaccharides which, in turn, activate defense genes. See generally, Day et al., 2001; Zhang et al., 2002; Wan et al., 2004; Kaku et al., 2006; and Libault et al., 2007.
[0014] Previous work has reported chitin recognition in rice and legumes. Stacey, G. and N. Shibuya, Plant and Soil 194: 161-169 (1997) The ability of Arabidopsis thaliana to recognize and respond to chitin has also been reported. A variety of genes have been shown to respond to chitin treatment. See e.g., Ramonell et al. Microarray analysis of chitin elicitation in Arabidopsis thaliana. Mol. Plant. Pathol. 3 (1): 301-311 (2002) and Zhang et al., Characterization of Early, Chitin-Induced Gene Expression in Arabidopsis Mol. Plant-Microbe Int. 15: 963-970 (2002) and Wan et al., Activation of a potential mitogen-activated protein kinase pathway in Arabidopsis by chitin. Mol. Plant. Pathol. 5(1): 125-135 (2004).
[0015] More specifically, chitin binding sites or proteins have been previously identified in membrane preparations of a variety of plant cells. Day et al., 2001; Ito et al., 1997; and Okada et al, 2002. More recently, a LysM domain-containing protein (CEBiP) has been shown to be involved in the binding and recognition of chitooligosaccharides in rice. Kaku et al., 2006. The LysM motif was originally identified in bacterial enzymes that degrade cell wall component peptidoglycan, which is structurally similar to chitin. Joris, 1992. Since CEBiP lacks a significant intracellular domain, it likely functions as part of a chitin receptor complex. Kaku et al., 2006. However, no such chitin receptor complexes have been identified.

SUMMARY

[0016] The present disclosure overcomes the problems outlined above and advances the art by providing methods to confer fungal resistance to plants. This disclosure addresses a new biotechnology-based approach to generate rust resistant soybean and to confer rust resistance upon soybean plants. The technology also involves the development and/or deployment of defense peptides against fungal pathogen, such as the Asian soybean rust fungus. The technology similarly applies to other pathogens in plants, such as the field bean (Phaseolus vulgaris) rust pathogen, Uromyces appendiculatus.
[0017] It is hereby disclosed a number of LysM-containing receptor like kinases (“LysM RLKs”) in soybean, as well as in other legume or non-legume plants. The lysine motif (LysM) domain is an ancient and ubiquitous protein module that binds peptidoglycan and structurally related molecules. A genomic survey in a large number of species spanning all kingdoms reveals that the combination of LysM and receptor kinase domains is present exclusively in plants. Table I lists a number of genes encoding LysM containing proteins from both prokaryotes and eukaryotes, along with their accession numbers from GenBank or other databases.
[0018] 
[00001] [TABLE-US-00001]
  TABLE 1
 
  LysM family genes in prokaryotes and eukaryotes
  LysM motif   kingdom   domain     species name   sources   accession number
 
  >AGRT52b   Bacteria   Proteobacteria   alpha-Argobacterium_tumefaciens_C58   UniProt/TrEMBL   Q8UEQ5
        proteobacteria      
  >ANASP1   Bacteria   Cyanobacteria   Nostoc_PCC   UniProt/TrEMBL   Q8YRU0
  >BACAN1a   Bacteria   Firmicutes   Bacillus_anthracis   UniProt/TrEMBL   Q81WS5
  >BACAN2b   Bacteria   Firmicutes   Bacillus_anthracis   UniProt/TrEMBL   Q81Y89
  >BACAN7   Bacteria   Firmicutes   Bacillus_anthracis   UniProt/TrEMBL   Q81SZ3
  >BORPE5   Bacteria   Proteobacteria   Beta-bordetella_pertussis   UniProt/TrEMBL   Q7W0R5
        proteobacteria      
  >BORPE6   Bacteria   Proteobacteria   Beta-bordetella_pertussis   UniProt/TrEMBL   Q7VY72
        proteobacteria      
  >BRAJA1   Bacteria   Proteobacteria   alpha-Bradyrhizobium_japonicum   UniProt/TrEMBL   Q89Y08
        proteobacteria      
  >BRAJA2   Bacteria   Proteobacteria   alpha-Bradyrhizobium_japonicum   UniProt/TrEMBL   Q89XF2
        proteobacteria      
  >BURPS1   Bacteria   Proteobacteria   Beta-Burkholderia_pasudomallei_1710b   UniProt/TrEMBL   Q63LR7
        proteobacteria      
  >BURPS4   Bacteria   Proteobacteria   Beta-Burkholderia_pasudomallei_1710b   UniProt/TrEMBL   Q63TI4
        proteobacteria      
  >BURPS6a   Bacteria   Proteobacteria   Beta-Burkholderia_pasudomallei_1710b   UniProt/TrEMBL   Q63V96
        proteobacteria      
  >CHLAU2   Bacteria   Chloroflexi   Chloroflexus_aurantiacus   UniProt/TrEMBL   Q3E5J5
  >ECOLI6   Bacteria   Proteobacteria   Gama-Escherichia_coli   UniProt/TrEMBL   P75954
        proteobacteria      
  >PELCD5a   Bacteria   Proteobacteria   Delta-Pelobacter_carbinolicus_DSM   UniProt/TrEMBL   Q3A2X4
        proteobacteria      
  >RALSO3   Bacteria   Proteobacteria   Beta-Ralstonia_solanacearum   UniProt/TrEMBL   Q8Y0H0
        proteobacteria      
  >RALSO6   Bacteria   Proteobacteria   Beta-Ralstonia_solanacearum   UniProt/TrEMBL   Q8XZ88
        proteobacteria      
  >RHOPA4   Bacteria   Proteobacteria   Alpha-Rhodopseudomonas_palustris   UniProt/TrEMBL   Q379H8
        proteobacteria      
  >SALCH2   Bacteria   Proteobacteria   Gama-Salmonella_choleraesuis   UniProt/TrEMBL   Q5J4C2
        proteobacteria      
  >SALCH5   Bacteria   Proteobacteria   Gama-Salmonella_choleraesuis   UniProt/TrEMBL   Q57QE0
        proteobacteria      
  >STRCO4   Bacteria   Firmicutes   Actino-Streptomyces_coelicolor   UniProt/TrEMBL   Q9ACX5
        bacteridae      
  >VIBCH4   Bacteria   Proteobacteria   Gama-Vibrio_cholerae   UniProt/TrEMBL   Q9KNA7
        proteobacteria      
  >VIBCH5a   Bacteria   Proteobacteria   Gama-Vibrio_cholerae   UniProt/TrEMBL   Q9KV14
        proteobacteria      
  >WOLSU1a   Bacteria   Proteobacteria   Epsilon-wolinella_succinogenes   UniProt/TrEMBL   Q7M7V0
        proteobacteria      
  >WOLSU1b   Bacteria   Proteobacteria   Epsilon-wolinella_succinogenes   UniProt/TrEMBL   Q7M7V0
        proteobacteria      
  >CAEEL1   Eukaryota   Metazoa   NematodaCaenorhabditis_elegans   UniProt/TrEMBL   P90882
  >CAEEL6   Eukaryota   Metazoa   NematodaCaenorhabditis_elegans   UniProt/TrEMBL   Q93715
  >CHLRE1   Eukaryota   Chlorophyta   Chlamydomonas_reinhardtii   UniProt/TrEMBL   Q9M5B9
  >DICDI2   Eukaryota   Mycetozoa   DictyosteliidaDictyostelium_discoideum   UniProt/TrEMBL   Q54BF7
  >DROME10   Eukaryota   Metazoa   ChordataDrosophila_melanoqaster   UniProt/TrEMBL   Q9V4P7
  >DROME9   Eukaryota   Metazoa   ChordataDrosophila_melanoqaster   UniProt/TrEMBL   Q9VNA1
  >HUMAN1   Eukaryota   Metazoa   ChordataHomo_sapiens   UniProt/TrEMBL   Q5TF95
  >HUMAN7   Eukaryota   Metazoa   ChordataHomo_sapiens   UniProt/TrEMBL   Q7Z3D4
  >MOUSE5   Eukaryota   Metazoa   ChordataMus_musculus   UniProt/TrEMBL   Q99LE3
  >MOUSE9   Eukaryota   Metazoa   ChordataMus_musculus   UniProt/TrEMBL   Q6DFV7
  >XENLA5   Eukaryota   Metazoa   ChordataXenopus_laevis   UniProt/TrEMBL   Q5BJ38
  >AtLYK1b   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g21630
  >AtLYK1c   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g21630
  >AtLYK2   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At3g01840
  >AtLYK3   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At1g51940
  >AtLYK4a   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g23770
  >AtLYK4b   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g23770
  >AtLYK4c   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g23770
  >AtLYK5a   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g33580
  >AtLYK5c   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g33580
  >AtLYP1b   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At1g21880
  >AtLYP2a   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At1g77630
  >AtLYP3a   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g17120
  >AtLYP3b   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At2g17120
  >AtLysMe1   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At3g52790
  >AtLysMe2   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At4g25433
  >AtLysMe3   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At5g62150
  >AtLysMn1   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At1g55000
  >AtLysMn2   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At5g08200
  >AtLysMn3   Eukaryota   Viridiplantae   StreptophytaArabidopsis_thaliana   TAIR   At5g23130
  >GmLYK10b   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2080D08.12
  >GmLYK10c   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2080D08.12
  >GmLYK11   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2042I24.15
  >GmLYK2   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2098N11.15
  >GmLYK4b   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2095P01.22
  >GmLYK4c   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2095P01.22
  >GmLYK8a   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2098N11.2
  >GmLYK8b   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2098N11.2
  >GmLYK9b   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2069O12.22
  >GmLYK9c   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study   GmW2069O12.22
  >GmLYP1b   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLYP2a   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLYP2b   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLYP3a   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLYP3b   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLysMe1   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLysMe2   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLysMe3   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLysMe4   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLysMn1   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLysMn2   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmLysMn3   Eukaryota   Viridiplantae   StreptophytaGlycine_max   TIGR  
  >GmNFR1ab   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study  
  >GmNFR1ac   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study  
  >GmNFR5aa   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study  
  >GmNFR5ab   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study  
  >GmNFR5ac   Eukaryota   Viridiplantae   StreptophytaGlycine_max   this study  
  >MtLYK10a   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC148994_13
          truncatula  
            sequencing  
            resources  
  >MtLYK10b   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC148994_13
          truncatula  
            sequencing  
            resources  
  >MtLYK10c   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC148994_13
          truncatula  
            sequencing  
            resources  
  >MtLYK12b   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC126779_3
          truncatula  
            sequencing  
            resources  
  >MtLYK12c   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC126779_3
          truncatula  
            sequencing  
            resources  
  >MtLYK13a   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC126779_4
          truncatula  
            sequencing  
            resources  
  >MtLYK13b   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC126779_4
          truncatula  
            sequencing  
            resources  
  >MtLYK3b   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatula   Gene Bank   AY372402
  >MtLYK3c   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatula   Gene Bank   AY372402
  >MtLYK9a   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC148241_11
          truncatula  
            sequencing  
            resources  
  >MtLYK9b   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC148241_11
          truncatula  
            sequencing  
            resources  
  >MtLYK9c   Eukaryota   Viridiplantae   StreptophytaMedicago_truncatulaMedicago   AC148241_11
          truncatula  
            sequencing  
            resources  
  >OsLYK2b   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os06g41980
  >OsLYK2c   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os06g41980
  >OsLYK3   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os06g41960
  >OsLYK4b   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os02g09960
  >OsLYK4c   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os02g09960
  >OsLYK5a   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os03g13080
  >OsLYK5c   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os03g13080
  >OsLYK6a   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os11g35330
  >OsLYK6b   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os11g35330
  >OsLYK6c   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os11g35330
  >OsLYP1b   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os03g04110
  >OsLYP2a   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os09g37600
  >OsLYP2b   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os09g37600
  >OsLYP3a   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os06g10660
  >OsLYP3b   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os06g10660
  >OsLYP5b   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os02g53000
  >OsLYP6a   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os11g34570
  >OsLYP6b   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os11g34570
  >OsLysMe1   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os01g57390
  >osLysMe2   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os01g57400
  >OsLysMe3   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os04g48380
  >OsLysMn1   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os03g49250
  >OsLysMn2   Eukaryota   Viridiplantae   StreptophytaOryza_sativa   TIGR   LOC_Os06g51360
  >PtLysMe4   Eukaryota   Viridiplantae   StreptophytaPopulus_trichocarpa   DOE JGI   EUGENE3.00051310
  >PtLysMe8   Eukaryota   Viridiplantae   StreptophytaPopulus_trichocarpa   DOE JGI   EUGENE3.00070396
  >PtLysMe9   Eukaryota   Viridiplantae   StreptophytaPopulus_trichocarpa   DOE JGI   EUGENE3.00110096
  >PtLysMe11   Eukaryota   Viridiplantae   StreptophytaPopulus_trichocarpa   DOE JGI   EUGENE3.00070285
 
[0019] In comparison to the LysM proteins in other kingdoms, plant LYK proteins possess unique features: (1) the combination of LysM and kinase domains exists exclusively in the plant lineage; (2) plant LYK proteins have no more than three LysM motifs; (3) if more than two LysM motifs exist within a single plant LYK protein, they are always distinct from each other at the protein sequence level; and (4) the LysM domain sequences in plant LYK proteins are highly diversified due to different combinations of heterogenous LysM motifs. Based on the sequence phylogenies, LysM motifs (named LYKa, LYKb, and LYKc from the N to the C terminus) in plant LYK proteins largely fall into five clades (FIG. 1A). This distribution of LysM motifs was found in all six plant species studied (i.e. LysM motifs from dicots and rice are clustered together in each clade, suggesting that the diversification event of plant LysM motifs predated the divergence of monocot and dicot plants).
[0020] The LysM motifs from non-kinase plant LysM proteins have also been investigated. These sequences have been retrieved using BLAST searches against genomic sequence databases of Arabidopsis, rice, and poplar and EST sequences of soybean. Based on their subcellular localization predictions and domain arrangements, non-kinase plant LysM proteins may be further categorized into three subgroups, including LysM-type receptor-like proteins (LYPs), extracellular LysM proteins (LysMe), and nonsecretory intracellular LysM proteins (LysMn; FIG. 1B). This grouping will be helpful in understanding the nature of each LysM protein and providing insightful clues to the biological functions.
[0021] FIG. 1B illustrates the general domain structure of different LysM containing proteins. As shown in FIG. 1B, LysM RLKs (also referred to as “LYK”) typically possess one or more LysM domains, a transmembrane domain and a kinase domain. The LysM domain is known for its capability to bind chitin. The transmembrane domain may serve to anchor the LysM RLKs in the membrane of the cells, whereas the kinase domain extends into the cytoplasm where it may phosphorylate specific substrates in the cell. In one embodiment, it is conceivable that the transmembrane domain of an LYK may be replaced with a different transmembrane domain from another LYK, or from another transmembrane protein,
[0022] As shown in FIG. 1 and FIG. 2, LysM domains in plants are highly diversified and that at least six distinct types of LysM motifs exist in plant LysM kinase proteins, which are shown as Types I-V and VII in FIG. 1B. Five additional types of LysM motifs exist in non-kinase plant LysM proteins, designated as Types VI, VIII-XI as shown in FIG. 1B. See also Zhang et al., Plant Physiol. 144, 623-636 (2007), which is hereby expressly incorporated by reference. FIG. 2 shows sequence alignment of representative LysM domains. FIG. 2A shows an alignment of 93 LysM-containing proteins in plants. Shaded areas indicate conserved residues in FIG. 2. FIG. 2B is an alignment of LysM domains from the LYK Group I, which contains LysM motif Types II and IV. FIG. 2C is an alignment of LysM domains from the LYK Group II, which contains LysM motif Types I, II and V. FIG. 2D is an alignment of LysM domains from the LYK Group III, which contains LysM motif Type VII. FIG. 2E is an alignment of LysM domains from the LYP group, which typically contains LysM motif Types VI and VII, or VI and VIII. See also FIG. 1B. FIG. 2F is an alignment of LysM domains from the LysMe group, which typically contains LysM motif Types IX or X. FIG. 2G is an alignment of LysM domains from the LysMn group, which typically contains LysM motif Type XI.
[0023] As predicted by Pfam, LYP proteins have exactly two LysM motifs and LysMe and LysMn proteins have only one LysM motif. Sequence alignments show that, among the 11 types of LysM motifs, motif sequences of LysMn (the motif within LysMn proteins, LysM motif type XI), one group of LysMe (the motif within LysMe proteins, LysM motif type X), and one group of LYPb (the second motif from the N terminus within LYP proteins, LysM motif VII) are extremely conserved. In these motifs, the amino acid identities averaged across the alignments are 91% for LysMe (type X), 86% for LysMn (type XI), and 75% for LYP (type VII). LysMn motif sequences always start with a His and end with a Pro. Similarly, LYPb motif sequences always end with a Pro. LYKa motifs are seven to 10 residues shorter.
[0024] In one aspect of this disclosure, soybean plants may be made resistant to soybean rust where no durable resistance is currently available. Certain soybean strains may be susceptible to rust diseases because they lack a functional signaling pathway that can perceive the existence of chitin or pass such a signal into the plant cell. Other strains may lack certain functional chitin responsive proteins and thus are not capable of mounting successful defenses against the invaders. It is hereby disclosed a methodology whereby a transgene encoding a component of the chitin signaling pathway may be introduced into a plant, such as a soybean plant. Expression of the transgene may enhance the perception of chitin by the transgenic plant, augment subsequent signaling that leads to gene activation inside the cells, and/or increase the capability of effector proteins in fighting the fungal pathogens.
[0025] In another aspect, mutations may be identified, induced or introduced into a plant, such as soybean, in order to obtain a mutant plant that have enhanced chitin perception or response. Certain mutations in LysM RLKs may enhance recognition of chitin by plant cells, whereas some other mutations in LysM RLKs may abolish chitin recognition. Similar situations may apply to other protein involved in fungal defense, including but not limited to the CRGs. The polynucleotide sequences disclosed herein may aid identification, mapping and/or genetic analysis of such mutants.
[0026] In one embodiment, a transgenic plant may be prepared by identifying in a plant one or more genes that contain a LysM receptor kinase family gene with a level of expression that is regulated by treatment of the plant with chitin. Such a plant may then be transformed with one or more LysM receptor kinase genes. The resulting transgenic plant may be challenged with chitin, its derivatives, or a pathogen to confirm an enhanced plant defense response, if desired.
[0027] The same general techniques disclosed herein may be employed in plants other than soybean to help create strains that are resistant to fungal infection. Different plants may be used to effect the transformation, such as soybean, Arabidopsis thaliana, or others. For instance, genes identified in one species may be introduced into another species in order to obtain transgenic plants that have enhanced fungal defense.
[0028] In yet another embodiment, a gene which belongs to the LysM receptor kinase family may be knocked out. Alternatively, a LysM receptor kinase family gene may be overexpressed. The resultant mutant plants may exhibit improved plant defense responses when challenged with chitin or its derivatives, for example, by spraying the leaves with chitin, or when challenged with a chitin-expressing organism.

