A genome-wide comparison of NB-LRR type of resistance gene analogs (RGA) in the plant Kingdom

Molecules and Cells

Volumn 33, Issue 4, 2012, Pages 385-392

  Kim, Jungeun ^a,b   Lim, Chan Ju ^a   Lee, Bong Woo ^a   Choi, Jae Pil ^a   Oh, Sang Keun ^a   Ahmad, Raza ^a   Kwon, Suk Yoon ^a   Ahn, Jisook ^a,b   Hur, Cheol Goo ^a,b  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b University of Science and Technology (UST)   (South Korea)

Author keywords

NB LRR; NB LRR cluster; Plant genome; RGA; RGA map

Indexed keywords

TOLL LIKE RECEPTOR ADAPTOR MOLECULE 1;

ACCURACY; ANGIOSPERM; ARABIDOPSIS; ARTICLE; CHLAMYDOMONAS REINHARDTII; CHROMOSOME 12; CHROMOSOME 13; CHROMOSOME 18; CHROMOSOME 9; COMPARATIVE STUDY; GENE CLUSTER; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; GENETIC RESISTANCE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GRAPE; HELIANTHUS ANNUUS; LETTUCE; MIMULUS; MONOCOT; NONHUMAN; PAPAYA; PHYSCOMITRELLA; PLANT GENETICS; POACEAE; RICE; SELAGINELLA;

BINDING SITES; COMPUTATIONAL BIOLOGY; GENETIC VARIATION; GENOME, PLANT; LEUCINE; PHYLOGENY; PLANT IMMUNITY; PLANT PROTEINS; PLANTS; REPETITIVE SEQUENCES, AMINO ACID; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

BRYOPHYTA; CHLOROPHYTA; DICOTYLEDONEAE; EMBRYOPHYTA; LILIOPSIDA; MAGNOLIOPHYTA; MIMULUS GUTTATUS; POACEAE;

EID: 84863494168     PISSN: 10168478     EISSN: 02191032     Source Type: Journal    
DOI: 10.1007/s10059-012-0003-8     Document Type: Article

References (30)