BRIEF DESCRIPTION OF THE DRAWINGS

[0029] FIG. 1 illustrates the eleven distinct types of LysM motifs in plants. (A) The evolutionary relationships of plant LysM motifs. (B) Subcellular localization and LysM domain structures of LysM proteins in plants.
[0030] FIG. 2 shows a sequence comparison of various plant LysM sequences that were obtained by computerized searching. FIG. 2A shows an alignment of 93 LysM-containing proteins: MtLYK10 (SEQ ID No. 75), MtLYK11 (SEQ ID No. 76), MtLysMe2 (SEQ ID No. 150; HtLYK1 (SEQ ID No. 71); MtLysHe1 (SEQ ID No. 151); AtLYK1 (SEQ ID No. 3); GmLYK2 (SEQ ID No. J6); HtLYK3 (SEQ ID No. 72); HtLYK4 (SEQ ID No. 73); HtLYK2 (SEQ ID No. 152); LjNFR1a (SEQ ID No. 1); PtLysHn8 (SEQ ID No. 153); PtLYK1 (SEQ ID No. 85); GmLYK8 (SEQ ID No. 63); PtLYK3 (SEQ ID No. 87); AtLYK5 (SEQ ID No. 5); GmLYK6 (SEQ ID No. 61); GmLYK4 (SEQ ID No. 58); HtLYK12 (SEQ ID No. 77); PtLYK6 (SEQ ID No. 90); PtLYK9 (SEQ ID No. 93); AtLYK4 (SEQ ID No. 6); OsLYK1 (SEQ ID No. 79); PtLYK5 (SEQ ID No. 89); GnLYK10 (SEQ ID No. 65); PtLYK7 (SEQ ID No. 91); AtLYK2 (SEQ ID No. 4); OsLYK2 (SEQ ID No. 80); PtLYP1 (SEQ ID No. 154); PtLYK4 (SEQ ID No. 88); PtLYK10 (SEQ ID No. 94); GmLYK9 (SEQ ID No. 64); GnNFR5a (SEQ ID No. 59); LjNFR5 (SEQ ID No. 2); PsSYH10 (SEQ ID No. 155); HtLYK13 (SEQ ID No. 78); HtLYK9 (SEQ ID No. 74); PtLYK2 (SEQ ID No. 86); OsLYK3 (SEQ ID No. 81); AtLYK3 (SEQ ID No. 5); PtLYK8 (SEQ ID No. 92); GnLYK11 (SEQ ID No. 66); PtLYP2 (SEQ ID No. 156); PtLYP3 (SEQ ID No. 157); PtLYP6 (SEQ ID No. 158); AtLYP3 (SEQ ID No. 159); GmLYP1 (SEQ ID No. 160); OsLYP1 (SEQ ID No. 161); PtLYP7 (SEQ ID No. 162); PtLYP5 (SEQ ID No. 163); PtLYP4 (SEQ ID No. 164); GmLYP4 (SEQ ID No. 165); GmLYP2 (SEQ ID No. 166); AtLYP2 (SEQ ID No. 167); AtLYP2 (SEQ ID No. 168); GmLYP3 (SEQ ID No. 169); GmLysHe1 (SEQ ID No. 170); MtLysH16 (171); PtLysHe7 (SEQ ID No. 172); GmLysHe2 (SEQ ID No. 173); GmLysHe4 (SEQ ID No. 174); PtLysHe6 (SEQ ID No. 175); GmLysHe3 (SEQ ID No. 176); GmLysHe6 (SEQ ID No. 177); GmLysHe5 (SEQ ID No. 178); PtLysHe3 (SEQ ID No. 179); PtLysHe5 (SEQ ID No. 180); PtLysMe10 (SEQ ID No. 181); AtLysHe3 (SEQ ID No. 182); OsLysHe4 (SEQ ID No. 183); AtLysHe2 (SEQ ID No. 184); AtLysHe1 (SEQ ID No. 185); PtLysHn9 (SEQ ID No. 186); PtLysHn7 (SEQ ID No. 187); PtLysHe8 (SEQ ID No. 188); PtLysMe11 (SEQ ID No. 189); PtLysHe4 (SEQ ID No. 190); GmLysHn2 (SEQ ID No. 191); GmLysHn4 (SEQ ID No. 192); PtLysHn6 (SEQ ID No. 193); OsLysHn3 (SEQ ID No. 194); GmLysHn3 (SEQ ID No. 195); GmLysHn5 (SEQ ID No. 196); AtLysHn2 (SEQ ID No. 197); PtLysMn11 (SEQ ID No. 198); AtLysHn3 (SEQ ID No. 199); GmLysHn1 (SEQ ID No. 200); AtLysHn1 (SEQ ID No. 201); PtLysHn2 (SEQ ID No. 202); PtLysHn1 (SEQ ID No. 203); OsLysHn1 (SEQ ID No. 204); PtLysMn10 (SEQ ID No. 205); and PtLysHe9 (SEQ ID No. 206). FIG. 2B is an alignment of LysM domains from the following proteins: MtLYK3 (SEQ ID No. 72), MtLYK4 (SEQ ID No. 73), MtLYK2 (SEQ ID No. 152), GmNFR1a (SEQ ID No. 54; GmNFR1b (SEQ ID No. 55); LjNFR1a (SEQ ID No. 1); MtLYK1 (SEQ ID No. 71); AtLYK1 (SEQ ID No. 3); GmLYK3 (SEQ ID No. 57); MtLYK3 (SEQ ID No. 72); MtLYK4 (SEQ ID No. 73); MtLYK2 (SEQ ID No. 152); GmNFR1a (SEQ ID No. 54); GmNFR1b (SEQ ID No. 55); LjNFR1a (SEQ ID No. 1); MtLYK1 (SEQ ID No. 71); AtLYK1 (SEQ ID No. 3); and GmLYK3 (SEQ ID No. 57). FIG. 2C is an alignment of LysM domains from GmNFR5a (SEQ ID No. 59); LjNFR5 (SEQ ID No. 2); MtLYK9 (SEQ ID No. 74); PtLYK2 (SEQ ID No. 86); GmLYK10 (SEQ ID No. 65); PtLYK7 (SEQ ID No. 91); AtLYK5 (SEQ ID No. 7); GmLYK8 (SEQ ID No. 63); MtLYK10 (SEQ ID No. 75); MtLYK11 (SEQ ID No. 76); LjLYK4 (SEQ ID No. 69); MtLYK12 (SEQ ID No. 77); GmLYK4 (SEQ ID No. 58); PtLYK6 (SEQ ID No. 90); PtLYK9(SEQ ID No. 93); AtLYK4 (SEQ ID No. 6); PtLYK10 (SEQ ID No. 94); PtLYK4 (SEQ ID No. 88); GmLYK9 (SEQ ID No. 62); MtLYK13 (SEQ ID No. 78); PsSYM10 (SEQ ID No. 155); PtLYK11 (SEQ ID No. 95); GmNFR5b (SEQ ID No. 60); GmNFR5a (SEQ ID No. 59); LjNFR5 (SEQ ID No. 2); MtLYK9 (SEQ ID No. 74); PtLYK2 (SEQ ID No. 86); GmLYK10 (SEQ ID No. 65); PtLYK7 (SEQ ID No. 91); AtLYK5 (SEQ ID No. 7); GmLYK8 (SEQ ID No. 63); MtLYK10 (SEQ ID No. 75); MtLYK11 (SEQ ID No. 76); LyLYK4 (SEQ ID No. 69); MtLYK12 (SEQ ID No. 77); GmLYK4 (SEQ ID No. 58); PtLYK6 (SEQ ID No. 90); PtLYK9 (SEQ ID No. 93); AtLYK4 (SEQ ID No. 6); PtLYK10 (SEQ ID No. 94); PtLYK4 (SEQ ID No. 88); GmLYK9 (SEQ ID No. 64); MtLYK13 (SEQ ID No. 78); PsSYM10 (SEQ ID No. 155); PtLYK11 (SEQ ID No. 95); and GmNFR5b (SEQ ID No. 60). FIG. 2D is an alignment of LysM domains from GmLYK6 (SEQ ID No. 61); PtLYK3 (SEQ ID No. 87); OsLYK1 (SEQ ID No. 79); PtLYK5 (SEQ ID No. 89); AtLYK2 (SEQ ID No. 4); GmLKY11 (SEQ ID No. 66); PtLYK8 (SEQ ID No. 92); AtLYK3 (SEQ ID No. 5); OsLYK2 (SEQ ID No. 80); PtLYK1 (SEQ ID No. 85); OsLYK3 (SEQ ID No. 81). FIG. 2E is an alignment of LysM domains from AtLyP1 (SEQ ID No. 167); AtLYP2 (SEQ ID No. 168); PtLYP5 (SEQ ID No. 163); PtLYP7 (SEQ ID No. 162); PtLYP4 (SEQ ID No. 164); GmLYP4 (SEQ ID No. 165); GmLYP2 (SEQ ID No. 166); OsLYP3 (SEQ ID No. 207); OsLYP5 (SEQ ID No. 208); OsLYP4 (SEQ ID No. 209); GmLYP3 (SEQ ID No. 169); OsLYP1 (SEQ ID No. 161); OsLYP6 (SEQ ID No. 210); OsLYP2 (SEQ ID No. 211); PtLYP2 (SEQ ID No. 156); PtLYP3 (SEQ ID No. 157); AtLYP3 (SEQ ID No. 159); GmLYP1 (SEQ ID No. 160; PtLYP6 (SEQ ID No. 158); and PtLYP1 (SEQ ID No. 154). FIG. 2F is an alignment of LysM domains from GMLYSMe1 (SEQ ID No. 170); PtLysMe7 (SEQ ID No. 172); AtLysMe1 (SEQ ID No. 185); AtLysMe3 (SEQ ID No. 182); GmLysMe4 (SEQ ID No. 174); GmLysMe2 (SEQ ID No. 173); GmLysMe3 (SEQ ID No. 176); GmLysMe5 (SEQ ID No. 178); GmLysMe6 (SEQ ID No. 177); PtLysMe6 (SEQ ID No. 175); PtLysMe3 (SEQ ID No. 179); PtLysMe5 (SEQ ID No. 180); PtLysMe10 (SEQ ID No. 181); OsLysMe4 (SEQ ID No. 183); AtLysMe2 (SEQ ID No. 184); PtLysMe11 (SEQ ID No. 189); PtLysMe8 (SEQ ID No. 188); PtLysMe4 (SEQ ID No. 190); OsLysMe2 (SEQ ID No. 212); OsLysMe1 (SEQ ID No. 213); PtLysMe9 (SEQ ID No. 206); OsLysMe3 (SEQ ID No. 214). FIG. 2G is an alignment of LysM domains from AtLYSMn1 (SEQ ID No. 201); AtLysMn1 (SEQ ID No. 201); GmLysMn1 (SEQ ID No. 200); PtLysMn2 (SEQ ID No. 202); PtLysMn1 (SEQ ID No. 203); OsLysMn1 (SEQ ID No. 204); GmLysMn2 (SEQ ID No. 191); GmLysMn4 (SEQ ID No. 192); PtLysMn6 (SEQ ID No. 193); OsLysMn3 (SEQ ID No. 194); GmLysMn3 (SEQ ID No. 195); GmLysMn5 (SEQ ID No. 196); AtLysMn2 (SEQ ID No. 197); PtLysMn11 (SEQ ID No. 198); AtLysMn3 (SEQ ID No. 199); OsLysMn2 (SEQ ID No. 215); PtLysMn10 (SEQ ID No. 205); PtLysMn7 (SEQ ID No. 187); PtLysMn9 (SEQ ID No. 186); and PtLysMn8 (SEQ ID No. 153).
[0031] FIG. 3 presents experimental results showing enhanced expression of the defense genes PR1 and PR-2 in the LysM receptor kinase mutant L3.
[0032] FIG. 4A shows an improved defense response of the L3 mutant to infection by the necotrophic fungus Botrytis cinerea.
[0033] FIG. 4B shows an improved defense response of the L3 mutant to infection by Pseudomonas syringae.
[0034] FIG. 5 shows a model of the involvement of the LysM receptor kinases in plant defense.
[0035] FIG. 6 shows that the knockout of the AtLysM RLK1 gene blocks the induction of the selected chitooligosaccharide-responsive genes (CRGs).
[0036] FIG. 7 shows disruption of the AtLysM RLK1 gene expression by the T-DNA insertions. WT=Wild-type Col-0; Mu=AtLysM RLK1 mutant. Actin-2 was used as an internal control.
[0037] FIG. 8 shows restoration of CRGs in the AtLysM RLK1 mutant by the ectopic expression of the AtLysM RLK1 gene. Actin-2 serves as an internal control.
[0038] FIG. 9 shows the tissue expression pattern of the AtLysM RLK1 gene. Actin-2 serves as an internal control.
[0039] FIG. 10 shows that AtLysM RLK1 is induced by chitooligosaccharides, but not by the flagellin-derived flg22 peptide.
[0040] FIG. 11 shows that the T-DNA insertions in the AtLysM RLK1 gene block the induction of virtually all CRGs.
[0041] FIG. 12 shows the functional categorization by annotations of 909 CRGs-GO Biological Process.
[0042] FIG. 13 shows that the AtLysM RLK1 mutant is more susceptible to fungal pathogens than wild-type plants and that exogenously applied chitooligosaccharides enhances resistance in the wild-type plants, but not in the mutant.
[0043] FIG. 14 shows that the selected CRGs are still induced in the AtLysM RLK1 mutant by a fungal pathogen, but to a reduced level.
[0044] FIG. 15 shows that mutations in the legume Nod signal receptor genes NFR1 and NFR5 do not affect the induction of the selected CRGs in Lotus japonicus.
[0045] FIG. 16 shows that the mutation in the AtLysM RLK1 gene does not affect other defense-related pathways.
[0046] FIG. 17 shows that the AtLysM RLK1 mutation does not block the induction of flagellin-responsive genes.
[0047] FIG. 18 shows similarity between the LysM receptor kinase-like genes in a variety of plants.
[0048] FIG. 19 shows the expression analysis of GmLysM receptor-like kinases in response to white-mold pathogen.
[0049] FIG. 20 shows the expression analysis of GmLysM receptor-like kinases in chitin-treated leaves.
[0050] FIG. 21 shows the results of tissue-specific expression analysis of LysM receptor-like kinases in soybean, M. truncatula, and rice.

DETAILED DESCRIPTION

[0051] The following detailed description is provided to aid those skilled in the art in practicing the present instrumentalities. Even so, this detailed description should not be construed to unduly limit the present invention as modifications and variations in the embodiments discussed herein can be made by those of ordinary skill in the art without departing from the spirit or scope of the present inventive discovery.
[0052] LysM domain-containing receptor-like kinases (“LysM RLKs,” “LYK” or “LysM receptor kinase family proteins”), such as NFR1 and NFR5 in legumes, have been shown to be critical for the perception of modified chitooligosaccharides—Nod signals—in the legume-rhizobial symbiotic nodulation process. See Limpens et al., 2003; Madsen et al., 2003; and Radutoiu et al., 2003. Similar LysM receptor kinase family genes (or LysM RLK genes) are also present in non-leguminous plants. Zhang et al., 2007. For example, five LysM RLK genes have been identified in the model plant Arabidopsis thaliana. LysM domain-containing proteins are also found in animals but LysM RLKs appear to be unique to plants. Zhang et al., 2007.
[0053] For purpose of this disclosure, a “LysM receptor kinase family gene” (LysM RLK gene) is any gene that encodes a protein with at least a Lysine motif (LysM) domain, a kinase domain and a transmembrane domain between the LysM and the kinase domain as shown in FIG. 1. In one aspect, the kinase domain is a serine/threonine kinase domain. A gene may be shown to belong to different subfamilies of LysM genes by sequence comparison with a known LysM gene, as exemplified by the sequence alignment of different LysM containing proteins in FIG. 2. This classification may be decided by a predetermined level of sequence identity in one or more functional domains of a known LysM receptor kinase, such as 70%, 80%, 90%, 95%, 96%, 97%, 98% 99% or 100% sequence identity with respect to a functional domain or an entire coding sequence.
[0054] Two sequences may be said to have “substantial sequence similarity” when they have a degree of sequence identity that persons of ordinary skill in the art may expect them to provide similar functionality; or in some cases, a person of skills in the art may expect individual domains within the sequences to possess similar functionality due to the sequence similarity. As measured by computer algorithms that are designed to quantitate sequence identity or similarity, this may be at least 70% identity, or more preferably, this may be any value from 90% and up, such as 95%, 96%, 97%, 98% or 99% identity, with 100% identity being an exact match. When two sequences are of different length, the sequence identity refers to cumulative sequence identity between those segments of both sequences that when aligned generate the best possible matches of individual residues throughout the full length of the sequences. In general, higher sequence similarity between two sequences indicates that the two sequences are more likely to perform similar, if not identical function.
[0055] The term CRGs (or CRG) refers to genes that may be activated upon perception of chitin or its derivatives by plant cells. Examples of CRGs may include MPK3, WRKY22, WRKY29, WRKY33, WRKY53 and any other genes whose expression levels may be up- or down-regulated when the cells are exposed to chitin or its derivatives. In one embodiment, genetic engineering may be used to render certain CRGs constitutively expressed, or, more preferably, expression of CRGs may be placed under control of certain regulatory elements such that CRG proteins may be expressed before fungi have been detected by the plant.
[0056] Under certain circumstances, it may be desirable to generate mutations in the coding sequence of certain genes, such as the LYK genes or CRGs. One of skills in the art may recognize that certain sequence variations may not significantly affect the functionality of a DNA or RNA molecule, or a protein. For instance, one may align and compare the sequences of the LYK family genes, as shown in FIG. 2, to determine which residues may be less conservative than others. The term “conservative” is used to depict those nucleotide or amino acid residues that have not undergone significant changes over the course of evolution. The conservative residues are typically shown as matching residues in a multi-sequence alignment. Guided by such an alignment, one may substitute those residues that are less conservative without compromising the functionality of the genes, RNAs, or proteins. Such manipulations of polynucleotide or polypeptide molecules are within the scope of this disclosure.
[0057] A “functional” LysM receptor kinase refers to a protein encoded by one of the LysM receptor kinase family genes that is capable of performing the full function that is typically performed by other LysM receptor kinase family proteins.
[0058] “Secretion sequence” means a sequence that directs newly synthesized secretory or membrane proteins to and through membranes of the endoplasmic reticulum, or from the cytoplasm to the periplasm across the inner membrane of bacteria, or from the matrix of mitochondria into the inner space, or from the stroma of chloroplasts into the thylakoid. Fusion of such a sequence to a gene that is to be expressed in a heterologous host ensures secretion of the recombinant protein from the host cell.
[0059] A “recombinant polynucleotide” means a polynucleotide that is free of one or both of the nucleotide sequences which flank the polynucleotide in the naturally-occurring genome of the organism from which the polynucleotide is derived. The term includes, for example, a polynucleotide or fragment thereof that is incorporated into a vector or expression cassette; into an autonomously replicating plasmid or virus; into the genomic DNA of a prokaryote or eukaryote; or that exists as a separate molecule independent of other polynucleotides. It also includes a recombinant polynucleotide that is part of a hybrid polynucleotide, for example, one encoding a polypeptide sequence.
[0060] “PCR” means polymerase chain reaction.
[0061] As used herein “polynucleotide” and “oligonucleotide” are used interchangeably and refer to a polymeric (2 or more monomers) form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Although nucleotides are usually joined by phosphodiester linkages, the term also includes polymeric nucleotides containing neutral amide backbone linkages composed of aminoethyl glycine units. This term refers only to the primary structure of the molecule. Thus, this term includes double- and single-stranded DNA and RNA. It also includes known types of modifications, for example, labels, methylation, “caps”, substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.), those containing pendant moieties, such as, for example, proteins (including for e.g., nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotide. Polynucleotides include both sense and antisense strands.
[0062] “Sequence” means the linear order in which monomers occur in a polymer, for example, the order of amino acids in a polypeptide or the order of nucleotides in a polynucleotide.
[0063] “Peptide,” “Protein” and “Polypeptide” are used interchangeably and mean a compound that consists of two or more amino acids that are linked by means of peptide bonds.
[0064] “Recombinant protein” means that the protein, whether comprising a native or mutant primary amino acid sequence, is obtained by expression of a gene carried by a recombinant DNA molecule in a cell other than the cell in which that gene and/or protein is naturally found. In other words, the gene is heterologous to the host in which it is expressed. It should be noted that any alteration of a gene, including the addition of a polynucleotide encoding an affinity purification moiety, makes that gene unnatural for the purposes of this definition, and thus that gene cannot be “naturally” found in any cell.
[0065] A “non-immunoglobulin peptide” means a peptide which is not an immunoglobulin, a recognized region of an immunoglobulin, or contains a region of an immunoglobulin. For example, a single chain variable region of an immunoglobulin would be excluded from this definition.
[0066] “Substantially pure” or “substantially purified” means that the substance is free from other contaminating proteins, nucleic acids, and other biologicals derived from the original source organism. Purity may be assayed by standard methods, and will ordinarily be at least about 40% pure, more ordinarily at least about 50% pure, generally at least about 60% pure, more generally at least about 70% pure, often at least about 75% pure, more often at least about 80% pure, typically at least about 85% pure, more typically at least about 90% pure, preferably at least about 95% pure, more preferably at least about 98% pure, and in even more preferred embodiments, at least 99% pure. The analysis may be weight or molar percentages, evaluated, e.g., by gel staining, spectrophotometry, or terminus labeling etc.
[0067] A “transgene” refers to a coding sequence that has been introduced into a host organism, which may be referred to as a transgenic organism, e.g., a transgenic animal, or a transgenic plant, when the transgene has been successfully introduced into said organism. Typically, a transgene is introduced into a host organism so that the coding sequence may be transcribed into RNA or, in most cases, be further expressed as a polypeptide. The introduction of a transgene into a host organism and subsequent expression of the transgene is generally known as a transgenic process. A transgenic plant may refer to a whole plant, or a tissue of a plant, such as a seed, that contains a transgene and has a potential to be grow into a plant.
[0068] A “mutation,” as used herein, means a change in the nucleotide sequence of a polynucleotide molecule or a change in the amino acid sequence of a polypeptide. The molecule carrying such a change may be referred to as a mutant molecule, and the change is typically measured by comparing the sequence of the mutant molecule with that of the polynucleotide or polypeptide molecule from which the mutant molecule is derived. An organism with a mutation in one of its endogenous genes may be called a mutant.
[0069] A mutation in a gene may occur on either the coding region or the non-coding region of the gene. A mutated copy of a gene may be said to be “derived” from a endogenous copy of the same gene when one or more spontaneous or induced mutations occur on an endogenous gene, at which point the endogenous gene becomes a mutated gene because it is no longer the same as the original wild-type gene. The resultant organism may be called a mutant.
[0070] In one aspect, the polynucleotide sequences disclosed herein, including but not limited to LysM receptor kinase family genes and various CRGs, may be used to identify those mutants with mutations in one of the LysM receptor kinase family genes. For instance, a large number of mutants may be generated by either spontaneous or induced mutation. These mutants may be screened to identify those mutations that occur in one of the LysM receptor kinase family genes. Suitable methods for such a screening may include, for example, PCR, sequencing, or hybridization.
[0071] In another aspect, these polynucleotide sequences, including but not limited to LysM receptor kinase family genes and various CRGs, may also be used to design DNA construct for targeted insertion, deletion, or substitution of a specific LysM receptor kinase family gene. For instance, a DNA fragment may be first inserted into the coding region of a LysM receptor kinase family gene, the construct thus obtained may then be introduced into a host to create an insertional mutant by homologous recombination.
[0072] The traits of a plant may be modified. A modified plant may be coconsidered “fungal resistant” if the chance of a plant becoming infected by a specific fungal pathogen is at least 30% less than that of a wild-type plant from which the modified plant is derived.
[0073] A molecule is “endogenous” to an organism if the molecule exists or is encoded by a molecule that exists in the organism without requiring a transgenic process. For purpose of this disclosure, the terms “expression” and “express” refer to transcription of DNA into RNA, or translation of RNA into protein, or both.
[0074] Besides null mutation that renders a protein completely non-functional, a mutation may also render a protein dominant negative when it only abolishes partial function of a protein. The resultant partially functioning protein may act as a “dominant negative” protein when it continues to perform the remaining function. For example, a mutated protein may continue to bind a co-factor without activating that co-factor because the activation function has been lost. When such a mutated protein is expressed in a cell, it binds to many co-factors without activating them, thus rendering them unavailable for the wild-type protein. In this situation, the mutant protein is said to be acting in a dominant negative fashion.
[0075] The term “knocking out” or “knock out” means rendering a gene non-functional. “Knocking down” means lowering the expression levels of a gene or decrease the relative activity of the encoded protein. A gene can be knocked out or knocked down through deletion, insertion, substitution of a fragment or a residue in the coding region or in the regulatory regions of a gene.
[0076] Within the scope of the disclosed instrumentalities are recombinant oligonucleotides encoding peptides having antifungal activity. These recombinant oligonucleotides can be used to produce recombinant polynucleotides which are commonly used as cloning or expression vectors although other uses are possible. A cloning vector is a self-replicating DNA molecule that serves to transfer a DNA segment into a host cell. The three most common types of cloning vectors are bacterial plasmids, phages, and other viruses. An expression vector is a cloning vector designed so that a coding sequence inserted at a particular site will be transcribed and translated into a protein.
[0077] Both cloning and expression vectors may contain nucleotide sequences that allow the vectors to replicate in one or more suitable host cells. In cloning vectors, this sequence is generally one that enables the vector to replicate independently of the host cell chromosomes, and also includes either origins of replication or autonomously replicating sequences. Various bacterial and viral origins of replication are well known to those skilled in the art and include, but are not limited to the pBR322 plasmid origin, the 2μ plasmid origin, and the SV40, polyoma, adenovirus, VSV and BPV viral origins. An expression vector may contain an origin of replication so that it can be replicated independently from the host's chromosome. More preferably, an expression vector carrying the transgene of interest may have a means by which the DNA fragment containing the transgene may be integrated onto a chromosome of the host plant and thus may be replicated along with the host chromosomes.
[0078] The polynucleotide sequences of the present disclosure may be used to produce antifungal peptides by the use of recombinant expression vectors containing the polynucleotide sequence disclosed herein. For purpose of this disclosure, antifungal peptides may mean polypeptides or fragments thereof that may help prevent fungal infection of a plant. Examples of antifungal peptides may include but not limited to polypeptides encoded by the LysM receptor kinase genes or the CRGs. In one embodiment, these antifungal peptide may be expressed in vitro and be applied onto a plant or be injected into a plant to achieve the desired antifungal effects. Suitable expression vectors include chromosomal, non-chromosomal and synthetic DNA sequences, for example, SV 40 derivatives; bacterial plasmids; phage DNA; baculovirus; yeast plasmids; vectors derived from combinations of plasmids and phage DNA; and viral DNA such as vaccinia, adenovirus, fowl pox virus, and pseudorabies. In addition, any other vector that is replicable and viable in the host may be used. Suitable host for in vitro expression may include bacterial, yeast, plant or insect cells, among others.
[0079] The nucleotide sequence of interest may be inserted into the vector by a variety of methods. In the most common method the sequence is inserted into an appropriate restriction endonuclease site(s) using procedures commonly known to those skilled in the art and detailed in, for example, Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed., Cold Spring Harbor Press, (1989) and Ausubel et al., Short Protocols in Molecular Biology, 2nd ed., John Wiley & Sons (1992).
[0080] In an expression vector, the sequence of interest may be operably linked to a suitable regulatory elements, including but not limited to a promoter or a enhancer, that may be recognized by the host cell to direct mRNA synthesis. Promoters generally refer to untranslated sequences located upstream from the start codon of a structural gene that regulate the transcription and translation of nucleic acid sequences under their control. Promoters may be classified as either inducible or constitutive promoters. Inducible promoters are promoters that initiate increased levels of transcription from DNA under their control in response to some change in the environment, e.g. the presence or absence of a nutrient or a change in temperature. Constitutive promoters, in contrast, maintain a relatively constant level of transcription.
[0081] A nucleic acid sequence is operably linked when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operatively linked to DNA for a polypeptide if it is expressed as a preprotein which participates in the secretion of the polypeptide; a promoter is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, operably linked sequences are contiguous and, in the case of a secretory leader, contiguous and in reading phase. Linking is achieved by ligation at restriction enzyme sites. If suitable restriction sites are not available, then synthetic oligonucleotide adapters or linkers can be used as is known to those skilled in the art. Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd ed., Cold Spring Harbor Press, (1989) and Ausubel et al., Short Protocols in Molecular Biology, 2nd ed., John Wiley & Sons (1992).
[0082] Common promoters used in expression vectors include, but are not limited to, LTR or SV40 promoter, the E. coli lac or trp promoters, and the phage lambda PL promoter. Useful inducible plant promoters include heat-shock promoters (Ou-Lee et al. (1986) Proc. Natl. Acad. Sci. USA 83: 6815; Ainley et al. (1990) Plant Mol. Biol. 14: 949), a nitrate-inducible promoter derived from the spinach nitrite reductase gene (Back et al. (1991)Plant Mol. Biol. 17: 9), hormone-inducible promoters (Yamaguchi-Shinozaki et al. (1990) Plant Mol. Biol. 15: 905; Kares et al. (1990) Plant Mol. Biol. 15: 905), and light-inducible promoters associated with the small subunit of RuBP carboxylase and LHCP gene families (Kuhlemeier et al. (1989) Plant Cell 1: 471; Feinbaum et al. (1991) Mol. Gen. Genet. 226: 449; Weisshaar et al. (1991) EMBO J. 10: 1777; Lam and Chua (1990) Science 248: 471; Castresana et al. (1988) EMBO J. 7: 1929; Schulze-Lefeit et al. (1989) EMBO J. 8: 651). Other promoters known to control the expression of genes in prokaryotic or eukaryotic cells can be used and are known to those skilled in the art. Expression vectors may also contain a ribosome binding site for translation initiation, and a transcription terminator. The vector may also contain sequences useful for the amplification of gene expression.
[0083] Expression and cloning vectors can, and usually do, contain a selection gene or selection marker. Typically, this gene encodes a protein necessary for the survival or growth of the host cell transformed with the vector. Examples of suitable markers include dihydrofolate reductase (DHFR) or neomycin resistance for eukaryotic cells and tetracycline or ampicillin resistance for E. coli. Selection markers in plants include resistance to bleomycin, gentamycin, glyphosate, hygromycin, kanamycin, methotrexate, phleomycin, phosphinotricin, spectinomycin, streptomycin, sulfonamide and sulfonylureas. Maliga et al., Methods in Plant Molecular Biology, Cold Spring Harbor Press, 1995, p. 39.
[0084] In addition, expression vectors can also contain marker sequences operatively linked to a nucleotide sequence for a protein that encode an additional protein used as a marker. The result is a hybrid or fusion protein comprising two linked and different proteins. The marker protein can provide, for example, an immunological or enzymatic marker for the recombinant protein produced by the expression vector. Suitable markers include, but are not limited to, alkaline phosphatase (AP), myc, hemagglutinin (HA), β-glucuronidase (GUS), luciferase, and green fluorescent protein (GFP).
[0085] The polynucleotide sequences of the present disclosure may also be part of an expression cassette that at a minimum comprises, operably linked in the 5′ to 3′ direction, a regulatory sequence such as a promoter, a polynucleotide encoding a peptide of the present disclosure, and a transcriptional termination signal sequence functional in a host cell. The promoter can be of any of the types discussed herein, for example, a tissue specific promoter, a developmentally regulated promoter, an organelle specific promoter, a seed specific promoter, a plastid specific promoter, etc. The expression cassette can further comprise an operably linked targeting, transit, or secretion peptide coding region capable of directing transport of the protein produced. The expression cassette can also further comprise a nucleotide sequence encoding a selectable marker and/or a purification moiety.
[0086] More particularly, the present disclosure includes recombinant constructs comprising an isolated polynucleotide sequence encoding the antifungal peptides of the present disclosure. The constructs can include a vector, such as a plasmid or viral vector, into which the sequence has been inserted, either in the forward or reverse orientation. The recombinant construct can further comprise regulatory sequences, including, for example, a promoter operatively linked to the sequence. Large numbers of suitable vectors and promoters are known to those skilled in the art and are commercially available.
[0087] Different domains from different LysM RLKs may be combined to obtain chimeric proteins. Such a chimeric protein may possess a number of desirable properties that are not otherwise exhibited by one single protein that naturally exist in plants. Such desirable properties may include but are not limited to increased sensibility to chitin and its derivatives, increased kinase activity or enhanced kinase specificity.
[0088] A further embodiment of the present disclosure relates to transformed host cells containing constructs comprising the oligonucleotide sequences of the present disclosure. For instance, various combination of the LysM RLK genes, in wild-type or mutated forms, may be introduced as transgenes into a host plant, such as soybean. In a preferred embodiment, the host plants is susceptible to fungal infection and the expression of the LysM RLK transgenes may confer certain degree of fungal resistance to the host. In addition to the LysM RLK genes, the transgenes may include other genes that may play a role in fungal defense, such as any of the CRGs whose forced expression may enhance the host's capability to defend against fungal pathogens.
[0089] The host cell can be a higher eukaryotic cell, such as a mammalian or plant cell, or a lower eukaryotic cell such as a yeast cell, or the host can be a prokaryotic cell such as a bacterial cell. Introduction of the construct into the host cell can be accomplished by a variety of methods including calcium phosphate transfection, DEAE-dextran mediated transfection, Polybrene, protoplast fusion, liposomes, direct microinjection into the nuclei, scrape loading, and electroporation. In plants, a variety of different methods can be employed to introduce transformation/expression vectors into plant protoplasts, cells, callus tissue, leaf discs, meristems, etc., to generate transgenic plants. These methods include, for example, Agrobacterium-mediated transformation, particle gun delivery, microinjection, electroporation, polyethylene glycol-mediated protoplast transformation, liposome-mediated transformation, etc. (reviewed in Potrykus (1991) Annu. Rev. Plant Physiol. Plant Mol. Biol. 42: 205).
[0090] Peptides produced by expression of the polynucleotides of the present disclosure can be obtained by transforming a host cell by any of the previously described methods, growing the host cell under appropriate conditions, inducing expression of the polynucleotide and isolating the protein(s) of interest. If the protein in retained within the host cell, the protein can be obtained by lysis of the host cells, while if the protein is a secreted protein, it can be isolated from the culture medium. Several methods are available for purification of proteins and are known to those of ordinary skill in the art. These include precipitation by, for example, ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, lectin chromatography, high performance liquid chromatography (HPLC), electrophoresis under native or denaturing conditions, isoelectric focusing, and immunoprecipitation.
[0091] Alternatively, peptides encoded by the polynucleotides of the present disclosure can be produced by chemical synthesis using either solid-phase peptide synthesis or by classical solution peptide synthesis also known as liquid-phase peptide synthesis. In oligomer-supported liquid phase synthesis, the growing product is attached to a large soluble polymeric group. The product from each step of the synthesis can then be separated from unreacted reactants based on the large difference in size between the relatively large polymer-attached product and the unreacted reactants. This permits reactions to take place in homogeneous solutions, and eliminates tedious purification steps associated with traditional liquid phase synthesis. Oligomer-supported liquid phase synthesis has also been adapted to automatic liquid phase synthesis of peptides.
[0092] For solid-phase peptide synthesis, the procedure entails the sequential assembly of the appropriate amino acids into a peptide of a desired sequence while the end of the growing peptide is linked to an insoluble support. Usually, the carboxyl terminus of the peptide is linked to a polymer from which it can be liberated upon treatment with a cleavage reagent. In a common method, an amino acid is bound to a resin particle, and the peptide generated in a stepwise manner by successive additions of protected amino acids to produce a chain of amino acids. Modifications of the technique described by Merrifield are commonly used (see, e.g., Merrifield, J. Am. Chem. Soc. 96: 2989-93, 1964). In an automated solid-phase method, peptides are synthesized by loading the carboxy-terminal amino acid onto an organic linker (e.g., PAM, 4-oxymethylphenylacetamidomethyl), which is covalently attached to an insoluble polystyrene resin cross-linked with divinyl benzene. The terminal amine may be protected by blocking with t-butyloxycarbonyl. Hydroxyl- and carboxyl-groups are commonly protected by blocking with O-benzyl groups. Synthesis is accomplished in an automated peptide synthesizer, a number of which are commercially available. Following synthesis, the product may be removed from the resin. The blocking groups are removed typically by using hydrofluoric acid or trifluoromethyl sulfonic acid according to established methods (e.g., Bergot and McCurdy, Applied Biosystems Bulletin, 1987). Following cleavage and purification, a yield of approximately 60 to 70% is typically produced. Purification of the product peptides is accomplished by, for example, crystallizing the peptide from an organic solvent such as methyl-butyl ether, then dissolving in distilled water, and using dialysis (if the molecular weight of the subject peptide is greater than about 500 daltons) or reverse high-pressure liquid chromatography (e.g., using a C18 column with 0.1% trifluoroacetic acid and acetonitrile as solvents) if the molecular weight of the peptide is less than 500 daltons. Purified peptide may be lyophilized and stored in a dry state until use. Analysis of the resulting peptides may be accomplished using the common methods of analytical high pressure liquid chromatography (HPLC) and electrospray mass spectrometry (ES-MS).
[0093] In general, transgenic plants comprising cells containing polynucleotides of the present disclosure can be produced by any of the foregoing methods; selecting plant cells that have been transformed on a selective medium; regenerating plant cells that have been transformed to produce differentiated plants; and selecting a transformed plant that expresses the protein(s) encoded by the polynucleotides of the present disclosure at a desired level.
[0094] Specific methods for transforming a wide variety of dicots and obtaining transgenic plants are well documented in the literature (Gasser and Fraley, Science 244:1293, 1989; Fisk and Dandekar, Scientia Horticulturae 55:5, 1993; Dandekar and Fisk, Plant transformation: agrobacterium-mediated gene transfer. Methods Mol. Biol. 2005; 286:35-46; Olhoft P M, Donovan C M, Somers D A, Soybean (Glycine max) transformation using mature cotyledonary node explants, Methods Mol. Biol. 2006; 343:385-96; Ko T S, Korban S S, Somers D A, Soybean (Glycine max) transformation using immature cotyledon explants, Methods Mol. Biol. 2006; 343:397-405; and all references cited therein).
[0095] Successful transformation and plant regeneration have also been achieved in a variety of monocots. Specific examples are as follows: asparagus (Asparagus officinalis; Bytebier et al. (1987) Proc. Natl. Acad. Sci. USA 84: 5345); barley (Hordeum vulgarae; Wan and Lemaux (1994) Plant Physiol. 104: 37); maize (Zea mays; Rhodes et al. (1988) Science 240: 204; Gordon-Kamm et al. (1990) Plant Cell 2: 603; Fromm et al. (1990) Bio/Technology 8: 833; Koziel et al. (1993) Bio/Technology 11: 194); oats (Avena sativa; Somers et al. (1992) Bio/Technology 10: 1589); orchardgrass (Dactylis glomerata; Horn et al. (1988) Plant Cell Rep. 7: 469); rice (Oryza sativa, including indica and japonica varieties; Toriyama et al. (1988) Bio/Technology 6: 10; Zhang et al. (1988) Plant Cell Rep. 7: 379; Luo and Wu (1988) Plant Mol. Biol. Rep. 6: 165; Zhang and Wu (1988) Theor. Appl. Genet. 76: 835; Christou et al. (1991) Bio/Technology 9: 957); rye (Secale cereale; De la Pena et al. (1987) Nature 325: 274); sorghum (Sorghum bicolor; Cassas et al. (1993) Proc. Natl. Acad. Sci. USA 90: 11212); sugar cane (Saccharum spp.; Bower and Birch (1992) Plant J. 2: 409); tall fescue (Festuca arundinacea; Wang et al. (1992) Bio/Technology 10: 691); turfgrass (Agrostis palustris; Zhong et al. (1993) Plant Cell Rep. 13: 1); and wheat (Triticum aestivum; Vasil et al. (1992) Bio/Technology 10: 667; Weeks et al. (1993) Plant Physiol. 102: 1077; Becker et al. (1994) Plant J. 5: 299). All these references relate to transformation techniques in dicots or monocots and are hereby expressly incorporated into this disclosure by reference.
[0096] Various LysM RLK genes show tissue specific expression in plants. Tissue specific promoters or other regulatory elements may play a role in controlling these tissue specific expression patterns. DNA recombination utilizing these regulatory elements may be employed to manipulate the expression pattern and/or levels of the various LysM RLK genes, or other genes in general. For instance, expression construct containing a tissue specific promoter may be used to drive the expression of a LysM RLK which is not otherwise expressed in the particular tissue.

EXAMPLES

[0097] The following examples are intended to provide illustrations of the application of the present disclosure. The following examples are not intended to completely define or otherwise limit the scope of the invention.

Example 1

Plant LysM Domains are Highly Diversified

[0098] The sequences of NFR1 (SEQ ID No. 1) and NFR5 (SEQ ID No. 2) genes from Lotus japonicus, as reported by Radutoiu et al. (2003) were used to identify genes encoding LysM domain-containing proteins by searching public databases of Arabidopsis, rice, poplar, M. truncatula, and L. japonicus. Soybean LYK genes were identified by shotgun sequencing bacterial artificial chromosomes (BACs) with homologies to LysM-encoding ESTs. The resulting putative LYK protein sequences from all species were then searched against the Pfam server to verify LysM and kinase domains. Collectively, a total of 49 LYK genes were identified in the six plant genomes, namely, those of Arabidopsis, rice, poplar, M. truncatula, L. japonicus and soybean, as summarized in Table 2. The predicted amino acid sequences of these genes or fragments were obtained and compared by sequence alignment, with representative alignments shown in FIG. 2.
[0099] 
[00002] [TABLE-US-00002]
  TABLE 2
 
LysM type receptor-like kinase genes from Arabidopsis, soybean, Lotus,
Medicago, rice and poplar.
  Name (SEQ ID No.)   Alias name   Sources
 
  AtLYK1 (SEQ ID No. 3)   At3g21630   TAIR
  AtLYK2 (SEQ ID No. 4)   At3g01840   TAIR
  AtLYK3 (SEQ ID No. 5)   At1g51940   TAIR
  AtLYK4 (SEQ ID No. 6)   At2g23770   TAIR
  AtLYK5 (SEQ ID No. 7)   At2g33580   TAIR
  GmNFR1α (SEQ ID 54)   GmW2098N11.16   this study
  GmNFR1β (SEQ ID 55)   GmW2098N15.9   this study
  GmLYK2 (SEQ ID 56)   GmW2098N11.15   this study
  GmLYK3 (SEQ ID 57)   GmW2026N19.18   this study
  GmLYK4 (SEQ ID 58)   GmW2095P01.22   this study
  GmNFR5α (SEQ ID 59)   GmW2035N07.17   this study
  GmNFR5β (SEQ ID 60)   GmW2095P01.23   this study
  GmLYK6 (SEQ ID 61)   GmW2075N23   this study
  GmLYK7 (SEQ ID 62)   GmW2035N07.16   this study
  GmLYK8 (SEQ ID 63)   GmW2098N11.2   this study
  GmLYK9 (SEQ ID 64)   GmW2069O12.22   this study
  GmLYK10 (SEQ ID 65)   GmW2080D08.12   this study
  GmLYK11 (SEQ ID 66)   GmW2042I24.15   this study
  LjNFR1 (SEQ ID 1)   AJ575248   Gene Bank
  LjLYK2 (SEQ ID 67)   TM0545.8   Kazusa
  LjLYK3 (SEQ ID 68)   TM0545.9   Kazusa
  LjLYK4 (SEQ ID 69)   TM0522.16   Kazusa
  LjNFR5 (SEQ ID 2)   AJ575255   Gene Bank
  LjLYK6 (SEQ ID 70)   TM0076a.10   Kazusa
  MtLYK1 (SEQ ID 71)   CR936945.12Medicago truncatula sequencing
      resources
  MtLYK3 (SEQ ID 72)   AY372402   Gene Bank
  MtLYK4 (SEQ ID 73)   AY372403   Gene Bank
  MtLYK9 (SEQ ID 74)   AC148241_11Medicago truncatula sequencing
      resources
  MtLYK10 (SEQ ID 75)   AC148994_13Medicago truncatula sequencing
      resources
  MtLYK11 (SEQ ID 76)   AC148994_15Medicago truncatula sequencing
      resources
  MtLYK12 (SEQ ID 77)   AC126779_3Medicago truncatula sequencing
      resources
  MtLYK13 (SEQ ID 78)   AC126779_4Medicago truncatula sequencing
      resources
  OsLYK1 (SEQ ID 79)   LOC_Os01g36550   TIGR
  OsLYK2 (SEQ ID 80)   LOC_Os06g41980   TIGR
  OsLYK3 (SEQ ID 81)   LOC_Os06g41960   TIGR
  OsLYK4 (SEQ ID 82)   LOC_Os02g09960   TIGR
  OsLYK5 (SEQ ID 83)   LOC_Os03g13080   TIGR
  OsLYK6 (SEQ ID 84)   LOC_Os11g35330   TIGR
  PtLYK1 (SEQ ID 85)   FGENESH1_PG.C_LG_VIII001701   DOE JGI
  PtLYK2 (SEQ ID 86)   FGENESH1_PG.C_LG_VII000997   DOE JGI
  PtLYK3 (SEQ ID 87)   EUGENE3.00051645   DOE JGI
  PtLYK4 (SEQ ID 88)   EUGENE3.00081504   DOE JGI
  PtLYK5 (SEQ ID 89)   EUGENE3.00400189   DOE JGI
  PtLYK6 (SEQ ID 90)   GRAIL3.0019013601   DOE JGI
  PtLYK7 (SEQ ID 91)   GRAIL3.0017002501   DOE JGI
  PtLYK8 (SEQ ID 92)   FGENESH1_PM.C_LG_I000490   DOE JGI
  PtLYK9 (SEQ ID 93)   EUGENE3.00570233   DOE JGI
  PtLYK10 (SEQ ID 94)   EUGENE3.00100714   DOE JGI
  PtLYK11 (SEQ ID 95)   eugene3.00570235   DOE JGI
 
[0100] More specifically, plant LysM protein sequences were first searched using the keyword LysM and BLASTp (1e-20) using the LysM domains of LjNFR1 (SEQ ID No. 1) and LjNFR5 (SEQ ID No. 2) against the following publicly available databases: Arabidopsis (Arabidopsis thaliana, database maintained by the Carnegie Institution of Washington Department of Plant Biology); rice (Oryza sativa, database maintained by the Institute for Genomic Research (TIGR)); poplar (Popillis spp., database maintained by DOE's Joint Genome Institute); Medicago truncatula, database maintained by the lab of Nevin Young at the University of Minnesota); and Lotus japonicus (database maintained by the Kazusa DNA Research Institute in Japan. Domain structures of the resulting potential LysM proteins were analyzed with Pfam software and Inter-ProScan to identify LysM proteins. Soybean (Glycine max) LysM proteins were searched via tBLASTn (1e-5) using the same query sequences as above against two publicly available EST databases, one maintained by the Institute for Genomic Research, the other maintained by Monsanto.
[0101] Primers were designed based on the resulting soybean EST sequences to probe a six-dimensional BAC pool for LysM-containing BACs via a PCR-based approach. The probed LYK-containing BACs were verified and shotgun sequenced to either finished phase (phase 3) at the Arizona Genome Sequencing Center or prefinished phase (phase 2) at the Washington University Genome Sequencing Center. BAC sequences were annotated using the dicot species model and Arabidopsis matrix of FGENESH. Annotated proteins were similarly analyzed to screen for LYK proteins. Signal peptides and transmembrane domains were predicted with SignalP using both nearest-neighbor and hidden Markov model (HMM) algorithms and transmembrane HMM, respectively.
[0102] The GenBank accession numbers of soybean BACs are EF533702 for GMWb098N11; EF533695 for GMWb098N15; EF533696 for GMWb026N19; EF533701 for GMWb095P01; EF533697 for GMWb035N07; EF533699 for GMWb069012; EF533700 for GMWb080D08; and EF533698 for GMWb042124. LysM protein sequences from species spanning all kingdoms were extracted from Pfam and searched for LysM motifs at an E-value cutoff of 0.1.
[0103] Sequence alignments were performed using ClustalX 1.83 (Thompson et al., 1997) with PHYLIP output format and edited in Jalview (Clamp et al., 2004). The average identities across the alignments for LysMe (type X), LysMn (type XI), and LYPb (type VII) were calculated based on the exported annotations in Jalview. An HMM profile calculated using hmmer (Eddy, 1998) for each alignment was used to realign (hmmalign) sequences at matching states (−m) to identify and remove indel regions.
[0104] Parsimony trees were generated using the program protpars of PHYLIP (Felsenstein, 2000), with maximum-likelihood branch lengths calculated using TREE-PUZZLE (Schmidt et al., 2002). Distance trees were calculated using the program Protdist and Fitch of the PHYLIP package. Maximum-likelihood trees were calculated using the program proml of the PHYLIP package. Bootstrap values were calculated using the program seqboot of the PHYLIP package. Trees were viewed and rooted using A Tree Viewer (Zmasek and Eddy, 2001). For calculation of nucleotide substitution rates, codon-aligned nucleic acid sequences were created using CodonAlign 2.0. All insertions and deletions were removed except that a gap of more than 30 nucleotides was preferably retained to demonstrate the lack of the p loop and the activation loop in the kinase domains of LjNFR5 orthologs (Limpens et al., 2003; Madsen et al., 2003; Arrighi et al., 2006). Nucleotide substitution levels were calculated using the program codeml of the PAML package (Yang, 1997) with a user-defined parsimony tree.
[0105] To build microsynteny maps, genomic sequences surrounding each LYK gene, about 0.5 to 0.9 Mb in length, were extracted from the above databases and from soybean BAC sequences, which are about 100 to 170 kb in length. The genomic sequences were annotated using dicot species model and Arabidopsis matrix of FGENESH for the five dicot plants and monocot species model and rice matrix for rice. The annotated protein sequences were compiled together into a peptide sequence database. Repetitive sequences were excluded from the databases. BLASTp was used to compare proteins against the database with an E-value cutoff of 1e-20 and a percent identity cutoff of 35% between species and 40% within same species and legumes. BLASTp results were then filtered once to remove retroelements. The microsynteny maps were finally drawn in Adobe Illustrator 10.0.