1. Ausubel, F.M. (2005). Are innate immune signaling pathways in plants and animals conserved? Nat. Immunol. 6, 973-979. (Pubitemid 41486181)
2. Bonas, U., and Van den Ackerveken, G. (1999). Gene-for-gene interactions: bacterial avirulence proteins specify plant disease resistance. Curr. Opin. Microbiol. 2, 94-98. (Pubitemid 29130222)
3. Chen, Q., Han, Z., Jiang, H., Tian, D., and Yang, S. (2010). Strong Positive selection drives rapid diversification of R-genes in Arabidopsis relatives. J. Mol. Evol. 70, 137-148.
4. Dangl, J.L., and Jones, J.D. (2001). Plant pathogens and integrated defence responses to infection. Nature 411, 826-833. (Pubitemid 32588110)
5. Eddy, S.R. (1998). Profile hidden Markov models. Bioinformatics 14, 755-763. (Pubitemid 28552108)
6. Jones, D.A., and Takemoto, D. (2004). Plant innate immunity -direct and indirect recognition of general and specific pathogen-associated molecules. Curr. Opin. Immunol. 16, 48-62. (Pubitemid 38198117)
7. Kohler, A., Rinaldi, C., Duplessis, S., Baucher, M., Geelen, D., Du-chaussoy, F., Meyers, B.C., Boerjan, W., and Martin, F. (2008). Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Mol. Biol. 66, 619-636.
8. Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580. (Pubitemid 33032862)
9. Kuang, H., Woo, S.S., Meyers, B.C., Nevo, E., and Michelmore, R.W. (2004). Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce. Plant Cell 16, 2870-2894. (Pubitemid 41075740)
10. Li, J., Ding, J., Zhang, W., Zhang, Y., Tang, P., Chen, J.Q., Tian, D., and Yang, S. (2010). Unique evolutionary pattern of numbers of gramineous NBS-LRR genes. Mol. Genet. Genomics 283, 427-438.
11. Lupas, A., Van Dyke, M., and Stock, J. (1991). Predicting coiled coils from protein sequences. Science 252, 1162-1164. (Pubitemid 21917026)
12. Martin, G.B., Bogdanove, A.J., and Sessa, G. (2003). Understanding the functions of plant disease resistance proteins. Annu. Rev. Plant Biol. 54, 23-61. (Pubitemid 37399986)
13. McDowell, J.M., and Simon, S.A. (2008). Molecular diversity at the plant-pathogen interface. Dev. Comp. Immunol. 32, 736-744.
14. Meyers, B.C., Dickerman, A.W., Michelmore, R.W., Sivaramakri-shnan, S., Sobral, B.W., and Young, N.D. (1999). Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. Plant J. 20, 317-332. (Pubitemid 129515914)
15. Meyers, B.C., Morgante, M., and Michelmore, R.W. (2002). TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes. Plant J. 32, 77-92. (Pubitemid 35180926)
16. Meyers, B.C., Kozik, A., Griego, A., Kuang, H., and Michelmore, R.W. (2003). Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell 15, 809-834. (Pubitemid 36453281)
17. Michelmore, R.W., and Meyers, B.C. (1998). Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res. 8, 1113-1130. (Pubitemid 29027217)
18. Moffett, P. (2009). Mechanisms of recognition in dominant R gene mediated resistance. Adv. Virus Res. 75, 1-33.
19. Monosi, B., Wisser, R.J., Pennill, L., and Hulbert, S.H. (2004). Full-genome analysis of resistance gene homologues in rice. Theor. Appl. Genet. 109, 1434-1447. (Pubitemid 40059266)
20. Parniske, M., Hammond-Kosack, K.E., Golstein, C., Thomas, C.M., Jones, D.A., Harrison, K., Wulff, B.B., and Jones, J.D. (1997). Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell 91, 821-832. (Pubitemid 28007738)
21. Porter, B.W., Paidi, M., Ming, R., Alam, M., Nishijima, W.T., and Zhu, Y.J. (2009). Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. Mol. Genet. Genomics 281, 609-626.
22. Sanseverino, W., Roma, G., De Simone, M., Faino, L., Melito, S., Stupka, E., Frusciante, L., and Ercolano, M.R. (2010). PRGdb: a bioinformatics platform for plant resistance gene analysis. Nucleic Acids Res. 38, D814-821.
23. Shiu, S.H., and Bleecker, A.B. (2001). Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc. Natl. Acad. Sci. USA 98, 10763-10768. (Pubitemid 32878695)
24. van Ooijen, G., van den Burg, H.A., Cornelissen, B.J., and Takken, F.L. (2007). Structure and function of resistance proteins in solanaceous plants. Annu. Rev. Phytopathol. 45, 43-72.
25. Yang, S., Feng, Z., Zhang, X., Jiang, K., Jin, X., Hang, Y., Chen, J.Q., and Tian, D. (2006). Genome-wide investigation on the genetic variations of rice disease resistance genes. Plant Mol. Biol. 62, 181-193. (Pubitemid 44372896)
26. Yang, S., Zhang, X., Yue, J.X., Tian, D., and Chen, J.Q. (2008). Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol. Genet. Genomics 280, 187-198.
27. Young, N.D. (2000). The genetic architecture of resistance. Curr. Opin. Plant Biol. 3, 285-290. (Pubitemid 30437866)
28. Zhang, M., Wu, Y.H., Lee, M.K., Liu, Y.H., Rong, Y., Santos, T.S., Wu, C., Xie, F., Nelson, R.L., and Zhang, H.B. (2010). Numbers of genes in the NBS and RLK families vary by more than fourfold within a plant species and are regulated by multiple factors. Nucleic Acids Res. 38, 6513-6525.
29. Zhou, T., Wang, Y., Chen, J.Q., Araki, H., Jing, Z., Jiang, K., Shen, J., and Tian, D. (2004). Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol. Genet. Genomics 271, 402-415. (Pubitemid 38824034)
30. Zipfel, C., and Felix, G. (2005). Plants and animals: a different taste for microbes? Curr. Opin. Plant Biol. 8, 353-360. (Pubitemid 40817376)