Example 2

Induction of Gene Expression in Arabidopsis Treated with Chitin

[0106] A total of five LysM receptor-like kinase genes were identified in Arabidopsis from the studies described in Example 1. The Genbank numbers of these five genes are AtLYK1 (GenBank accession # At3g21630), AtLYK2 (GenBank accession # At3g01840), AtLYK3 (GenBank accession # At1g51940), AtLYK4 (GenBank accession # At2g23770), AtLYK5 (GenBank accession # At2g33580), and, which are designated as SEQ ID. Nos. 3-7, respectively. A DNA microarray experiment was performed by treating Arabidopsis plants with chitin. Leaves were treated by spraying with chitin (100 μM)+0.2% Tween-20. The Affymetrix 24K Arabidopsis genome chip was utilized according to the manufacture's instructions for this test. The data obtained showed that transcription of 3 of the 5 Arabidopsis LysM RLK genes, At2g33580 (13-fold), At3g21630 (2-fold) and At2g23770 (2-fold), was significantly increased by treating the plants with chitin. The data implicate these genes in plant chitin response.

Example 3

LysM RLK Mutants in Arabidopsis

[0107] To test whether non-leguminous LysM RLKs may be involved in the perception of chitooligosaccharides and the subsequent induction of downstream genes that have been implicated in fungal defense, T-DNA insertion mutants were obtained for all five LysM RLK genes (i.e., At1g51940, At2g23770, At2g33580, At3g01840, and At3g21630) in Arabidopsis. The gene At3g21630 (SEQ ID. No. 3) is also termed AtLYK1 or AtLysM RLK1. Homozygous mutants were then treated with a purified chitooligosaccharide (chitooctaose) and the expression levels of known CRGs, such as MPK3 (At3g45640, SEQ ID. No. 8), WRKY22 (At4g01250, SEQ ID. No. 9), WRKY29 (At4g23550, SEQ ID. No. 10), WRKY33 (At2g38470, SEQ ID. No. 11), and WRKY53 (At4g23810, SEQ ID. No. 12), were measured.
[0108] More particularly, Arabidopsis seedlings were grown hydroponically as described by Ramonell et al., 2005. Fourteen-day old seedlings were treated with chitooctaose (Sigma, St. Louis, Mo., USA) at a concentration of 1 μM or with distilled water (as a control) for 30 minutes. To test flagellin-responsive genes, 14-day old seedlings were also treated with the flagellinderived flg22 peptide (dissolved in dimethyl sulfoxide, DMSO) at a final concentration of 10 μM or with an equivalent amount of DMSO (as a control) for 30 minutes. To test other defense pathways, Arabidopsis seedlings were also treated for 24 hours with 5 mM SA, 100 μM MeJA, and 0.5 mM ACC (all obtained from Sigma, St. Louis, Mo., USA) and dissolved in 0.1% ethanol. The control plants were similarly treated with an equivalent amount of ethanol. After treatment, the seedlings were collected and frozen in liquid nitrogen for RNA isolation.
[0109] Total RNA was isolated using the Trizol Reagent according to the manufacturer's instructions (Invitrogen, Carlsbad, Calif.). The isolated RNA was further purified using Qiagen RNeasy Mini Columns according to the manufacturer's instruction (Qiagen, Valencia, Calif., USA) and treated with Turbo™ DNase (Ambion, Austin, Tex., USA). For semi-quantitative RT-PCR or quantitative 17 PCR, cDNA was synthesized using M-MLV reverse transcriptase according to the manufacturer's instructions (Promega, Madison, Wis., USA).
[0110] Semi-quantitative RT-PCR. The gene-specific primer pairs (forward and reverse) for detecting the following selected chitooligosaccharide-responsive genes (CRGs) are:
[0111] 
[00003] [TABLE-US-00003]
    For MPK3 (At3g45640):
  (SEQ ID No. 13)
    5′-CTCACGGAGGACAGTTCATAAG-3′
    and
 
  (SEQ ID No. 14)
    5′-GAGATCAGATTCTGTCGGTGTG-3′
 
    For WRKY22 (At4g01250):
  (SEQ ID No. 15)
    5′-GTAAGCTCATCAGCTACTACCAC-3′
    and
 
  (SEQ ID No. 16)
    5′-ACCGCTAGATGATCCTCAACAG-3′
 
    for WRKY29 (At4g23550):
  (SEQ ID No. 17)
    5′-ATGGACGAAGGAGACCTAGAAG-3′
    and
 
  (SEQ ID No. 18)
    5′-CCGCTTGGTGCGTACTCGTTTC-3′
 
    For WRKY33 (At2g38470):
  (SEQ ID No. 19)
    5′-CTCCGACCACAACTACAACTAC-3′
    and
 
  (SEQ ID No. 20)
    5′-GGCTCTCTCACTGTCTTGCTTC-3′
 
    For WRKY53 (At4g23810):
  (SEQ ID No. 21)
    5′-CCTACGAGAGATCTCTTCTTCTG-3′
    and
 
  (SEQ ID No. 22)
    5′-AGATCGGAGAACTCTCCACGTG-3′
[0112] As an internal control, the following forward and reverse primers of actin-2 (At3 g18780) were included in the same PCR reaction with each primer pair of the above genes:
[0113] 
[00004] [TABLE-US-00004]
  (SEQ ID No. 23)
    5′-GACTAAGAGAGAAAGTAAGAGATAATCCAG-3′
    and
 
  (SEQ ID No. 24)
    5′-CAGCCTTTGATTTCAATTTGCATGTAAGAG-3′.
[0114] PCR reactions were conducted using Taq polymerase (Promega, Madison, Wis., USA) under the following conditions: 94° C., 3 minutes; 94° C., 30 seconds; 55° C., 30 seconds; 72° C., 1.5 minutes; 25 cycles; 72° C., 3 minutes. The corresponding CRG genes in Lotus japonicus were identified by blasting the cDNA sequences of the above Arabidopsis CRGs (and also actin-2) against the TIGR Lotus japonicus Gene Index. The closest hits were chosen and arbitrarily named after their Arabidopsis counterparts with the prefix Lj (standing for Lotus japonicus). The following primer pairs were designed to detect these genes:
[0115] 
[00005] [TABLE-US-00005]
    For LjMPK3 (TC8079):
  (SEQ ID No. 25)
    5′-CACCCTTGCGTAGAGAGTTTACTGATGTC-3′,
    and
 
  (SEQ ID No. 26)
    5′-GTTGACGAGGATATTGAGGAAGTTGTCTG-3′;
 
    For LjWRKY22 (AV423663):
  (SEQ ID No. 27)
    5′-TCACCTTGCTGGTTCTGGTTCTGGTTCTG-3′,
    and
 
  (SEQ ID No. 28)
    5′-TCTGATAGGGGTGCAACCCCATCTTCTTC-3′;
 
    For LjWRKY33 (TC14849):
  (SEQ ID No. 29)
    5′-AGTTGTGGTTCAGACCACCAGTGACATTG-3′
    and
 
  (SEQ ID No. 30)
    5′-ACCCCATTGAGTTTCCAAACCCTGATGAG-3′;
 
    For LjWRKY53 (TC9074):
  (SEQ ID No. 31)
    5′-CCCATCAAAAGAACCAACCACAACAAGAG-3′
    and
 
  (SEQ ID No. 32)
    5′-ATCCGCACGCACTTGAACCATGTATTGTG-3′;
 
    For LjActin-2 (TC14247):
  (SEQ ID No. 33)
    5′-AAGGTTCGTAAACGATGGCTGATGCTGAG-3′
    and
 
  (SEQ ID No. 34)
    5′-ACCTTGATCTTCATGCTGCTAGGAGCAAG-3′.
[0116] LjActin-2 was used as an internal control.
[0117] Quantitative PCR. To quantify gene expression using quantitative PCR, the forward and reverse primers of each gene were as follows:
[0118] 
[00006] [TABLE-US-00006]
    For PR-1 (At2g14610, SEQ ID. No. 35):
  (SEQ ID No. 36)
    5′-AACACGTGCAATGGAGTTTGTGGTCACT-3′
    and
 
  (SEQ ID No. 37)
    5′-ACCATTGTTACACCTCACTTTGGCACAT-3′;
 
    For PDF1.2 (At5g44420, SEQ ID. No. 38):
  (SEQ ID No. 39)
    5′-AGTGCATTAACCTTGAAGGAGCCAAACAT-3′
    and
 
  (SEQ ID No. 40)
    5′-AACAGATACACTTGTGTGCTGGGAAGACA-3′;
 
    For MPK3 (At3g45640):
  (SEQ ID No. 41)
    5′-TGGCCATTGATCTTGTTGACAGAATGTTGA-3′
    and
 
  (SEQ ID No. 42)
    5′-TCGTGCAATTTAGCAAGGTACTGGTGATT-3′;
 
    for WRKY53 (At4g23810):
  (SEQ ID No. 43)
    5′-TTTAGGCGCCAAATTCCCAAGGAGTTATT-3′
    and
 
  (SEQ ID No. 44)
    5′-TCTGGACTTGTTTCGTTGCCCAACAGTTT-3′;
 
    For actin-2 (At3g18780):
  (SEQ ID No. 45)
    5′-GGTATTCTTACCTTGAAGTATCCTATTG-3′
    and
 
  (SEQ ID No. 46)
    5′-CTCATTGTAGAAAGTGTGATGCCAGATC-3′.
[0119] Actin-2 was used as an internal control to normalize gene expression across different samples. The reactions were conducted on a 7500 Real-Time PCR System (Applied Biosystems, Foster City, Calif., USA) using the SYBR® Green Master Mix (Applied Biosystems, Foster City, Calif., USA) with the following PCR conditions: 95° C., 10 minutes; 95° C., 15 seconds; 60° C., 1 minute; 40 cycles; followed by the dissociation curve analysis to verify single amplicon. The fold change in the target gene, normalized to actin-2 and relative to the gene expression in the control sample, was calculated as described in Ramonell et al., 2002.
[0120] The AtLysM RLK1 insertion mutant (096F09) used in the current work was generated in the context of the GABI-Kat program and provided by Bernd Weisshaar (MPI for Plant Breeding Research, Cologne, Germany). See Shibuya et al., 2001. The homozygous plants were identified by genotyping using the following gene-specific primers:
[0121] 
[00007] [TABLE-US-00007]
  (SEQ ID No. 47)
    5′-AGAATATATCCACGAGCACACGGTTCCAG-3′(forward),
    and
 
  (SEQ ID No. 48)
    5′-GACGAAAAGAGAGTGGATAAAGCAACCAC-3′(reverse)

together with the T-DNA left border primer:
[0122] 
[00008] [TABLE-US-00008]
  (SEQ ID No. 49)
    5′-CCCATTTGGACGTGAATGTAGACAC-3′.
[0123] These two primers were also used to detect the expression of the AtLysM RLK1 gene via RT-PCR. The other primers used to detect the transcript 5′ of the insertion site were as follows:
[0124] 
[00009] [TABLE-US-00009]
  (SEQ ID No. 50)
    5′-ATGAAGCTAAAGATTTCTCTAATCGCTC-3′,
    and
 
  (SEQ ID No. 51)
    5′-GAAATGCACCATTTGGATCTCTTCCAG-3′
[0125] The mutants of the other 4 Arabidopsis LysM RLK genes were obtained from the SALK Institute and Syngenta Incorporation through the Arabidopsis Basic Research Center (ABRC) or from the Martienssen lab at the Cold Spring Harbor Laboratory.
[0126] One insertion mutant designated as L3 with an insertion in gene At1g51940 exhibited an interesting phenotype. This mutant showed enhanced expression of some defense-related genes, such as PR-2 and PR-1, as shown in FIG. 3. The PR-2 gene (AT3G57260, SEQ ID. No. 52) encodes a β-1,3-glucanase, which is an enzyme that degrades the fungal cell wall component glucan to inhibit fungal infection. PR-1 (SEQ ID. No. 35) has also been shown to be involved in plant defense against pathogens, especially bacterial pathogens. This enhanced expression of defense genes suggests that the mutant may be resistant to fungal pathogens. The test of this mutant with a fungal pathogen called Botrytis cinerea demonstrated that the mutant is resistant to this fungal pathogen, as shown in FIG. 4A. B. cinerea is a necrotrophic fungus, and dead plants were assessed as those having no remaining green, only yellowish leaves. The L3 mutant demonstrated increased resistance relative to the wild-type plant.
[0127] In addition, the L3 mutant showed decreased susceptibility to the bacterial pathogen Pseudomonas syringae strain DC3000, as shown in FIG. 4B. The enhanced resistance is likely due to the knockout of the specific LysM receptor kinase gene. Analysis of expression of the At1g51940 gene in the L3 mutant failed to detect the mRNA. Therefore, the lack of At1g51940 gene expression correlates with elevated PR1 expression and enhanced disease resistance. This suggests that At1g51940 may act normally to repress the disease resistance response according to a model pathway of the involvement of the LYSM RK in plant defense, as shown in FIG. 5. Therefore, it is possible to make plants more resistant to fungal pathogens by either knocking out or knocking down the expression of this gene. Furthermore, dominant negative forms of this protein may also be made and employed to modulate plant fungal resistance.
[0128] Another insertion mutant, corresponding to At3g21630, or AtLYK1 (designated hereafter as AtLysM RLK1), almost completely blocked the induction of all the selected CRGs (FIG. 6A), suggesting a critical role of AtLysM RLK1 in the perception of chitooligosaccharides. Both the mutant (Mu) and wildtype (WT) plants were treated with purified chitooctaose or water (as a control) for 30 minutes and gene expression of the selected CRGs was detected using semi-quantitative RT-PCR. Actin-2 was used as an internal control. The amplification of both actin-2 and a CRG was conducted in the same tube.
[0129] The AtLysM RLK1 gene (SEQ ID. No. 3) is 2988 nucleotides (nts) long, with 11 introns (FIG. 6B) and a coding sequence of 1854 nts. Square boxes represent exons. Solid lines between them are introns. The start codon (ATG) and stop codon (TAG) are included in the first and last exon, respectively. The two T-DNA insertions (T-DNA1 and 2) inserted in the 10th intron in the AtLysM RLK1 mutant are indicated above the gene. LB: left border; RB: right border. The AtLysM RLK1 gene encodes a LysM RLK of 617 amino acids (SEQ ID No. 53), with an extracellular domain (containing 3 predicted LysM motifs), a transmembrane domain (TM), and an intracellular serine/threonine kinase domain. FIG. 6C illustrates the predicted domain structure of AtLysM RLK1. S: signal peptide; LysM: LysM domain; TM: transmembrane domain; Ser/Thr Kinase: Serine/Threonine kinase domain. AtLysM RLK1 has been shown to be phylogenetically related to the Nod signal receptor NFR1. Zhang et al., 2007.
[0130] Two T-DNA insertions were identified in the AtLysM RLK1 mutant, separated by 4 nts, in the 10th intron (FIG. 6B). RT-PCR analysis using primers corresponding to the exon regions on the side of the 10th intron failed to detect mRNA expression in the AtLysM RLK1 mutant; however, a truncated transcript derived from the gene sequence before the intron was detected by RT-PCR (FIGS. 7A and 7B), suggesting the T-DNA insertions in the intron blocked full-length transcription of the gene.
[0131] To confirm that the observed changes in CRGs expression were caused by the mutation in the AtLysM RLK1 gene, the mutant was complemented with the full-length AtLysM RLK1 cDNA driven by the constitutive Cauliflower Mosaic Virus (CMV) 35S promoter. More specifically, the full-length CDS (1854 nucleotides long) was obtained by RT-PCR and cloned in the Eco RV site of the pBluescript vector. The confirmed sequence was further cloned into the modified binary 16 vector pCAMBIA1200 that contains a 35S promoter-Multiple Cloning Sites (MCS)-poly A signal, downstream of the 35S promoter. The final construct was electroporated into Agrobacterium tumafaciens EHA105 according to the procedures described by Stacey and Shibuya, 1997. The resultant A. tumafaciens was then used to transform the homozygous AtLysM RLK1 mutant via floral dipping as described by Passarinho et al., 2002.
[0132] Multiple transgenic lines were obtained. The complemented plants were treated with chitooctaose or water (as a control) at a final concentration of 1 μM for 30 minutes. RT-PCR data show that the selected CRGs were induced to a level in the selected complemented plants (Com-1 and Com-2) similar to the level in the wild type (WT) plants (FIG. 8). Com-1 and Com-2 are two independent complemented lines and WT is wild-type Col-0 plants.
[0133] Thus, the complemented plants showed restored induction of those selected CRGs, confirming that it was the insertions in the AtLysM RLK1 gene that caused the observed change in gene expression. The complementation data also ruled out the possibility that a truncated protein translated from the observed truncated transcript may have affected the expression of the selected CRGs.
[0134] The expression pattern of the AtLysM RLK1 gene was also studied. RT-PCR data show that AtLysM RLK1 is expressed ubiquitously in the whole plant, in tissues such as root, rosette leaf, cauline leaf, stem, inflorescence, silique, flower bud, open flower, and pollen, with the lowest expression levels in pollen (FIG. 9). Interestingly, this gene was induced by chitooligosaccharides, but not by the flg22 peptide derived from flagellin, a PAMP (pathogen-associated molecular pattern) produced by pathogenic bacteria (FIG. 10) (Gomez-Gomez et al., 2000), suggesting a specific role of this gene in chitooligosaccharide signaling. More specifically, for experiment (A), fourteen-day-old, hydroponically grown seedlings were treated for 30 minutes with chitooctaose at a final concentration of 1 μM or with distilled water (as a control); for experiment (B), the seedlings were treated with flg22 (dissolved in DMSO) at a final concentration of 10 μM or with an equivalent amount of DMSO (as a control).
[0135] Gene expression profiles in the AtLysM RLK1 mutant in response to chitooctaose were studied using the Affymetrix Arabidopsis Whole Genome Array ATH1 (with ˜22000 genes), with wild-type plants as a control. Data analysis showed that a total of 909 genes responded more than 1.5 fold (P<0.05) to chitooctaose elicitation in both the wild-type and mutant plants 30 minutes after the treatment (FIG. 11A). A row represents a gene and each column represents a sample. WT-8mer=wild-type Col-0 treated with chitooctaose; WT-water=wild-type Col-0 treated with distilled water; Mu-water=the AtLysM RLK1 mutant treated with distilled water; Mu-8mer=the AtLysM RLK1 mutant treated with chitooctaose. The color bar below the cluster picture: the red color indicates the expression level of a gene is above the mean expression of the gene across all samples; the green color indicates expression lower than the mean. These genes can be separated into two groups: up- and down-regulated by chitooctaose, as represented by the two large clusters in FIG. 11A.
[0136] Out of the 909 genes tested, 890 showed a change in transcript levels in the wild-type plants in response to chitooctaose, with 663 up-regulated and 227 down-regulated (FIG. 11B, 11C and Table 3). Up-regulated genes: 1.5 fold, P<0.05. Down-regulated genes: 1.5 fold, P<0.05. By contrast, only 33 genes out of 909 were responsive in the mutant, with 16 up-regulated and 17 down-regulated (FIGS. 11B and 11C; Table 4). Among the 33 genes, 14 genes (3 up- and 11 down-regulated) were also similarly regulated in the wild-type plants (rows 1 to 15 in Table 4), leaving only 19 genes that appeared to be differentially regulated by chitooctaose in the mutant (rows 16-34 in Table 4). However, 13 of these genes showed a similar regulation trend (up- or down-regulation) in the wild-type plants to that in the mutant, although such a trend was not considered significant in the wild-type plants (rows 16 to 28 in Table 4).
[0137] 
[00010] [TABLE-US-00010]
  TABLE 3
 
  Genes that are Responsive to chitooctaose in Wild-type
        WT   Mu    
  Probe set   Annotation   Accession   FC   FC   WT P   Mu P
 
  245613_at   hypothetical protein   At4g14450   72.79   −1.8   0.019018   0.836714
  249197_at   putative protein contains similarity to   At5g42380   51.63   1.06   0.019359   0.866994
    calmodulin; supported by full-length cDNA:          
    Ceres: 99348.          
  258947_at   hypothetical protein similar to calmodulin-like   At3g01830   43.33   1.58   0.012148   0.103554
  protein GB: CAB42906 [Arabidopsis thaliana]; Pfam          
    HMM hit: EF hand; supported by full-length cDNA:          
    Ceres: 7252.          
  260399_at   putative lipoxygenase similar to lipoxygenase   At1g72520   41.48   −1.11   0.009183   0.804844
  GB: CAB56692 [Arabidopsis thaliana]; supported by          
  cDNA: gi_15810254_gb_AY056166.1          
  257540_at   hypothetical protein   At3g21520   34.95   1.08   0.001687   0.921695
  256526_at   disease resistance protein, putative similar to disease   At1g66090   33.68   −1.13   0.01628   0.597847
  resistance protein RPP1-WsA [Arabidopsis thaliana]          
    GI: 3860163; supported by full-length cDNA: Ceres:          
    93530.          
  250796_at   putative protein similar to unknown protein   At5g05300   31.56   1.1   0.004167   0.773037
    (gb|AAF01528.1)          
  261474_at   anionic peroxidase, putative similar to anionic   At1g14540   30.96   −1.02   0.001414   0.955549
  peroxidase GI: 170202 from [Nicotiana sylvestris]          
  245755_at   hypothetical protein predicted by   At1g35210   30.5   −1.11   0.01789   0.881393
    genemark.hmm; supported by full-length cDNA:          
    Ceres: 42217.          
  254231_atputative protein AR411-Arabidopsis thaliana (thale   At4g23810   28.21   −1.25   0.018401   0.425568
    cress), PID: g1669603; supported by cDNA:          
    gi_13507100_gb_AF272748.1_AF272748          
  248322_at   putative protein similar to unknown protein   At5g52760   26.14   1.31   0.004693   0.152597
    (emb|CAA71173.1)          
  249770_at   unknown protein; supported by full-length cDNA:   At5g24110   25.43   −1.06   0.035483   0.869658
    Ceres: 6469.          
  247215_at   Expressed protein; supported by full-length cDNA:   At5g64905   24.84   1.24   0.04883   0.449026
    Ceres: 3657.          
  265725_at   putative alanine acetyl transferase   At2g32030   23.73   1.08   0.027584   0.473742
  266821_at   putative ethylene response element binding protein   At2g44840   23.69   −1.22   0.019899   0.271281
    (EREBP); supported by full-length cDNA:          
    Ceres: 6397.          
  248904_at   Expressed protein; supported by full-length cDNA:   At5g46295   23.69   −1.49   0.007953   0.428724
    Ceres: 18973.          
  261648_at   salt-tolerance zinc finger protein identical to salt-   At1g27730   22.71   −1.09   0.016239   0.33423
    tolerance zinc finger protein GB: CAA64820          
  GI: 1565227 from [Arabidopsis thaliana]; supported          
  by cDNA: gi_14334649_gb_AY034998.1          
  262085_at   hypothetical protein predicted by genemark.hmm   At1g56060   22.37   1.36   0.001015   0.285112
  261021_at   hypothetical protein similar to reticuline oxidase-like   At1g26380   22.2   2.37   0.004697   0.108353
    protein GB: CAB45850 GI: 5262224 from          
  [Arabidopsis thaliana]; supported by cDNA:          
    gi_13430839_gb_AF360332.1_AF360332          
  263182_at   Expressed protein; supported by full-length cDNA:   At1g05575   19.34   −1.02   0.005652   0.804382
    Ceres: 27081.          
  249417_at   calcium-binding protein-like cbp1 calcium-binding   At5g39670   18.84   −1.03   0.012777   0.874622
  protein, Lotus japonicus, EMBL: LJA251808;          
    supported by cDNA:          
  gi_16648829_gb_AY058192.1          
  254120_at   putative mitochondrial uncoupling protein   At4g24570   18.47   −1.26   0.006894   0.121685
  mitochondrial uncoupling protein, Arabidopsis          
  thaliana (thale cress), PATX: E1316826; supported          
    by full-length cDNA: Ceres: 119476.          
  264153_at   disease resistance protein RPS4, putative similar to   At1g65390   17.77   −1.01   0.006757   0.837017
    disease resistance protein RPS4 GI: 5459305 from          
  [Arabidopsis thaliana]          
  249264_s_at   disease resistance protein-like   At5g41740   17.16   1.01   0.016032   0.965149
  246821_at   calmodulin-binding-like protein calmodulin-   At5g26920   16.58   −1.22   0.002033   0.305516
  binding protein TCB60, Nicotiana tabacum,          
    EMBL: U58971          
  265327_at   unknown protein   At2g18210   16.02   −1.08   0.007312   0.847704
  252131_atBCS1 protein-like protein Homo sapiens h-bcs1   At3g50930   15.81   1.28   0.020727   0.19657
    (BCS1) mRNA, nuclear gene encoding          
    mitochondrial protein which is involved in the          
    expression of functional mitochondrial ubiquinol-          
    cytochrome c reductase complex probably via the          
    control of expression of Riesk          
  245840_at   hypothetical protein predicted by   At1g58420   15.76   −1.16   0.001929   0.649675
    genemark.hmm; supported by full-length cDNA:          
    Ceres: 124269.          
  245041_at   AR781, similar to yeast pheromone receptor   At2g26530   15.71   −1.4   0.011514   0.105739
    identical to GB: D88743, corrected a frameshift          
    found in the original record (at 69530 bp), sequence          
    submitted has been verified from 10 sequence          
    electropherograms. The translation now starts from          
    an upstream ATG.          
  248799_at   ethylene responsive element binding factor 5   At5g47230   15.6   −1.36   0.005208   0.117072
    (ATERF5) (sp|O80341); supported by cDNA:          
    gi_14326511_gb_AF385709.1_AF385709          
  250149_at   cinnamoyl CoA reductase-like protein cinnamoyl   At5g14700   15.46   −1.13   0.022877   0.554222
  CoA reductase, Populus tremuloides,          
    EMBL: AF217958; supported by full-length cDNA:          
    Ceres: 17229.          
  256306_at   lipase, putative contains Pfam profile: PF01764:   At1g30370   15.3   1.11   0.00866   0.751633
    Lipase          
  246777_at   RING-H2 zinc finger protein-like RING-H2 zinc   At5g27420   14.67   −1.44   0.011803   0.037951
  finger protein ATL6-Arabidopsis thaliana,          
    EMBL: AF132016; supported by full-length cDNA:          
    Ceres: 106078.          
  263783_at   putative WRKY-type DNA binding protein;   At2g46400   14.41   1.26   0.005589   0.126494
    supported by cDNA:          
  gi_15430276_gb_AY046275.1          
  245369_at   Expressed protein; supported by full-length cDNA:   At4g15975   14.34   1.03   0.00366   0.920236
    Ceres: 124835.          
  251336_at   putative protein hypothetical protein F4I18.26-   At3g61190   14.31   1.07   0.007665   0.724447
  Arabidopsis thaliana, PIR: T02471; supported by full-          
    length cDNA: Ceres: 30454.          
  260046_at   Expressed protein; supported by cDNA:   At1g73800   13.55   1   0.010217   0.9771
  gi_16648699_gb_AY058126.1          
  260068_at   putative calmodulin-binding protein similar to   At1g73805   13.35   1.16   0.007383   0.51944
    calmodulin-binding protein GB: AAB37246          
  [Nicotiana tabacum]          
  266071_at   unknown protein   At2g18680   13.32   1.11   0.004216   0.713949
  253643_at   hypothetical protein; supported by full-length   At4g29780   13.05   −1.11   0.002383   0.344174
    cDNA: Ceres: 249769.          
  264213_at   hypothetical protein contains similarity to lectin   At1g65400   12.76   −1.17   0.021498   0.255697
  polypeptide GI: 410436 from [Cucurbita maxima]          
  262382_at   virus resistance protein, putative similar to virus   At1g72920   12.68   −1.4   0.003189   0.073493
  resistance protein GI: 558886 from [Nicotiana          
  glutinosa]          
  247543_at   DNA binding protein-like DNA binding protein   At5g61600   12.31   −1.31   0.014862   0.112814
  EREBP-4, Nicotiana tabacum,          
    PIR: T02434; supported by full-length cDNA:          
    Ceres: 92102.          
  256442_at   hypothetical protein predicted by   At3g10930   11.62   −1.07   0.025288   0.782271
    genefinder; supported by full-length cDNA:          
    Ceres: 12509.          
  253060_atputative protein predicted protein, Arabidopsis   At4g37710   11.56   1.34   0.005721   0.412461
  thaliana; supported by full-length cDNA:          
    Ceres: 207350.          
  253915_atputative protein centrin, Marsilea vestita; supported   At4g27280   11.5   −1.07   0.01185   0.333253
    by full-length cDNA: Ceres: 13072.          
  249928_at   CCR4-associated factor-like protein   At5g22250   11.41   −1.17   0.009043   0.204172
  245711_at   putative c2h2 zinc finger transcription factor   At5g04340   11.35   −1.11   0.016673   0.392119
  261892_at   transcription factor, putative similar to WRKY   At1g80840   11.27   1.09   0.006954   0.498704
    transcription factor GB: BAA87058 GI: 6472585          
  from [Nicotiana tabacum]; supported by full-length          
    cDNA: Ceres: 6437.          
  261394_at   wall-associated kinase 2, putative similar to wall-   At1g79680   11.05   1.08   0.003074   0.819188
  associated kinase 2 GI: 4826399 from [Arabidopsis          
  thaliana]          
  251774_at   nematode resistance protein-like protein Hs1pro-1   At3g55840   11.02   −1.37   0.007795   0.481526
  nematode resistance gene, Beta procumbens,          
    EMBL: BPU79733; supported by full-length cDNA:          
    Ceres: 149697.          
  265723_at   putative disease resistance protein   At2g32140   10.99   1.18   0.016981   0.537825
  255339_athypothetical protein similar to A. thaliana   At4g04480   10.83   1.32   0.012367   0.514455
    hypothetical protein F1N20.130, GenBank accession          
    number AL022140          
  251054_at   receptor like protein kinase receptor like protein   At5g01540   10.66   −1.01   0.003949   0.917593
  kinase-Arabidopsis thaliana, EMBL: ATLECGENE;          
    supported by cDNA:          
    gi_13605542_gb_AF361597.1_AF361597          
  253827_at   Expressed protein; supported by cDNA:   At4g28085   10.37   −1.09   0.010797   0.530514
  gi_15028040_gb_AY045877.1          
  255945_at   putative protein   At5g28610   10.06   1.21   0.010366   0.464865
  249618_atputative protein predicted proteins, Arabidopsis   At5g37490   9.99   −1.09   0.004719   0.814525
  thalina          
  248934_at   serine/threonine protein kinase-like protein   At5g46080   9.94   −1.17   0.007605   0.645509
  261037_at   lipoxygenase identical to GB: CAB56692 from   At1g17420   9.88   −1.1   0.002351   0.775492
  (Arabidopsis thaliana)          
  267623_at   unknown protein   At2g39650   9.87   −1.12   0.006744   0.439834
  259428_at   MAP kinase, putative similar to MAP kinase 5   At1g01560   9.84   1.54   0.002458   0.135149
  GI: 4239889 from [Zea mays]          
  246927_s_atnodulin-like protein nodulin, Glycine max,   At5g25260   9.74   1.6   0.004623   0.163075
    EMBL: AF065435          
  264758_at   late embryogenesis abundant protein, putative   At1g61340   9.73   1.17   0.016626   0.389155
    similar to late embryogenesis abundant protein          
  GI: 1350540 from [Picea glauca]          
  245329_at   Expressed protein; supported by full-length cDNA:   At4g14365   9.7   1.42   0.002486   0.029582
    Ceres: 37809.          
  262072_at   hypothetical protein predicted by   At1g59590   9.54   −1.12   0.009452   0.599212
    genemark.hmm; supported by full-length cDNA:          
    Ceres: 99553.          
  255844_at   putative protein kinase contains a protein kinase   At2g33580   9.42   1.11   0.006611   0.553845
    domain profile (PDOC00100)          
  253632_at   senescence-associated protein homolog senescence-   At4g30430   9.29   1.22   0.004184   0.351697
    associated protein 5-Hemerocallis hybrid          
    cultivar, PID: g3551954; supported by full-length          
    cDNA: Ceres: 122632.          
  257511_at   hypothetical protein   At1g43000   9.29   −1.13   0.020984   0.846669
  253999_at   1-aminocyclopropane-1-carboxylate synthase-like   At4g26200   9.24   −1.56   0.004129   0.115048
  protein ACC synthase, Malus domestica, U73816          
  265920_s_at   unknown protein   At2g15120   9.13   1.33   0.001682   0.33404
  263800_at   hypothetical protein predicted by genscan; supported   At2g24600   8.97   1.02   0.014457   0.769925
  by cDNA: gi_15810330_gb_AY056204.1          
  248164_at   putative protein similar to unknown protein   At5g54490   8.97   −1.17   0.008767   0.190232
    (pir||T05752); supported by full-length cDNA:          
    Ceres: 109272.          
  265597_at   Expressed protein; supported by cDNA:   At2g20145   8.96   −1   0.023429   0.965819
    gi_13605516_gb_AF361584.1_AF361584          
  248327_at   putative protein similar to unknown protein   At5g52750   8.93   −1.04   0.017097   0.808905
    (emb|CAA71173.1); supported by full-length cDNA:          
    Ceres: 19542.          
  252908_at   putative protein   At4g39670   8.56   1.17   0.012661   0.466742
  251400_atputative protein prib5, Ribes nigrum,   At3g60420   8.53   1.64   0.029245   0.023237
    EMBL: RNI7578; supported by full-length cDNA:          
    Ceres: 31361.          
  261475_at   anionic peroxidase, putative similar to anionic   At1g14550   8.51   1.41   0.01103   0.395333
  peroxidase GI: 170202 from [Nicotiana sylvestris]          
  256185_at   dof zinc finger protein identical to dof zinc finger   At1g51700   8.47   −1.09   0.001565   0.51485
  protein [Arabidopsis thaliana] GI: 3608261;          
    supported by cDNA:          
    gi_3608260_dbj_AB017564.1_AB017564          
  250493_at   putative protein various predicted proteins,   At5g09800   8.28   −1.06   0.010787   0.857557
  Arabidopsis thaliana          
  252679_at   CCR4-associated factor 1-like protein   At3g44260   8.27   −1.27   0.000484   0.065446
    CAF1_MOUSE CCR4-ASSOCIATED FACTOR 1-          
  Mus musculus, SWISSPROT: CAF1_MOUSE;          
    supported by cDNA:          
  gi_15292828_gb_AY050848.1          
  265797_at   Expressed protein; supported by full-length cDNA:   At2g35715   8.26   −1.27   0.005817   0.60028
    Ceres: 9996.          
  248448_at   putative protein contains similarity to ethylene   At5g51190   8.25   −1.1   0.009635   0.575899
    responsive element binding factor; supported by full-          
    length cDNA: Ceres: 2347.          
  255884_at   hypothetical protein predicted by   At1g20310   8.15   −1.19   0.022852   0.204061
    genemark.hmm; supported by full-length cDNA:          
    Ceres: 8562.          
  261449_at   putative ATPase similar to GB: AAF28353 from   At1g21120   7.97   1.46   0.004955   0.182958
  [Fragaria x ananassa]          
  265841_at   putative glycogenin   At2g35710   7.96   −1.27   0.011587   0.280483
  251895_at   class IV chitinase (CHIV)   At3g54420   7.95   −1.09   0.003142   0.722712
  263935_at   unknown protein   At2g35930   7.89   −1.06   0.006185   0.342267
  255502_at   contains similarity to a protein kinase domain (Pfam:   At4g02410   7.89   −1.07   0.003365   0.691648
    pkinase.hmm, score: 166.20) and to legume lectins          
    beta domain (Pfam: lectin_legB.hmm, score: 139.32)          
  258787_at   hypothetical protein predicted by genscan; supported   At3g11840   7.84   −1.13   0.036463   0.37994
    by full-length cDNA: Ceres: 100676.          
  266658_at   Expressed protein; supported by full-length cDNA:   At2g25735   7.71   −1.47   0.003942   0.026409
    Ceres: 7152.          
  245250_at   ethylene responsive element binding factor-like   At4g17490   7.54   1.06   0.008242   0.704323
    protein (AtERF6); supported by cDNA:          
    gi_3298497_dbj_AB013301.1_AB013301          
  247487_atputative protein predicted protein, Arabidopsis   At5g62150   7.39   1.01   0.005388   0.945249
  thaliana          
  261470_at   ethylene-responsive element binding factor, putative   At1g28370   7.33   −1.17   0.005528   0.478834
    similar to ethylene-responsive element binding factor          
  GI: 8809573 from [Nicotiana sylvestris]; supported by          
    full-length cDNA: Ceres: 27635.          
  262381_at   virus resistance protein, putative similar to virus   At1g72900   7.27   −1.19   0.006528   0.311035
  resistance protein GI: 558886 from [Nicotiana          
  glutinosa]          
  248123_at   putative protein similar to unknown protein   At5g54720   7.23   1.29   0.006214   0.245803
    (gb|AAD32884.1)          
  263379_at   putative CCCH-type zinc finger protein also an   At2g40140   7.21   1.01   0.004911   0.848966
    ankyrin-repeat protein          
  263584_at   NAM (no apical meristem)-like protein similar to   At2g17040   7.13   −1.29   0.006099   0.12014
  petunia NAM (X92205) and A. thaliana sequences          
    ATAF1 (X74755) and ATAF2 (X74756); probable          
    DNA-binding protein; supported by cDNA:          
    gi_13605646_gb_AF361804.1_AF361804          
  259566_at   hypothetical protein   At1g20520   7.04   −1.14   0.024145   0.734624
  267028_at   putative WRKY-type DNA binding protein   At2g38470   7.02   −1.19   0.009642   0.27064
  265008_at   Mlo protein, putative similar to Mlo protein   At1g61560   6.99   1.2   0.00298   0.470024
  GI: 1877220 from [Hordeum vulgare]; supported by          
    cDNA: gi_14091581_gb_AF369567.1_AF369567          
  247693_at   putative protein leucine zipper-containing protein,   At5g59730   6.97   1.01   0.004438   0.963142
  Lycopersicon esculentum, PIR: S21495; supported by          
  cDNA: gi_14334437_gb_AY034910.1          
  257748_at   hypothetical protein predicted by genemark.hmm   At3g18710   6.82   −1.16   0.009082   0.446456
  258351_at   hypothetical protein contains similarity to ion   At3g17700   6.78   −1.02   0.004386   0.920019
  channel protein from [Arabidopsis thaliana];          
    supported by cDNA:          
    gi_8131897_gb_AF148541.1_AF148541          
  251745_at   putative protein zinc finger transcription factor   At3g55980   6.71   −1.36   0.001393   0.169064
  (PEI1), Arabidopsis thaliana, EMBL: AF050463;          
    supported by cDNA:          
  gi_15810486_gb_AY056282.1          
  257536_at   unknown protein   At3g02800   6.46   1.24   0.011172   0.244827
  246108_at   putative protein retinal glutamic acid-rich protein,   At5g28630   6.43   −1.14   0.017801   0.374617
    bovine, PIR: A40437; supported by full-length cDNA:          
    Ceres: 24151.          
  256046_at   unknown protein   At1g07135   6.42   −1.28   0.005287   0.339032
  258436_at   putative RING zinc finger protein similar to RING-   At3g16720   6.39   −1.2   0.002525   0.290143
    H2 zinc finger protein ATL6 GB: AAD33584 from          
  [Arabidopsis thaliana]; supported by full-length          
    cDNA: Ceres: 4581.          
  254255_at   serine/threonine kinase-like protein   At4g23220   6.39   1.58   0.01157   0.225448
  serine/threonine kinase, Brassica oleracea; supported          
    by cDNA:          
    gi_14423417_gb_AF386946.1_AF386946          
  248686_at   33 kDa secretory protein-like; supported by cDNA:   At5g48540   6.37   1.07   0.007302   0.530534
  gi_15292980_gb_AY050924.1          
  248726_at   RAS superfamily GTP-binding protein-like;   At5g47960   6.34   −1   0.011505   0.996984
    supported by cDNA:          
    gi_12004622_gb_AF218121.1_AF218121          
  256633_at   unknown protein   At3g28340   6.32   −1.23   0.013314   0.277616
  256183_at   MAP kinase kinase 4 (ATMKK4) identical to MAP   At1g51660   6.32   1.03   0.001255   0.842274
  kinase kinase 4 [Arabidopsis thaliana]; supported by          
    cDNA: gi_13265419_gb_AF324667.2_AF324667          
  247949_at   cytochrome P450   At5g57220   6.31   −1.03   0.00798   0.740555
  250098_at   putative protein; supported by full-length cDNA:   At5g17350   6.21   −1.09   0.005623   0.628534
    Ceres: 1198.          
  255504_at   drought-induced-19-like 1 similar to drought-   At4g02200   6.14   1.1   0.002902   0.428306
    induced-19, GenBank accession number X78584          
    similar to F2P16.10, GenBank accession number          
    2191179 identical to T10M13.20          
  253414_at   putative protein   At4g33050   6.08   −1.1   0.002073   0.284317
  262731_at   hypothetical protein similar to gb|AF098458 latex-   At1g16420   6.07   1.18   0.016528   0.727417
  abundant protein (LAR) from Hevea brasiliensis          
  247848_at   resistance protein-like disease resistance protein   At5g58120   6.07   −1.04   0.01295   0.876046
  RPP1-WsA, Arabidopsis thaliana, EMBL: AF098962          
  254926_at   ACC synthase (AtACS-6); supported by cDNA:   At4g11280   6.04   −1.17   0.005123   0.161176
    gi_16226285_gb_AF428292.1_AF428292          
  249719_at   Expressed protein; supported by full-length cDNA:   At5g35735   6.04   −1.08   0.005081   0.233393
    Ceres: 32450.          
  247208_at   nodulin-like; supported by full-length cDNA:   At5g64870   6.04   1.22   0.001605   0.225756
    Ceres: 142026.          
  257478_at   hypothetical protein similar to putative   At1g16130   5.96   −1.23   0.008918   0.562604
    serine/threonine-specific protein kinase GI: 7270012          
  from [Arabidopsis thaliana]          
  246993_at   Cys2/His2-type zinc finger protein 1   At5g67450   5.95   −1.06   0.005299   0.855156
    (dbj|BAA85108.1)          
  252060_at   putative protein other hypothetical proteins in   At3g52430   5.94   1.2   0.005073   0.34486
  Arabidopsis thaliana; supported by cDNA:          
    gi_6457330_gb_AF188329.1_AF188329          
  267381_at   unknown protein; supported by cDNA:   At2g26190   5.9   −1.09   0.006528   0.587987
    gi_16930468_gb_AF419588.1_AF419588          
  245038_atsimilar to latex allergen from Hevea brasiliensis;   At2g26560   5.89   −1.06   0.019374   0.83179
    supported by full-length cDNA: Ceres: 1999.          
  266800_at   hypothetical protein predicted by genefinder   At2g22880   5.86   −1.01   0.003336   0.993661
  259211_at   unknown protein identical to GB: AAD56318   At3g09020   5.82   1.08   0.00649   0.5476
  (Arabidopsis thaliana)          
  253485_at   Expressed protein; supported by full-length cDNA:   At4g31800   5.82   −1.13   0.00494   0.428126
    Ceres: 40692.          
  260211_at   hypothetical protein similar to YGL010w-like   At1g74440   5.77   1.06   0.003351   0.730279
  protein GB: AAC32136 [Picea mariana]          
  256093_at   predicted protein; supported by cDNA:   At1g20823   5.74   −1.35   0.016068   0.107243
  gi_15027984_gb_AY045849.1          
  267451_at   putative AP2 domain transcription factor   At2g33710   5.72   −1.17   0.015334   0.725714
  260411_at   hypothetical protein similar to GB: AAB61488   At1g69890   5.71   −1.29   0.011204   0.168552
  [Arabidopsis thaliana]; supported by full-length          
    cDNA: Ceres: 34864.          
  254592_at   heat shock transcription factor-like protein heat   At4g18880   5.7   −1.08   0.009829   0.552909
  shock transcription factor, Zea mays, PIR2: S61448          
  264000_at   putative mitochondrial dicarboxylate carrier protein;   At2g22500   5.68   −1.18   0.004964   0.182153
    supported by full-length cDNA: Ceres: 20723.          
  263475_at   Expressed protein; supported by full-length cDNA:   At2g31945   5.63   1   0.00655   0.971652
    Ceres: 258917.          
  254408_at   serine/threonine kinase-like protein serine/threonine   At4g21390   5.63   1.2   0.003477   0.605633
  kinase BRLK, Brassica oleracea, gb: Y12531          
  245209_at   putative protein similarity to predicted protein,   At5g12340   5.63   −1.23   0.004077   0.532051
  Arabidopsis thaliana          
  259629_at   disease resistance protein contains domains   At1g56510   5.61   −1.13   0.009583   0.608416
    associated with disease resistance genes in plants:          
    TIR/NB-ARC/LRR          
  247655_at   zinc finger protein Zat12; supported by full-length   At5g59820   5.56   1.2   0.004335   0.099425
    cDNA: Ceres: 40576.          
  266834_s_at   putative protein phosphatase 2C   At2g30020   5.52   −1.03   0.005778   0.730603
  256181_at   light repressible receptor protein kinase, putative   At1g51820   5.51   −1.08   0.002365   0.605128
    similar to light repressible receptor protein kinase          
  GI: 1321686 from (Arabidopsis thaliana)          
  251705_at   DNA-binding protein-like DNA-binding protein 4   At3g56400   5.5   −1.03   0.00667   0.83389
  WRKY4-Nicotiana tabacum,          
    EMBL: AF193771; supported by full-length cDNA:          
    Ceres: 34847.          
  251097_at   receptor like protein kinase receptor like protein   At5g01560   5.48   −1.09   0.00945   0.858858
  kinase-Arabidopsis thaliana, EMBL: ATLECGENE          
  248392_at   integral membrane protein-like   At5g52050   5.45   −1.21   0.005162   0.477438
  254158_at   putative protein dihydrofolate reductase-   At4g24380   5.44   −1.17   0.013347   0.342417
  Schizosaccharomyces          
  pombe, PID: e1320950; supported by full-length          
    cDNA: Ceres: 27155.          
  260406_at   putative glutathione transferase similar to glutathione   At1g69920   5.41   2.07   0.009635   0.082596
  transferase GB: CAA09188 [Alopecurus          
  myosuroides]          
  254241_at   serine/threonine kinase-like protein serine/threonine   At4g23190   5.37   1.09   0.001802   0.566443
  kinase, Brassica oleracea          
  265674_at   unknown protein; supported by full-length cDNA:   At2g32190   5.3   1.24   0.013333   0.440285
    Ceres: 40344.          
  264757_at   receptor protein kinase (IRK1), putative similar to   At1g61360   5.28   −1.05   0.002166   0.73136
    receptor protein kinase (IRK1) GI: 836953 from          
  [Ipomoea trifida]          
  248875_at   disease resistance protein-like   At5g46470   5.28   −1.01   0.004999   0.943089
  247708_at   putative protein COP1-interacting protein CIP8,   At5g59550   5.28   −1.21   0.003861   0.156044
  Arabidopsis thaliana, EMBL: AF162150; supported          
  by cDNA: gi_15450686_gb_AY052711.1          
  260239_at   putative receptor protein kinase similar to   At1g74360   5.26   1.27   0.014165   0.212238
    brassinosteroid insensitive 1 GB: AAC49810          
    (putative receptor protein kinase); contains Pfam          
    profiles: PF00560 Leucine Rich Repeat (17 repeats),          
    PF00069 Eukaryotic protein kinase domain;          
    supported by cDNA: gi_158          
  255549_at   predicted protein of unknown function   At4g01950   5.23   −1.02   0.009729   0.893458
  266992_atsimilar to Mlo proteins from H. vulgare; supported   At2g39200   5.21   −1.12   0.008101   0.282992
    by cDNA:          
    gi_14091593_gb_AF369573.1_AF369573          
  261973_at   hypothetical protein predicted by genemark.hmm   At1g64610   5.19   −1.09   0.005786   0.674167
  254242_at   serine/threonine kinase-like protein serine/   At4g23200   5.19   1.03   0.007882   0.840853
  threonine kinase, Brassica oleracea          
  260477_at   Ser/Thr protein kinase isolog   At1g11050   5.15   −1.34   0.029135   0.243484
  265670_s_at   unknown protein; supported by full-length cDNA:   At2g32210   5.07   1.19   0.014682   0.138268
    Ceres: 31665.          
  265199_s_at   putative glucosyl transferase   At2g36770   5.07   1.33   0.003771   0.194926
  247493_atcopine-like protein copine I, Homo sapiens,   At5g61900   5.07   1.04   0.003077   0.714944
    EMBL: HSU83246; supported by full-length cDNA:          
    Ceres: 146738.          
  265737_at   putative phosphatidic acid phosphatase; supported   At2g01180   5.04   −1.05   0.00382   0.74519
    by full-length cDNA: Ceres: 19163.          
  260243_at   hypothetical protein similar to putative protein   At1g63720   5.01   1.07   0.019639   0.772243
  GB: CAA18164 [Arabidopsis thaliana]; supported by          
    cDNA: gi_13878144_gb_AF370335.1_AF370335          
  252045_at   putative protein arm repeat containing protein ARC1-   At3g52450   5.01   1.25   0.012091   0.125673
  Brassica napus, PID: g2558938          
  250153_at   putative protein TMV response-related gene product,   At5g15130   5   1.05   0.011689   0.809857
  Nicotiana tabacum, EMBL: AB024510          
  247047_at   putative protein contains similarity to unknown   At5g66650   4.98   −1.01   0.006647   0.888192
    protein (gb AAC17084.1); supported by cDNA:          
  gi_14596230_gb_AY042903.1          
  261476_at   hypothetical protein contains similarity to alpha-   At1g14480   4.97   1.14   0.02789   0.562278
    latroinsectotoxin precursor GI: 9537 from          
  [Latrodectus tredecimguttatus]          
  247205_at   unknown protein; supported by full-length cDNA:   At5g64890   4.96   1.59   0.010532   0.389292
    Ceres: 9242.          
  261450_s_at   O-methyltransferase, putative similar to   At1g21110   4.95   1.5   0.02203   0.137219
  GB: AAF28353 from [Fragaria x ananassa]          
  252474_at   putative protein several hypothetical proteins-   At3g46620   4.94   −1.06   0.006633   0.705845
  Arabidopsis thaliana          
  257840_at   protein kinase, putative contains Pfam profile:   At3g25250   4.93   1.19   0.013824   0.496857
    PF00069 Eukaryotic protein kinase domain          
  248964_at   cytochrome P450   At5g45340   4.93   −1.52   0.003815   0.013613
  247071_at   putative protein similar to unknown protein (emb   At5g66640   4.92   −1.02   0.010559   0.987089
    CAB16816.1)          
  246270_at   putative protein   At4g36500   4.92   −1.2   0.002823   0.230335
  261033_at   unknown protein; supported by full-length cDNA:   At1g17380   4.84   −1.01   0.017643   0.96188
    Ceres: 37370.          
  260261_at   unknown protein   At1g68450   4.78   −1.03   0.006946   0.882923
  249485_at   receptor protein kinase-like protein receptor-protein   At5g39020   4.74   1.03   0.002268   0.823569
  kinase-like protein, Arabidopsis thaliana,          
    PIR: T45786          
  256487_at   disease resistance gene, putative similar to downy   At1g31540   4.73   1.14   0.01107   0.679977
  mildew resistance protein RPP5 [Arabidopsis          
  thaliana] GI: 6449046          
  249983_at   putative protein S-receptor kinase PK3 precursor,   At5g18470   4.69   1.03   0.006021   0.801393
    maize, PIR: T02753; supported by full-length cDNA:          
    Ceres: 154037.          
  258682_at   putative ribosomal-protein S6 kinase (ATPK19)   At3g08720   4.68   1.12   0.009464   0.260404
    identical to putative ribosomal-protein S6 kinase          
  (ATPK19) GB: D42061 [Arabidopsis thaliana]          
    (FEBS Lett. 358 (2), 199-204 (1995)); supported by          
  cDNA: gi_15292784_gb_AY050826.1          
  254487_at   calcium-binding protein-like calcium-binding   At4g20780   4.63   −1.43   0.015022   0.176224
  protein, Solanum tuberosum, gb: L02830          
  265728_at   hypothetical protein predicted by genscan   At2g31990   4.62   −1.14   0.025876   0.616683
  258792_at   hypothetical protein predicted by   At3g04640   4.62   −1.08   0.003809   0.521094
    genefinder, supported by full-length cDNA:          
    Ceres: 8992.          
  253535_at   putaive DNA-binding protein DNA-binding protein   At4g31550   4.62   −1.17   0.001616   0.072643
  WRKY3-Petroselinum crispum,          
    PIR2: S72445; supported by full-length cDNA:          
    Ceres: 11953.          
  257751_at   hypothetical protein predicted by   At3g18690   4.6   −1.01   0.006195   0.939184
    genemark.hmm; supported by full-length cDNA:          
    Ceres: 104278.          
  261367_at   protein kinase, putative similar to many predicted   At1g53080   4.59   1.31   0.008723   0.439817
    protein kinases          
  247240_at   putative protein strong similarity to unknown protein   At5g64660   4.57   −1.08   0.004191   0.392312
    (emb|CAB89350.1)          
  261526_at   protein kinase identical to protein kinase GI: 2852447   At1g14370   4.56   −1.08   0.004758   0.475696
  from [Arabidopsis thaliana]; supported by cDNA:          
    gi_2852446_dbj_D88206.1_D88206          
  254948_at   putative protein various predicted proteins,   At4g11000   4.55   1.03   0.020674   0.901116
  Arabidopsis thaliana          
  245119_at   unknown protein; supported by cDNA:   At2g41640   4.54   −1.2   0.013528   0.323955
    gi_16930450_gb_AF419579.1_AF419579          
  248319_at   unknown protein   At5g52710   4.5   −1.19   0.022646   0.498394
  245765_at   hypothetical protein similar to putative disease   At1g33600   4.5   −1.01   0.00753   0.943437
    resistance protein GB: AAC14512 GI: 2739389 from          
  [Arabidopsis thaliana]          
  248821_at   protein serine threonine kinase-like   At5g47070   4.49   1.13   0.005807   0.220356
  245272_at   hypothetical protein; supported by cDNA:   At4g17250   4.49   −1   0.016447   0.969266
  gi_16323154_gb_AY057681.1          
  255595_at   putative chitinase similar to peanut type II chitinase,   At4g01700   4.48   1.09   0.009232   0.455046
    GenBank accession number X82329, E.C. 3.2.1.14          
  249918_atputative protein predicted protein, Arabidopsis   At5g19240   4.48   1.11   0.005605   0.490746
  thaliana          
  263565_at   unknown protein   At2g15390   4.45   −1.28   0.011298   0.375612
  261713_at   protein kinase, putative identical to bHLH protein   At1g32640   4.43   1.12   0.002007   0.392042
  GB: CAA67885 GI: 1465368 from [Arabidopsis          
  thaliana]; supported by cDNA:          
  gi_14335047_gb_AY037203.1          
  262772_at   puative calcium-transporting ATPase similar to   At1g13210   4.4   −1.06   0.004192   0.641809
  gb|AF038007 FIC1 gene from Homo sapiens and is a          
    member of the PF|00122 E1-E2 ATPase family.          
    ESTs gb|T45045 and gb|AA394473 come from this          
    gene          
  258364_at   unknown protein   At3g14225   4.4   −1.49   0.013195   0.305266
  257022_at   zinc finger protein, putative similar to Cys2/His2-   At3g19580   4.39   −1.04   0.01073   0.818188
    type zinc finger protein 2 GB: BAA85107 from          
  [Arabidopsis thaliana]; supported by cDNA:          
  gi_15028256_gb_AY046043.1          
  252053_at   syntaxin-like protein synt4; supported by full-length   At3g52400   4.38   1.02   0.002866   0.837782
    cDNA: Ceres: 37248.          
  250695_at   lectin-like protein kinase   At5g06740   4.38   −1.34   0.030543   0.436678
  246293_at   SigA binding protein; supported by cDNA:   At3g56710   4.38   −1.01   0.005488   0.98387
  gi_14596086_gb_AY042831.1          
  249032_at   putative protein contains similarity to disease   At5g44910   4.37   1.06   0.010921   0.589391
    resistance protein          
  265189_at   unknown protein; supported by cDNA:   At1g23840   4.34   1.12   0.020118   0.585186
  gi_14335017_gb_AY037188.1          
  265668_at   putative alanine acetyl transferase; supported by   At2g32020   4.31   1.45   0.006627   0.053107
    full-length cDNA: Ceres: 21201.          
  264232_at   putative protein kinase Pfam HMM hit: Eukaryotic   At1g67470   4.3   −1.07   0.003961   0.651045
    protein kinase domain; identical to GB: AAC18787          
  (Arabidopsis thaliana)          
  263948_at   similar to harpin-induced protein hin1 from tobacco;   At2g35980   4.28   1.34   0.007735   0.319605
    supported by full-length cDNA: Ceres: 26418.          
  261748_at   hypothetical protein predicted by   At1g76070   4.27   −1.05   0.034903   0.781675
    genemark.hmm; supported by full-length cDNA:          
    Ceres: 39494.          
  252278_atNAC2-like protein NAC2-Arabidopsis thaliana,   At3g49530   4.25   −1.01   0.001287   0.915747
    EMBL: AF201456; supported by cDNA:          
  gi_16604578_gb_AY059734.1          
  247137_at   calcium-dependent protein kinase; supported by   At5g66210   4.23   −1.01   0.004474   0.902625
    full-length cDNA: Ceres: 18901.          
  255568_at   putative DNA-binding protein; supported by   At4g01250   4.21   −1.2   0.010495   0.218487
  cDNA: gi_15028172_gb_AY045909.1          
  259479_at   Expressed protein; supported by full-length cDNA:   At1g19020   4.2   1.23   0.002707   0.175614
    Ceres: 31015.          
  245247_at   scarecrow-like 13 (SCL13); supported by cDNA:   At4g17230   4.2   1.06   0.010533   0.625637
    gi_16930432_gb_AF419570.1_AF419570          
  252470_at   protein kinase 6-like protein protein kinase 6-   At3g46930   4.19   1.13   0.012875   0.362838
  Glycine max, PIR2: S29851          
  256050_at   leucine zipper protein, putative similar to leucine   At1g07000   4.16   1.04   0.018298   0.855313
  zipper protein GI: 10177020 from [Arabidopsis          
  thaliana]          
  261405_at   unknown protein; supported by full-length cDNA:   At1g18740   4.15   −1.11   0.00951   0.382476
    Ceres: 40753.          
  267288_at   similar to cold acclimation protein WCOR413   At2g23680   4.12   1.06   0.026303   0.758149
  [Triticum aestivum]          
  252592_at   mitogen-activated protein kinase 3; supported by   At3g45640   4.12   −1.15   0.004807   0.119458
    cDNA: gi_14423447_gb_AF386961.1_AF386961          
  247125_at   putative protein contains similarity to unknown   At5g66070   4.11   1   0.001239   0.979764
    protein (gb|AAF18680.1)          
  265184_at   unknown protein; supported by full-length cDNA:   At1g23710   4.09   −1.18   0.014497   0.24269
    Ceres: 36437.          
  247773_at   putative protein   At5g58630   4.09   −1.08   0.006176   0.825067
  263478_at   putative receptor-like protein kinase; supported by   At2g31880   4.08   1.14   0.00624   0.158364
  cDNA: gi_16648754_gb_AY058153.1          
  251910_at   serine/threonine-specific kinase like protein   At3g53810   4.05   −1.02   0.002869   0.843094
    serine/threonine-specific kinase (EC 2.7.1.—)          
  precursor-Arabidopsis thaliana, PIR: S68589          
  245662_at   hypothetical protein predicted by genemark.hmm   At1g28190   4.04   −1.23   0.0328   0.44426
  259997_at   unknown protein similar to N-   At1g67880   4.03   1   0.005767   0.973619
    acetylglucosaminyltransferase III GB: AAC53064          
  [Mus musculus]          
  252179_at   putative protein UDP-glucose: (glucosyl) LPS   At3g50760   4.03   −1.04   0.00304   0.802486
  alpha1,3-glucosyltransferase WaaO, E. coli,          
    EMBL: AF019746          
  252928_at   putative protein more than 30 predicted proteins,   At4g38940   4.01   1.07   0.000729   0.325455
  Arabidopsis; supported by full-length cDNA:          
    Ceres: 40069.          
  251832_at   putative protein tomato leucine zipper-containing   At3g55150   4.01   1.41   0.010257   0.134388
  protein, Lycopersicon esculentum, PIR: S21495          
  266396_at   unknown protein   At2g38790   4   1.05   0.027395   0.850892
  259400_at   receptor-like protein kinase, putative similar to   At1g17750   3.97   −1.02   0.042252   0.932069
    receptor-like protein kinase INRPK1 GI: 1684913          
  from [Ipomoea nil]          
  255654_at   Similar to receptor kinase   At4g00970   3.97   −1.11   0.010838   0.737951
  254587_at   resistance protein RPP5-like downy mildew   At4g19520   3.97   −1.05   0.00768   0.89806
  resistance protein RPP5, Arabidopsis thaliana,          
    PATX: G2109275          
  255753_at   myb factor, putative similar to myb factor   At1g18570   3.95   1.03   0.004424   0.830522
  GI: 1946266 from [Oryza sativa]; supported by          
    cDNA: gi_3941465_gb_AF062887.1_AF062887          
  246532_at   putative protein beta-glucan-elicitor receptor-   At5g15870   3.94   −1.02   0.015841   0.913394
  Glycine max, EMBL: D78510          
  246631_at   unknown protein; supported by full-length cDNA:   At1g50740   3.93   1.04   0.006841   0.56351
    Ceres: 34587.          
  252533_atputative protein predicted proteins, Arabidopsis   At3g46110   3.9   1.02   0.017185   0.893955
  thaliana          
  267384_at   unknown protein highly similar to   At2g44370   3.88   1.08   0.005016   0.736235
    GP|2435515|AF024504          
  258650_at   putative protein kinase similar to protein kinase   At3g09830   3.88   1.11   0.012936   0.571912
  (APK1A) GB: Q06548 [Arabidopsis thaliana];          
    contains Pfam profile: PF00069 Eukaryotic protein          
    kinase domain          
  249339_at   putative protein similar to unknown protein   At5g41100   3.88   −1.05   0.004061   0.72083
    (gb|AAB80666.1)          
  248794_at   ethylene responsive element binding factor 2   At5g47220   3.87   −1.23   0.011156   0.098663
    (ATERF2) (sp|O80338); supported by full-length          
    cDNA: Ceres: 3012.          
  245457_s_at   disease resistance RPP5 like protein   At4g16960   3.86   1.18   0.010259   0.375561
  248316_at   putative protein similar to unknown protein   At5g52670   3.84   −1.03   0.006334   0.875191
    (emb|CAA71173.1)          
  253046_at   cytochrome P450-like protein cytochrome P450,   At4g37370   3.83   2.17   0.019261   0.016853
  Glycyrrhiza echinata, AB001379; supported by full-          
    length cDNA: Ceres: 253698.          
  262374_s_at   flax rust resistance protein, putative similar to flax   At1g72930   3.81   1.03   0.004406   0.567071
  rust resistance protein GI: 4588066 from [Linumusitatissimum];          
    supported by full-length cDNA:          
    Ceres: 2795.          
  258537_at   putative disease resistance protein similar to disease   At3g04210   3.81   1.09   0.005941   0.472196
    resistance protein RPP1-WsC GB: AAC72979          
  [Arabidopsis thaliana]; supported by cDNA:          
  gi_15982829_gb_AY057522.1          
  252648_at   disease resistance protein homolog disease   At3g44630   3.81   −1.23   0.007177   0.068548
  resistance protein RPP1-WsB-Arabidopsis thaliana,          
    EMBL: AF098963          
  247913_at   unknown protein   At5g57510   3.81   1.12   0.009476   0.608703
  267411_at   putative disease resistance protein   At2g34930   3.8   −1.06   0.015151   0.825604
  265440_at   pEARLI 4 protein Same as GB: L43081; supported   At2g20960   3.8   −1.08   0.001968   0.382136
    by cDNA: gi_871781_gb_L43081.1_ATHPEARA          
  245252_at   ethylene responsive element binding factor 1   At4g17500   3.8   −1.47   0.008058   0.087956
    (frameshift !); supported by cDNA:          
    gi_3434966_dbj_AB008103.1_AB008103          
  259033_at   putative pectinacetylesterase similar to   At3g09410   3.79   1.64   0.003796   0.052828
    pectinacetylesterase precursor GB: CAA67728          
  [Vigna radiata]          
  246233_at   putative protein   At4g36550   3.79   −1.43   0.028755   0.228285
  255599_at   cyclic nucleotide gated channel (CNGC4) like   At4g01010   3.78   −1.02   0.00606   0.91649
  protein Arabidopsis thaliana cyclic nucleotide gated          
    channel (CNGC4), PID: g4378659          
  262901_at   hypothetical protein predicted by genemark.hmm   At1g59910   3.77   −1.08   0.006294   0.540378
  259952_at   putative disease resistance protein similar to Cf-4   At1g71400   3.74   1.08   0.001393   0.408545
  GB: CAA05268 from (Lycopersicon hirsutum)          
  246858_at   receptor-like protein kinase-like receptor-like   At5g25930   3.73   1.02   0.015786   0.964753
  protein kinase 5, Arabidopsis thaliana, PIR: S27756          
  250435_at   putative protein various predicted proteins,   At5g10380   3.72   1.22   0.007856   0.106321
  Arabidopsis thaliana          
  261650_at   envelope Ca2+-ATPase identical to envelope Ca2+-   At1g27770   3.71   1.05   0.00839   0.580228
    ATPase GB: AAD01212 GI: 516118 from          
  (Arabidopsis thaliana); supported by cDNA:          
    gi_493621_dbj_D13983.1_ATHRCECAA          
  252906_at   putative gamma-glutamyltransferase gamma-   At4g39640   3.71   1.07   0.012355   0.562612
  glutamyltransferase, Arabidopsis thaliana,          
    PIR2: S58286          
  251636_at   calcium-dependent protein kinase calcium-   At3g57530   3.71   −1.26   0.016722   0.11982
  dependent protein kinase-Fragaria x ananassa,          
    EMBL: AF035944          
  247426_at   putative protein contains similarity to calmodulin-   At5g62570   3.67   1.02   0.018802   0.878551
    binding protein          
  266685_at   hypothetical protein   At2g19710   3.66   −1   0.018487   0.952139
  249903_at   disease resistance protein-like   At5g22690   3.65   −1.04   0.010635   0.754135
  247925_at   TCH4 protein (gb|AAA92363.1); supported by   At5g57560   3.65   −1.28   0.003003   0.132214
    cDNA: gi_14194112_gb_AF367262.1_AF367262          
  248611_at   putative protein contains similarity to WRKY-type   At5g49520   3.63   −1.45   0.010966   0.13904
    DNA-binding protein          
  265221_s_at   putative glutamate decarboxylase; supported by   At2g02010   3.62   −1.12   0.01727   0.698419
    cDNA: gi_13605709_gb_AF361836.1_AF361836          
  259792_at   unknown protein; supported by cDNA:   At1g29690   3.62   −1.05   0.013953   0.685925
  gi_15809819_gb_AY054177.1          
  256576_at   zinc finger protein (PMZ), putative identical to   At3g28210   3.62   1.34   0.019514   0.107277
    putative zinc finger protein (PMZ) GB: AAD37511          
  GI: 5006473 [Arabidopsis thaliana]          
  254784_at   growth factor like protein antisense basic fibroblast   At4g12720   3.62   1.06   0.012904   0.638871
  growth factor GFG-Rattus norvegicus,          
    PID: g1518635; supported by full-length cDNA:          
    Ceres: 148575.          
  247177_at   unknown protein; supported by cDNA:   At5g65300   3.62   1.1   0.004863   0.387978
    gi_13877834_gb_AF370180.1_AF370180          
  245226_at   gene_id: K17E7.15~unknown protein   At3g29970   3.6   1.76   0.01017   0.066452
  256756_at   ATPase II, putative similar to GB: AAD34706 from   At3g25610   3.59   −1.01   0.009255   0.929097
  [Homo sapiens] (Biochem. Biophys. Res. Commun.          
    257 (2), 333-339 (1999))          
  253140_at   RING-H2 finger protein RHA3b; supported by full-   At4g35480   3.56   −1.04   0.013391   0.651703
    length cDNA: Ceres: 31493.          
  250289_at   putative protein; supported by full-length cDNA:   At5g13190   3.56   1.18   0.000966   0.176346
    Ceres: 5392.          
  247811_at   leucine zipper-containing protein leucine zipper-   At5g58430   3.56   −1.01   0.001344   0.933016
  containing protein, Lycopersicon esculentum,          
    PIR: S21495          
  261899_at   cinnamoyl CoA reductase, putative similar to   At1g80820   3.55   −1.11   0.01598   0.720481
    cinnamoyl CoA reductase GB: AAF43141          
  GI: 7239228 from [Populus tremuloides]; supported          
    by full-length cDNA: Ceres: 32255.          
  245866_s_at   unknown protein   At1g57990   3.55   −1.09   0.011056   0.501011
  264867_at   unknown protein   At1g24150   3.53   −1   0.030643   0.978236
  261193_at   unknown protein; supported by cDNA:   At1g32920   3.53   −1.12   0.009489   0.382199
  gi_15450636_gb_AY052686.1          
  261339_at   protein kinase, putative similar to many predicted   At1g35710   3.51   1.32   0.013195   0.062019
    protein kinases          
  267490_at   putative receptor-like protein kinase   At2g19130   3.5   1   0.015702   0.997521
  259561_at   hypothetical protein; supported by cDNA:   At1g21250   3.49   1.52   0.005151   0.042781
  gi_14532585_gb_AY039917.1          
  263228_at   putative reticuline oxidase-like protein similar to   At1g30700   3.48   1.07   0.007823   0.648304
  GB: P30986 from [Eschscholzia californica]          
    (berberine bridge-forming enzyme), ESTs          
    gb|F19886, gb|Z30784 and gb|Z30785 come from          
    this gene; supported by cDNA:          
    gi_16930506_gb_AF419607.1_AF419607          
  255627_at   Expressed protein; supported by full-length cDNA:   At4g00955   3.48   1.08   0.009206   0.72176
    Ceres: 93818.          
  254256_at   serine/threonine kinase-like protein serine/threonine   At4g23180   3.45   −1.2   0.002919   0.140829
  kinase, Brassica oleracea; supported by cDNA:          
    gi_13506744_gb_AF224705.1_AF224705          
  260135_at   calmodulin-related protein similar to GB: P25070   At1g66400   3.44   −1.11   0.013883   0.371779
  from [Arabidopsis thaliana], contains Pfam profile:          
    PF00036 EF hand (4 copies); supported by full-          
    length cDNA: Ceres: 95959.          
  260206_at   putative protein kinase contains Pfam profile:   At1g70740   3.43   −1.12   0.012329   0.420329
    PF00069 Eukaryotic protein kinase domain          
  259887_at   putative protein kinase similar to protein kinase   At1g76360   3.42   1.1   0.008975   0.501823
    (APK1A); contains Pfam profile: PF00069          
    Eukaryotic protein kinase domain          
  262383_at   disease resistance protein, putative similar to disease   At1g72940   3.41   1.18   0.011942   0.230832
  resistance protein GI: 9758876 from [Arabidopsis          
  thaliana]          
  256177_at   protein kinase, putative contains Pfam profile:   At1g51620   3.41   1.23   0.01444   0.359679
    PF00069: Eukaryotic protein kinase domain          
  245777_at   unknown protein contains similarity to   At1g73540   3.41   −1.25   0.026487   0.341823
    diphosphoinositol polyphosphate phosphohydrolase          
  GI: 3978224 from [Homo sapiens]          
  249221_at   serine/threonine protein kinase-like protein   At5g42440   3.4   −1.02   0.005295   0.883947
  245448_at   disease resistance RPP5 like protein   At4g16860   3.4   −1.15   0.027985   0.375642
  254869_at   protein kinase-like protein KI domain interacting   At4g11890   3.37   2.12   0.007665   0.003284
    kinase 1-Zea mays, PIR2: T02053          
  256755_at   calmodulin, putative similar to GB: P07463 from   At3g25600   3.37   −1.05   0.007284   0.663209
  [Paramecium tetraurelia] (Cell 62 (1), 165-174          
    (1990))          
  264107_s_at   putative receptor-like protein kinase   At2g13790   3.34   1.16   0.008131   0.293891
  266017_at   unknown protein; supported by cDNA:   At2g18690   3.32   1.36   0.008527   0.108178
  gi_14517479_gb_AY039575.1          
  263776_s_at   putative cyclic nucleotide-regulated ion channel   At2g46440   3.32   1.21   0.026465   0.278033
    protein          
  245193_at   F12A21.6 hypothetical protein   At1g67810   3.32   1.17   0.00613   0.205789
  256522_at   unknown protein; supported by full-length cDNA:   At1g66160   3.3   −1.22   0.004073   0.074994
    Ceres: 35218.          
  248703_at   dermal glycoprotein precursor, extracellular-like   At5g48430   3.28   1.09   0.005001   0.574329
  260434_at   hypothetical protein predicted by genscan+   At1g68330   3.27   −1.14   0.006128   0.614427
  252652_at   putative chloroplast prephenate dehydratase similar   At3g44720   3.23   1.08   0.004759   0.192206
    to bacterial PheA gene products          
  260023_at   unknown protein   At1g30040   3.21   1.26   0.004354   0.301041
  251640_at   putative protein; supported by full-length cDNA:   At3g57450   3.21   −1.03   0.002724   0.717428
    Ceres: 12522.          
  264314_at   unknown protein; supported by cDNA:   At1g70420   3.18   1.24   0.00926   0.33473
  gi_15010575_gb_AY045589.1          
  262549_at   hypothetical protein similar to hypothetical protein   At1g31290   3.18   1.36   0.017342   0.141779
  GB: AAF24586 GI: 6692121 from [Arabidopsis          
  thaliana]          
  261459_at   O-methyltransferase, putative similar to   At1g21100   3.18   1.37   0.006504   0.199125
  GB: AAF28353 from [Fragaria x ananassa];          
    supported by cDNA:          
  gi_15982843_gb_AY057529.1          
  249139_at   Cys2/His2-type zinc finger protein 3   At5g43170   3.18   −1.11   0.014619   0.403291
    (dbj|BAA85109.1); supported by full-length cDNA:          
    Ceres: 9878.          
  248980_at   putative protein similar to unknown protein   At5g45090   3.18   −1.03   0.006572   0.837241
    (pir||T04765)          
  264660_at   putative glutamyl-tRNA reductase 2 precursor   At1g09940   3.17   −1.02   0.009351   0.857849
  similar to GB: P49294 and to A. thaliana HEMA2          
    (gb|U27118)          
  254014_at   NPR1 like protein regulatory protein NPR1-   At4g26120   3.17   1.03   0.021113   0.898299
  Arabidopsis thaliana, PID: g1773295          
  252126_at   putative disease resistance protein   At3g50950   3.17   1.08   0.00517   0.256863
  262228_at   protein kinase, putative similar to protein kinase 1   At1g68690   3.16   1.18   0.018754   0.421396
  GB: BAA94509 GI: 7573596 from [Populus nigra];          
    supported by cDNA:          
  gi_14334805_gb_AY035076.1          
  259626_at   bZIP transcription factor, putative contains Pfam   At1g42990   3.15   1.08   0.006031   0.361959
    profile: PF00170: bZIP transcription factor;          
    supported by cDNA:          
  gi_15028322_gb_AY045964.1          
  254063_at   receptor kinase-like protein receptor-like protein   At4g25390   3.15   −1.09   0.021274   0.509081
  kinase, RLK3-Arabidopsis thaliana, PID: e1363211          
  259443_at   chitinase, putative similar to chitinase GI: 1237025   At1g02360   3.14   1.33   0.010757   0.097826
  from [Arachis hypogaea]          
  266615_s_at   putative monooxygenase; supported by full-length   At2g29720   3.13   −1   0.006073   0.993995
    cDNA: Ceres: 34214.          
  251507_at   putative protein CND41, chloroplast nucleoid DNA   At3g59080   3.13   −1.26   0.019246   0.076416
  binding protein-Nicotiana tabacum,          
    EMBL: D26015; supported by cDNA:          
    gi_15983375_gb_AF424562.1_AF424562          
  246870_at   ferrochelatase-I   At5g26030   3.12   −1.03   0.007971   0.563075
  261063_at   transcription factor scarecrow-like 14, putative   At1g07520   3.09   1.05   0.0041   0.648222
  similar to GB: AAD24412 from [Arabidopsis          
  thaliana] (Plant J. 18 (1), 111-119 (1999))          
  260296_at   putative disease resistance protein similar to disease   At1g63750   3.07   −1.24   0.035995   0.346342
    resistance protein (RPP1-WsC) GB: AAC72979          
  [Arabidopsis thaliana]          
  248868_at   putative protein similar to unknown protein   At5g46780   3.07   1.08   0.012841   0.668687
    (gb|AAC61815.1); supported by full-length cDNA:          
    Ceres: 254442.          
  267069_at   unknown protein   At2g41010   3.06   −1   0.022932   0.942266
  261143_at   unknown protein   At1g19770   3.06   −1.07   0.003012   0.469481
  255116_at   receptor protein kinase-like protein receptor protein   At4g08850   3.06   1.13   0.013035   0.33618
  kinase-like protein-Arabidopsis thaliana,          
    PIR2: T05898          
  253284_at   putative protein hydroxyproline-rich glycoprotein   At4g34150   3.05   1.01   0.004615   0.829133
  precursor, Nicotiana tabacum, PIR2: S06733;          
    supported by cDNA:          
    gi_15724315_gb_AF412098.1_AF412098          
  252903_at   putative protein various predicted proteins,   At4g39570   3.05   −1.05   0.005467   0.697229
  Arabidopsis thaliana          
  254847_at   putative phospholipase D-gamma phospholipase D-   At4g11850   3.04   −1.01   0.014523   0.911568
  gamma-Arabidopsis thaliana, PID: g2653885;          
    supported by cDNA:          
    gi_2653884_gb_AF027408.1_AF027408          
  251937_atputative protein predicted protein, Arabidopsis   At3g53400   3.04   1.04   0.035806   0.858509
  thaliana          
  256366_at   protein kinase, putative contains Pfam profile:   At1g66880   3.03   1.12   0.002701   0.411044
    PF00069: Eukaryotic protein kinase domain          
  247393_at   unknown protein   At5g63130   3.03   −1.65   0.018398   0.063566
  260556_at   putative endochitinase   At2g43620   3.02   1.32   0.003455   0.0287
  259445_at   dioxygenase, putative similar to dioxygenase   At1g02400   3.01   1.16   0.012122   0.130623
  GI: 1666096 from [Marah macrocarpus]          
  259298_at   putative disease resistance protein similar to Cf-2   At3g05370   3.01   −1.08   0.040444   0.621247
    disease resistance protein GB: AAC15780 from          
  [Lycopersicon pimpinellifolium]          
  257644_at   unknown protein; supported by full-length cDNA:   At3g25780   3.01   1.19   0.022772   0.336306
    Ceres: 3457.          
  253628_at   xyloglucan endo-1,4-beta-D-glucanase-like protein   At4g30280   3.01   1.29   0.005842   0.110446
    xyloglucan endo-1,4-beta-D-glucanase (EC 3.2.1.—)          
  XTR-3-Arabidopsis          
  thaliana, PIR2: S71222; supported by full-length          
    cDNA: Ceres: 142204.          
  249072_at   putative protein similar to unknown protein   At5g44060   3.01   1.08   0.007698   0.56653
    (gb|AAD10670.1)          
  253257_at   extra-large G-protein-like extra-large G-protein,   At4g34390   3   −1.06   0.004333   0.352585
  Arabidopsis thaliana, AF060942          
  253124_atputative protein unknown protein Arabidopsis   At4g36030   3   −1.07   0.016993   0.706449
  thaliana, PATX: E248475          
  250676_at   harpin-induced protein-like; supported by cDNA:   At5g06320   3   1.02   0.003772   0.798472
    gi_9502175_gb_AF264699.1_AF264699          
  266037_at   putative protein kinase contains a protein kinase   At2g05940   2.99   1.03   0.011895   0.742301
    domain profile (PDOC00100); supported by cDNA:          
  gi_15810412_gb_AY056245.1          
  254314_at   extensin-like protein hybrid proline-rich protein,   At4g22470   2.98   −1.04   0.013677   0.797081
  Zea mays, PIR2: JQ1663          
  252825_at   small GTP-binding protein-like SR1 Nt-rab6,   At4g39890   2.97   1.25   0.014269   0.471148
  Nicotiana tabacum, L29273; supported by cDNA:          
    gi_14423429_gb_AF386952.1_AF386952          
  260401_at   unknown protein similar to hypothetical protein   At1g69840   2.96   1.19   0.013016   0.197702
  GB: CAA10289 [Cicer arietinum]          
  250821_at   putative protein similar to unknown protein   At5g05190   2.95   −1.11   0.008801   0.532383
    (emb|CAB88044.1)          
  245265_at   hypothetical protein; supported by cDNA:   At4g14400   2.95   1.34   0.046774   0.092249
  gi_15810232_gb_AY056155.1          
  264289_at   hypothetical protein similar to hypothetical protein   At1g61890   2.94   1.17   0.016735   0.217477
  GI: 2894569 from [Arabidopsis thaliana]; supported          
  by cDNA: gi_15028186_gb_AY045916.1          
  259410_at   hypothetical protein predicted by genemark.hmm   At1g13340   2.94   1.45   0.015002   0.097363
  253958_atputative protein RING zinc finger protein, Gallus   At4g26400   2.94   1.06   0.002619   0.621194
  gallus          
  249078_at   phytochelatin synthase (gb|AAD41794.1);   At5g44070   2.94   −1.02   0.008033   0.806261
    supported by cDNA:          
  gi_14532653_gb_AY039951.1          
  267293_at   hypothetical protein   At2g23810   2.93   −1.06   0.004637   0.578539
  259992_at   putative heat shock transcription factor contains   At1g67970   2.93   −1.01   0.006051   0.910383
    Pfam profile: PF00447 HSF-type DNA-binding          
    domain; N-terminal portion similar to heat shock          
    transcription factor proteins: GB: CAA74397          
  [Arabidopsis thaliana], GB: S25478 [Lycopersicon          
  esculentum]          
  252862_at   putative L-ascorbate oxidase L-ascorbate oxidase,   At4g39830   2.93   1.13   0.009756   0.383415
  Cucumis sativus, PIR1: KSKVAO          
  249550_at   protein kinase-like protein wall-associated kinase 4   At5g38210   2.93   −1.13   0.00676   0.38925
  (wak4), Arabidopsis thaliana, EMBL: ATH9695          
  247279_at   arabinogalactan-protein (gb|AAC77823.1);   At5g64310   2.93   −1.01   0.00661   0.937671
    supported by full-length cDNA: Ceres: 25423.          
  265450_at   hypothetical protein predicted by genefinder   At2g46620   2.92   −1.03   0.014924   0.733991
  251479_at   serine/threonine-specific kinase lecRK1   At3g59700   2.91   −1.08   0.008769   0.515335
    precursor, lectin receptor-like          
  249418_atputative protein predicted protein, Arabidopsis   At5g39780   2.91   1.1   0.015458   0.521455
  thaliana          
  266247_at   hypothetical protein predicted by genscan   At2g27660   2.89   −1.11   0.009688   0.350456
  249252_at   putative protein contains similarity to unknown   At5g42010   2.89   −1.05   0.014073   0.747236
    protein (gb|AAF19687.1)          
  255291_at   putative calcium dependent protein kinase   At4g04700   2.88   −1.04   0.023496   0.890022
  253747_at   serine threonine-specific kinase like protein serine   At4g29050   2.87   −1.09   0.011457   0.626019
  threonine-specific kinase lecRK1-Arabidopsis          
  thaliana, PIR2: S68589          
  250323_at   putative protein hydroxyproline-rich glycoprotein,   At5g12880   2.87   1.06   0.009216   0.469664
    kidney bean, PIR: A29356          
  262801_at   unknown protein; supported by full-length cDNA:   At1g21010   2.86   1.08   0.017653   0.443505
    Ceres: 17521.          
  251061_at   putative protein hypothetical protein ARC1-   At5g01830   2.86   1.18   0.015743   0.623238
  Brassica napus, PIR: T08872          
  265132_at   unknown protein; supported by cDNA:   At1g23830   2.84   −1.07   0.017467   0.652241
  gi_16604403_gb_AY058100.1          
  260439_at   hypothetical protein predicted by   At1g68340   2.84   −1.04   0.003917   0.840841
    genscan+; supported by full-length cDNA:          
    Ceres: 3385.          
  260227_at   unknown protein similar to hypothetical proteins   At1g74450   2.83   −1.16   0.009649   0.269848
  GB: AAD39276 [Arabidopsis thaliana],          
  GB: CAB53491 [Oryza sativa]; supported by full-          
    length cDNA: Ceres: 108193.          
  261453_at   O-methyltransferase, putative similar to   At1g21130   2.82   −1.15   0.010888   0.513201
  GB: AAF28353 from [Fragaria x ananassa];          
    supported by full-length cDNA:          
    Ceres: 101583.          
  254432_at   reticuline oxidase-like protein reticuline oxidase,   At4g20830   2.82   1.19   0.046062   0.572211
  Eschscholzia californica, PIR: A41533; supported by          
    cDNA: gi_15983492_gb_AF424621.1_AF424621          
  253971_at   fructose-bisphosphate aldolase-like protein   At4g26530   2.82   −1.02   0.016712   0.805977
  fructose-bisphosphate aldolase, Arabidopsis thaliana,          
    PIR1: ADMU; supported by full-length cDNA:          
    Ceres: 34690.          
  262165_at   putative acyl-CoA: 1-acylglycerol-3-phosphate   At1g75020   2.81   −1.13   0.010295   0.275107
    acyltransferase similar to acyl-CoA: 1-acylglycerol-          
    3-phosphate acyltransferase GB: CAB09138          
  (Brassica napus); contains Pfam profile: PF01553          
    Acyltransferase; supported by full-length cDNA:          
    Ceres: 115679.          
  258275_at   unknown protein; supported by full-length cDNA:   At3g15760   2.81   −1.09   0.002884   0.259472
    Ceres: 8259.          
  255564_s_at   hypothetical protein T15B16.8   At4g01750   2.81   1.28   0.004474   0.364426
  253377_at   putative protein NBS/LRR disease resistance protein   At4g33300   2.81   1.03   0.008788   0.64371
  (RFL1)-Arabidopsis thaliana, PID: g3309619          
  260220_at   putative MYB family transcription factor contains   At1g74650   2.8   −1.05   0.014801   0.787419
    Pfam profile: PF00249 Myb-like DNA-binding          
    domain          
  256583_at   hypothetical protein   At3g28850   2.8   1.08   0.009872   0.39554
  252193_at   R2R3-MYB transcription factor; supported by   At3g50060   2.8   −1.67   0.007202   0.02821
    cDNA: gi_15983427_gb_AF424588.1_AF424588          
  247509_at   heat shock factor 6   At5g62020   2.8   1.11   0.004718   0.497285
  246368_at   light repressible receptor protein kinase, putative   At1g51890   2.8   1.32   0.007014   0.17566
    similar to light repressible receptor protein kinase          
  GI: 1321686 from [Arabidopsis thaliana]          
  259507_at   unknown protein   At1g43910   2.79   1.41   0.005884   0.156323
  251769_at   receptor kinase-like protein receptor kinase   At3g55950   2.79   1.02   0.037029   0.858886
    homolog CRINKLY4, maize, PIR: T04108          
  250335_at   lysophospholipase-like protein lysophospholipase   At5g11650   2.78   1.07   0.004853   0.539031
  homolog LPL1, Oryza sativa,          
    EMBL: AF039531; supported by full-length cDNA:          
    Ceres: 15284.          
  248134_at   putative protein contains similarity to integral   At5g54860   2.78   1.09   0.010767   0.465367
    membrane protein          
  246988_at   putative protein strong similarity to unknown protein   At5g67340   2.78   1.18   0.01807   0.609865
    (pir||T00518)          
  247707_at   scarecrow-like 11-like scarecrow-like 11,   At5g59450   2.76   −1.06   0.028093   0.649019
  Arabidopsis thaliana, EMBL: AF036307; supported          
  by cDNA: gi_14334655_gb_AY035001.1          
  256497_at   ORF1, putative similar to ORF1 GI: 457716 from   At1g31580   2.75   1.39   0.004888   0.080053
  (Arabidopsis thaliana); supported by cDNA:          
  gi_16649160_gb_AY059950.1          
  264008_at   unknown protein   At2g21120   2.74   −1.01   0.003042   0.876414
  264716_at   matrix metalloproteinase, putative similar to matrix   At1g70170   2.73   −1.02   0.005524   0.873758
  metalloproteinase GI: 7159629 from [Cucumis          
  sativus]          
  261445_at   unknown protein; supported by cDNA:   At1g28380   2.73   −1.06   0.02128   0.701956
  gi_16604598_gb_AY059744.1          
  256968_at   unknown protein   At3g21070   2.73   −1.14   0.014315   0.494381
  256763_at   unknown protein   At3g16860   2.73   −1.06   0.01099   0.724699
  255605_at   hypothetical protein   At4g01090   2.73   −1.18   0.02941   0.263496
  254652_at   DNA binding-like protein SPF1 protein, sweet   At4g18170   2.73   1.05   0.048645   0.839297
    protein, PIR2: S51529 and WRKY protein family,          
  Petroselinum crispum, MNOS: S72443,          
    MNOS: S72444, MNOS: S72445          
  247532_at   putative protein disease resistance protein kinase Pto,   At5g61560   2.73   −1.03   0.020053   0.845513
  Lycopersiocon esculentum, PIR: A49332          
  264106_at   unknown protein   At2g13780   2.71   1.2   0.013998   0.074305
  265075_at   hypothetical protein similar to embryo-abundant   At1g55450   2.7   −1.08   0.016743   0.546091
  protein GB: L47672 GI: 1350530 from [Picea glauca];          
    supported by cDNA:          
  gi_14335021_gb_AY037190.1          
  256793_at   unknown protein; supported by full-length cDNA:   At3g22160   2.69   −1.09   0.013465   0.391312
    Ceres: 8081.          
  258551_at   hypothetical protein predicted by   At3g06890   2.68   −1.02   0.016594   0.966946
    genscan+; supported by full-length cDNA:          
    Ceres: 262487.          
  255740_at   wall-associated kinase, putative similar to wall-   At1g25390   2.68   −1.15   0.012139   0.281008
  associated kinase 1 GI: 3549626 from [Arabidopsis          
  thaliana]; supported by cDNA:          
  gi_15529241_gb_AY052245.1          
  246099_at   blue copper binding protein; supported by full-   At5g20230   2.67   1.7   0.008061   0.011289
    length cDNA: Ceres: 7767.          
  264616_at   unknown protein   At2g17740   2.67   1   0.022917   0.884668
  254042_at   xyloglucan endo-1,4-beta-D-glucanase (XTR-6);   At4g25810   2.66   1.07   0.002288   0.480301
    supported by cDNA:          
    gi_1244757_gb_U43488.1_ATU43488          
  246289_at   putative protein predicted protein At2g41010-   At3g56880   2.66   −1.02   0.010884   0.82618
  Arabidopsis thaliana; EMBL: AC004261; supported          
    by full-length cDNA: Ceres: 39584.          
  266792_at   putative sucrose/H+ symporter   At2g02860   2.65   1.05   0.005194   0.618209
  265853_at   putative RING zinc finger protein   At2g42360   2.64   1.27   0.007875   0.101121
  258786_at   putative syntaxin contains Pfam profile: PF00804   At3g11820   2.64   1.16   0.005501   0.095192
    syntaxin; supported by full-length cDNA:          
    Ceres: 38899.          
  247940_at   phosphatidylserine decarboxylase   At5g57190   2.64   −1.08   0.02156   0.742477
  257083_s_at   non-race specific disease resistance protein, putative   At3g20590   2.63   −1.1   0.022335   0.571353
    contains non-consensus CT donor splice site at exon          
    1; potential pseudogene; similar to non-race specific          
    disease resistance protein GB: AAB95208          
  [Arabidopsis thaliana]          
  264434_at   hypothetical protein predicted by genscan; supported   At1g10340   2.61   1.14   0.016538   0.421888
    by cDNA:          
    gi_13937239_gb_AF372975.1_AF372975          
  263804_at   putative protein kinase contains a protein kinase   At2g40270   2.61   1.02   0.002801   0.766513
    domain profile (PDOC00100); supported by full-          
    length cDNA: Ceres: 123911.          
  249896_at   unknown protein; supported by cDNA:   At5g22530   2.61   1.12   0.01975   0.439704
  gi_14532613_gb_AY039931.1          
  249459_at   peroxidase ATP24a   At5g39580   2.61   −1.24   0.011537   0.098646
  247740_at   receptor-like protein kinase precursor-like receptor-   At5g58940   2.61   1.11   0.013363   0.45095
    like protein kinase precursor, Madagascar          
    periwinkle, PIR: T10060          
  246931_at   putative protein apoptosis-related protein PNAS-4,   At5g25170   2.6   1.01   0.003003   0.89146
  Homo sapiens, EMBL: AF229834; supported by full-          
    length cDNA: Ceres: 263500.          
  265713_at   putative integral membrane protein   At2g03530   2.59   −1.18   0.010284   0.275593
  263931_at   unknown protein; supported by full-length cDNA:   At2g36220   2.59   1.04   0.032332   0.640228
    Ceres: 12251.          
  264834_at   unknown protein similar to ESTs gb|AA605440 and   At1g03730   2.58   1.02   0.006042   0.863016
    gb|H37232; supported by full-length cDNA:          
    Ceres: 30716.          
  259852_at   disulfide bond formation protein, putative similar to   At1g72280   2.58   1.24   0.014598   0.356183
  GI: 6642925 from [Mus musculus]          
  252539_at   putative protein   At3g45730   2.58   1.3   0.009508   0.150314
  252378_at   receptor kinase-like protein protein kinase Xa21-   At3g47570   2.58   1.12   0.02363   0.435178
  Oryza sativa, PIR: A57676; supported by cDNA:          
  gi_15810450_gb_AY056264.1          
  251684_at   putative protein   At3g56410   2.57   1.08   0.023561   0.592162
  261719_at   hypothetical protein similar to hypothetical protein   At1g18380   2.56   1.36   0.016331   0.094821
  GB: AAF25996 GI: 6714300 from [Arabidopsis          
  thaliana]          
  254248_at   serine/threonine kinase serine/threonine kinase,   At4g23270   2.56   −1.04   0.006144   0.687459
  Brassica oleracea          
  253204_at   GTP binding protein beta subunit; supported by   At4g34460   2.56   −1.01   0.007411   0.949586
  cDNA: gi_15028006_gb_AY045860.1          
  249361_at   protein kinase-like protein protein kinase ATN1,   At5g40540   2.55   −1   0.004647   0.984046
  Arabidopsis thaliana, PIR: S61766          
  248665_at   Expressed protein; supported by full-length cDNA:   At5g48655   2.55   1.02   0.009359   0.848153
    Ceres: 12974.          
  253455_at   putative protein   At4g32020   2.54   −1.01   0.00825   0.888496
  248978_at   putative protein contains similarity to disease   At5g45070   2.54   −1.05   0.030143   0.671649
    resistance protein          
  248870_at   putative protein similar to unknown protein   At5g46710   2.54   1.03   0.004547   0.48662
    (pir||T05076); supported by full-length cDNA:          
    Ceres: 42747.          
  252170_at   hypothetical protein; supported by cDNA:   At3g50480   2.53   1.09   0.00647   0.431092
    gi_13605735_gb_AF361849.1_AF361849          
  264636_at   hypothetical protein predicted by   At1g65490   2.52   1.04   0.019945   0.653146
    genemark.hmm; supported by full-length cDNA:          
    Ceres: 2118.          
  264400_at   glucose-6-phosphate/phosphate-translocator   At1g61800   2.51   −1.13   0.035853   0.380949
    precursor, putative similar to glucose-6-          
    phosphate/phosphate-translocator precursor          
  GI: 2997591 from [Pisum sativum]; supported by          
  cDNA: gi_14596172_gb_AY042874.1          
  245567_at   germin precursor oxalate oxidase   At4g14630   2.51   −1.12   0.010395   0.322763
  264083_at   ethylene reponse factor-like AP2 domain   At2g31230   2.5   −1.09   0.007348   0.596007
    transcription factor          
  261220_at   ER lumen protein-retaining receptor similar to   At1g19970   2.5   1.11   0.01247   0.321046
  SP: O44017 from [Entamoeba histolytica]          
  259546_at   unknown protein   At1g35350   2.49   −1.02   0.009622   0.86289
  266101_at   unknown protein; supported by cDNA:   At2g37940   2.47   1.05   0.006689   0.366431
  gi_16604321_gb_AY058059.1          
  262384_at   disease resistance protein, putative similar to disease   At1g72950   2.47   −1.07   0.017043   0.63375
  resistance protein GI: 9758876 from [Arabidopsis          
  thaliana]          
  251423_at   regulatory protein-like regulatory protein preg,   At3g60550   2.47   1.04   0.005454   0.86361
  Neurospora crassa, PIR: S52974          
  259312_at   putative RING-H2 zinc finger protein ATL6 similar   At3g05200   2.46   −1.11   0.020543   0.252889
  to GB: AAD33584 from [Arabidopsis thaliana];          
    supported by cDNA:          
    gi_4928402_gb_AF132016.1_AF132016          
  267624_at   putative protein kinase   At2g39660   2.45   −1.1   0.015362   0.313576
  266230_at   hypothetical protein predicted by genscan and   At2g28830   2.45   1.03   0.03586   0.739871
    genefinder; supported by cDNA:          
  gi_14334729_gb_AY035038.1          
  260656_at   hypothetical protein predicted by genemark.hmm   At1g19380   2.45   1.12   0.012154   0.152235
  253664_at   NADPH-ferrihemoprotein reductase (ATR2)   At4g30210   2.45   1.06   0.014893   0.463357
  251259_at   putative protein phosphoprotein phosphatase (EC   At3g62260   2.45   1.09   0.008555   0.495561
  3.1.3.16) 1A-alpha-Homo sapiens,          
    PIR: S22423; supported by full-length cDNA:          
    Ceres: 20050.          
  267357_at   putative nematode-resistance protein; supported by   At2g40000   2.44   1.16   0.031618   0.266241
    full-length cDNA: Ceres: 35056.          
  254521_at   putative protein similar to unknown protein   At5g44810   2.44   −1.09   0.041638   0.416086
    (gb|AAC79139.1)          
  263419_at   putative protein kinase contains a protein kinase   At2g17220   2.43   1.09   0.008341   0.27009
    domain profile (PDOC00100); supported by full-          
    length cDNA: Ceres: 13257.          
  253323_atputative protein protein phosphatase Wip1, Homo   At4g33920   2.43   −1.13   0.025096   0.456412
  sapiens, PID: g2218063; supported by full-length          
    cDNA: Ceres: 40123.          
  258983_at   putative aminotransferase similar to beta-alanine-   At3g08860   2.42   1.14   0.006331   0.051755
  pyruvate aminotransferase GB: BAA19549 [Rattus          
  norvegicus], alanine-glyoxylate aminotransferase          
  GB: Q64565 [Rattus norvegicus]; Pfam HMM hit:          
    Aminotransferases class-III pyridoxal-phosphate          
  249583_at   CALMODULIN-RELATED PROTEIN 2, TOUCH-   At5g37770   2.42   −1.17   0.006305   0.208762
    INDUCED (TCH2); supported by full-length cDNA:          
    Ceres: 25475.          
  258046_at   MAP kinase kinase 5 identical to GB: BAA28831   At3g21220   2.41   1.13   0.013633   0.416118
  from [Arabidopsis thaliana]; supported by cDNA:          
    gi_3219272_dbj_AB015316.1_AB015316          
  250990_at   serine/threonine-specific protein kinase NAK;   At5g02290   2.41   −1.12   0.012886   0.320809
    supported by full-length cDNA: Ceres: 27477.          
  249423_at   Expressed protein; supported by full-length cDNA:   At5g39785   2.41   −1.13   0.026115   0.657212
    Ceres: 118847.          
  248814_at   putative protein similar to unknown protein   At5g46910   2.4   −1.03   0.007949   0.787827
    (pir||T06699)          
  254204_atputative protein CGI-58 protein-Homo   At4g24160   2.38   −1.04   0.010591   0.590709
  sapiens, PID: g4929585          
  252485_at   disease resistance protein RPP13-like protein   At3g46530   2.37   −1.05   0.012107   0.677972
  disease resistance protein RPP8-Arabidopsis          
  thaliana, EMBL: AF089710; supported by cDNA:          
  gi_14334999_gb_AY037179.1          
  265620_at   unknown protein   At2g27310   2.35   −1.2   0.049206   0.345125
  264756_at   receptor protein kinase (IRK1), putative similar to   At1g61370   2.35   −1.07   0.010494   0.634376
    receptor protein kinase (IRK1) GI: 836953 from          
  [Ipomoea trifida]          
  266993_at   nodulin-like protein; supported by cDNA:   At2g39210   2.33   1.12   0.017636   0.371447
    gi_16930478_gb_AF419593.1_AF419593          
  256735_at   hypothetical protein predicted by genemark.hmm   At3g29400   2.33   −1.12   0.006192   0.192654
  256425_at   disease resistance protein, putative similar to disease   At1g33560   2.33   1.04   0.010206   0.488005
    resistance protein RPP1-WsB GB: BAB01321          
  GI: 9279731 from (Arabidopsis thaliana)          
  250829_atdisease resistance-like protein rpp8, Arabidopsis   At5g04720   2.33   −1.08   0.013721   0.38143
  thaliana, EMBL: AF089711; supported by cDNA:          
  gi_15292720_gb_AY050794.1          
  248698_at   receptor-like protein kinase; supported by cDNA:   At5g48380   2.33   1.13   0.021685   0.326459
    gi_13605826_gb_AF367312.1_AF367312          
  247594_at   putative protein farnesylated protein GMFP5,   At5g60800   2.33   1.37   0.027382   0.054007
  Glycine max, EMBL: U64916          
  266166_at   putative glucosyltransferase; supported by full-   At2g28080   2.32   −1.05   0.018474   0.764619
    length cDNA: Ceres: 13761.          
  262745_at   lipase, putative contains Pfam profile: PF00657   At1g28600   2.32   −1.12   0.015545   0.267784
    Lipase/Acylhydrolase with GDSL-like          
    motif; supported by full-length cDNA: Ceres: 37307.          
  257407_at   unknown protein   At1g27100   2.32   −1.19   0.009875   0.068971
  258282_at   unknown protein   At3g26910   2.31   1.14   0.003241   0.168885
  252373_at   disease resistance protein EDS1; supported by   At3g48090   2.31   −1.07   0.011996   0.442811
  cDNA: gi_15028150_gb_AY046025.1          
  250956_at   putative protein   At5g03210   2.31   −1.02   0.03092   0.993512
  248851_s_at   disease resistance protein-like; supported by cDNA:   At5g46490   2.3   1.09   0.009234   0.638209
  gi_16323098_gb_AY057653.1          
  254924_at   MAP kinase(ATMPK5) possible internal deletion   At4g11330   2.29   −1.14   0.010478   0.330061
    at position 161, missing one A residue; reference          
    GI: 457401; supported by cDNA:          
    gi_457401_dbj_D21841.1_ATHATMPK5          
  250279_at   ABA-responsive protein-like ABA-responsive   At5g13200   2.29   −1.11   0.021853   0.295383
    protein, Hordeum vulgare, EMBL: AF026538          
  263221_at   UDP-galactose 4-epimerase-like protein similar to   At1g30620   2.28   1.23   0.015145   0.343241
    proteins from many bacterial species including          
  [Bacillus subtilis] and [Methanobacterium          
  thermoautotrophicum]          
  261718_at   wall-associated kinase, putative similar to wall-   At1g18390   2.28   1.07   0.008635   0.505026
    associated kinase 2 GB: CAB42872 GI: 4826399          
  from [Arabidopsis thaliana]          
  250398_atputative protein predicted proteins, Arabidopsis   At5g11000   2.28   1.16   0.012015   0.299864
  thaliana; supported by full-length cDNA:          
    Ceres: 263168.          
  256922_at   hypothetical protein contains similarity to flavonol   At3g19010   2.27   −1.04   0.029488   0.80973
  synthase (FLS) GB: Q41452 from [Solanum          
  tuberosum], contains Pfam profile: PF00671          
    Iron/Ascorbate oxidoreductase family; supported by          
    full-length cDNA: Ceres: 41506.          
  267530_at   putative receptor-like protein kinase   At2g41890   2.26   −1.11   0.028311   0.389366
  256627_at   unknown protein; supported by cDNA:   At3g19970   2.26   1.05   0.015238   0.715164
  gi_14532501_gb_AY039875.1          
  255880_at   hypothetical protein predicted by genscan+   At1g67060   2.26   −1.01   0.015412   0.926607
  254660_at   receptor serine/threonine kinase-like protein   At4g18250   2.26   −1.06   0.024187   0.802259
    receptor serine/threonine kinase PR5K,          
    PATCHX: G1235680          
  264528_at   hypothetical protein similar to Human XE169   At1g30810   2.25   1.03   0.00644   0.758062
    protein (gi|3033385); similar to EST gb|T88128          
  257784_at   geranylgeranylated protein, putative similar to   At3g26970   2.25   1.17   0.00182   0.287058
  ATGP4 GB: AAD00115 from [Arabidopsis thaliana]          
  255344_s_at   putative receptor-like protein kinase   At4g04540   2.25   1.01   0.022152   0.792265
  255080_at   arabinogalactan-protein homolog arabinogalactan-   At4g09030   2.25   −1.04   0.036604   0.768432
  protein-Arabiclopsis thaliana, PID: g3883126;          
    supported by cDNA:          
    gi_10880496_gb_AF195891.1_AF195891          
  259325_at   unknown protein   At3g05320   2.24   −1.15   0.016669   0.38111
  252851_at   putative protein CLATHRIN COAT ASSEMBLY   At4g40080   2.24   −1.08   0.014274   0.543837
  PROTEIN AP180-Mus musculus,          
    SWISSPROT: Q61548; supported by full-length          
    cDNA: Ceres: 8970.          
  257071_at   unknown protein; supported by cDNA:   At3g28180   2.23   1.04   0.014928   0.697835
  gi_15810494_gb_AY056286.1          
  253476_at   S-receptor kinase-like protein serine/threonine-   At4g32300   2.23   −1.04   0.009096   0.440827
  specific protein kinase PK10 precursor, Oryza sativa,          
    PIR2: S50767          
  254292_at   putative protein   At4g23030   2.22   1.13   0.007331   0.570308
  249393_at   disease resistance-like protein resistance gene Cf-4,   At5g40170   2.22   −1.04   0.016127   0.647441
  Lycopersicon hirsutum, EMBL: LHJ002235          
  249320_at   disease resistance protein-like non-consensus TT   At5g40910   2.22   1.13   0.049144   0.285783
    donor splice site at exon 1          
  246327_at   receptor-like serine/threonine kinase, putative similar   At1g16670   2.22   1.02   0.008469   0.775987
    to receptor-like serine/threonine kinase GI: 2465923          
  from [Arabidopsis thaliana]; supported by cDNA:          
  gi_16649102_gb_AY059921.1          
  267537_at   putative guanylate kinase; supported by cDNA:   At2g41880   2.21   −1.02   0.012268   0.883883
    gi_7861794_gb_AF204675.1_AF204675          
  251987_at   CYTOCHROME P450 71B5; supported by cDNA:   At3g53280   2.21   −1.27   0.010305   0.155225
    gi_3164131_dbj_D78601.1_D78601          
  248981_at   regulatory protein NPR1-like; transcription factor   At5g45110   2.21   1.11   0.020899   0.556465
    inhibitor I kappa B-like          
  265611_at   unknown protein; supported by full-length cDNA:   At2g25510   2.2   −1.04   0.010382   0.533642
    Ceres: 10730.          
  259071_at   unknown protein similar to hin1 GB: CAA68848   At3g11650   2.2   −1.02   0.008823   0.776008
  [Nicotiana tabacum]; supported by cDNA:          
    gi_9502173_gb_AF264698.1_AF264698          
  249029_at   disease resistance protein-like   At5g44870   2.2   1.01   0.033247   0.925701
  265648_at   putative beta-1,3-glucanase; supported by full-   At2g27500   2.19   −1.07   0.015702   0.521836
    length cDNA: Ceres: 1126.          
  252921_at   putative protein DNA damage-inducible protein-   At4g39030   2.19   1.57   0.026714   0.071711
  Synechocystis sp., PIR2: S77364          
  266749_at   putative protein kinase contains a protein kinase   At2g47060   2.18   −1.05   0.013372   0.636302
    domain profile (PDOC00100)          
  266231_at   putative protein kinase   At2g02220   2.18   −1.01   0.008538   0.969684
  254878_at   heat shock transcription factor-like protein heat   At4g11660   2.18   1.15   0.015925   0.386918
  shock transcription factor HSF29, Glycine max,          
    PIR2: S59541          
  258764_at   putative pectinesterase contains similarity to   At3g10720   2.17   −1   0.01345   0.975443
  pectinesterase GB: AAB57671 [Citrus sinensis]          
  266975_at   hypothetical protein predicted by grail   At2g39380   2.16   1.09   0.019477   0.60417
  254921_at   putative protein hypothetical protein F16G20.230-   At4g11300   2.16   −1.01   0.016335   0.995903
  Arabidopsis thaliana, PIR2: T05391; supported by          
    full-length cDNA: Ceres: 17771.          
  259937_s_at   putative ABC transporter contains Pfam profile:   At1g71330   2.14   1.25   0.009288   0.060426
    PF00005 ABC transporter          
  255524_at   hypothetical protein similar to pectinesterase   At4g02330   2.14   −1.08   0.006633   0.352183
  250018_at   putative protein similar to unknown protein   At5g18150   2.14   −1.05   0.005427   0.652846
    (emb|CAB87627.1)          
  249987_atputative protein predicted proteins, Arabidopsis   At5g18490   2.14   1.03   0.016862   0.931777
  thaliana; supported by full-length cDNA:          
    Ceres: 32414.          
  265722_at   putative chlorophyll a/b binding protein; supported   At2g40100   2.13   1.35   0.029801   0.022089
    by full-length cDNA: Ceres: 6454.          
  262540_at   hypothetical protein predicted by genemark.hmm   At1g34260   2.13   1.1   0.022736   0.377889
  264767_at   hypothetical protein similar to putative   At1g61380   2.12   1.15   0.012495   0.215443
    serine/threonine kinase GI: 4585880 from          
  [Arabidopsis thaliana]; supported by full-length          
    cDNA: Ceres: 13461.          
  251192_at   alpha galactosyltransferase-like protein alpha   At3g62720   2.12   −1.11   0.0119   0.381401
  galactosyltransferase-Trigonella foenum-graecum,          
    EMBL: TFO245478; supported by cDNA:          
    gi_15983425_gb_AF424587.1_AF424587          
  249984_atputative protein rsc43, Dictyostelium discoideum,   At5g18400   2.12   1.05   0.006326   0.639984
    EMBL: AF011338; supported by full-length cDNA:          
    Ceres: 6084.          
  249237_at   putative protein similar to unknown protein   At5g42050   2.12   1.01   0.019097   0.90689
    (sp|P37707); supported by full-length cDNA:          
    Ceres: 6903.          
  249021_at   putative protein similar to unknown protein   At5g44820   2.12   −1.03   0.014955   0.780757
    (pir||T04881)          
  266452_at   hypothetical protein predicted by genscan; supported   At2g43320   2.11   1.01   0.010229   0.93189
  by cDNA: gi_14517475_gb_AY039573.1          
  266168_at   putative protease inhibitor; supported by full-length   At2g38870   2.11   1.07   0.011954   0.24411
    cDNA: Ceres: 11662.          
  257264_at   hypothetical protein contains Pfam profile: PF01657   At3g22060   2.11   1.41   0.033325   0.224965
    Domain of unknown function; supported by cDNA:          
  gi_14334417_gb_AY034900.1          
  252133_at   hypothetical protein hypothetical protein-   At3g50900   2.11   −1.16   0.048974   0.506058
  Arabidopsis thaliana chromosome 4 AP2 contig,          
    PID: e353223; supported by full-length cDNA:          
    Ceres: 10044.          
  248230_at   putative protein similar to unknown protein   At5g53830   2.11   −1.24   0.009004   0.419028
    (gb|AAF34839.1); supported by cDNA:          
    gi_13926341_gb_AF372918.1_AF372918          
  247571_at   snap25a; supported by full-length cDNA:   At5g61210   2.11   1.1   0.033279   0.210386
    Ceres: 14562.          
  253147_at   protein kinase-like protein serine/threonine-   At4g35600   2.1   1.1   0.007538   0.342113
  specific protein kinase APK1, Arabidopsis thaliana,          
    PIR2: S28615          
  252976_s_atPhospholipase like protein Arabidopsis thaliana   At4g38550   2.1   1.02   0.005166   0.820109
    pEARLI 4 mRNA, PID: g871782          
  260975_at   receptor-like serine/threonine kinase, putative   At1g53430   2.09   −1.06   0.02462   0.698322
    similar to receptor-like serine/threonine kinase