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International Journal of Genomics
Volume 2015 (2015), Article ID 231358, 11 pages
http://dx.doi.org/10.1155/2015/231358
Research Article

Identification of Immune Related LRR-Containing Genes in Maize (Zea mays L.) by Genome-Wide Sequence Analysis

Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China

Received 17 May 2015; Accepted 27 September 2015

Academic Editor: Jinfa Zhang

Copyright © 2015 Wei Song et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. T. Nürnberger, F. Brunner, B. Kemmerling, and L. Piater, “Innate immunity in plants and animals: striking similarities and obvious differences,” Immunological Reviews, vol. 198, no. 1, pp. 249–266, 2004. View at Publisher · View at Google Scholar · View at Scopus
  2. F. M. Ausubel, “Are innate immune signaling pathways in plants and animals conserved?” Nature Immunology, vol. 6, no. 10, pp. 973–979, 2005. View at Publisher · View at Google Scholar · View at Scopus
  3. T. Boller and S. Y. He, “Innate immunity in plants: an arms race between pattern recognition receptors in plants and effectors in microbial pathogens,” Science, vol. 324, no. 5928, pp. 742–744, 2009. View at Publisher · View at Google Scholar · View at Scopus
  4. M. S. Dixon, D. A. Jones, J. S. Keddie, C. M. Thomas, K. Harrison, and J. D. G. Jones, “The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins,” Cell, vol. 84, no. 3, pp. 451–459, 1996. View at Publisher · View at Google Scholar · View at Scopus
  5. A. F. Bent, B. N. Kunkel, D. Dahlbeck et al., “RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes,” Science, vol. 265, no. 5180, pp. 1856–1860, 1994. View at Publisher · View at Google Scholar · View at Scopus
  6. B. C. Meyers, A. W. Dickerman, R. W. Michelmore, S. Sivaramakrishnan, B. W. Sobral, and N. D. Young, “Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily,” The Plant Journal, vol. 20, no. 3, pp. 317–332, 1999. View at Publisher · View at Google Scholar · View at Scopus
  7. J. L. Dangl and J. D. G. Jones, “Plant pathogens and integrated defence responses to infection,” Nature, vol. 411, no. 6839, pp. 826–833, 2001. View at Publisher · View at Google Scholar · View at Scopus
  8. J. D. G. Jones and J. L. Dangl, “The plant immune system,” Nature, vol. 444, no. 7117, pp. 323–329, 2006. View at Publisher · View at Google Scholar · View at Scopus
  9. F. Jupe, L. Pritchard, G. J. Etherington et al., “Identification and localisation of the NB-LRR gene family within the potato genome,” BMC Genomics, vol. 13, no. 1, article 75, 2012. View at Publisher · View at Google Scholar · View at Scopus
  10. S. Tan and S. Wu, “Genome wide analysis of nucleotide-binding site disease resistance genes in Brachypodium distachyon,” Comparative and Functional Genomics, vol. 2012, Article ID 418208, 12 pages, 2012. View at Publisher · View at Google Scholar · View at Scopus
  11. W.-Y. Song, G.-L. Wang, L.-L. Chen et al., “A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21,” Science, vol. 270, no. 5243, pp. 1804–1806, 1995. View at Publisher · View at Google Scholar · View at Scopus
  12. J. Li, J. Wen, K. A. Lease, J. T. Doke, F. E. Tax, and J. C. Walker, “BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling,” Cell, vol. 110, no. 2, pp. 213–222, 2002. View at Publisher · View at Google Scholar · View at Scopus
  13. X. Gou, K. He, H. Yang et al., “Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana,” BMC Genomics, vol. 11, no. 1, article 19, 2010. View at Publisher · View at Google Scholar · View at Scopus
  14. C.-J. Park, D. F. Caddell, and P. C. Ronald, “Protein phosphorylation in plant immunity: insights into the regulation of pattern recognition receptor-mediated signaling,” Frontiers in Plant Science, vol. 3, no. 177, pp. 1–9, 2012. View at Publisher · View at Google Scholar · View at Scopus
  15. L. Gómez-Gómez and T. Boller, “FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis,” Molecular Cell, vol. 5, no. 6, pp. 1003–1011, 2000. View at Publisher · View at Google Scholar · View at Scopus
  16. Y. Amano, H. Tsubouchi, H. Shinohara, M. Ogawa, and Y. Matsubayashi, “Tyrosine-sulfated glycopeptide involved in cellular proliferation and expansion in Arabidopsis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 46, pp. 18333–18338, 2007. View at Publisher · View at Google Scholar · View at Scopus
  17. S. Mosher, H. Seybold, P. Rodriguez et al., “The tyrosine-sulfated peptide receptors PSKR1 and PSY1R modify the immunity of Arabidopsis to biotrophic and necrotrophic pathogens in an antagonistic manner,” The Plant Journal, vol. 73, no. 3, pp. 469–482, 2013. View at Publisher · View at Google Scholar · View at Scopus
  18. L. Gómez-Gómez and T. Boller, “Flagellin perception: a paradigm for innate immunity,” Trends in Plant Science, vol. 7, no. 6, pp. 251–256, 2002. View at Publisher · View at Google Scholar · View at Scopus
  19. S.-H. Shiu and A. B. Bleecker, “Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases,” Proceedings of the National Academy of Sciences of the United States of America, vol. 98, no. 19, pp. 10763–10768, 2001. View at Publisher · View at Google Scholar · View at Scopus
  20. B. C. Meyers, A. Kozik, A. Griego, H. Kuang, and R. W. Michelmore, “Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis,” Plant Cell, vol. 15, no. 4, pp. 809–834, 2003. View at Publisher · View at Google Scholar · View at Scopus
  21. S. Luo, J. Peng, K. Li, M. Wang, and H. Kuang, “Contrasting evolutionary patterns of the Rp1 resistance gene family in different species of Poaceae,” Molecular Biology and Evolution, vol. 28, no. 1, pp. 313–325, 2011. View at Publisher · View at Google Scholar · View at Scopus
  22. T. Zhou, Y. Wang, J.-Q. Chen et al., “Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes,” Molecular Genetics and Genomics, vol. 271, no. 4, pp. 402–415, 2004. View at Publisher · View at Google Scholar · View at Scopus
  23. X. Cheng, H. Jiang, Y. Zhao, Y. Qian, S. Zhu, and B. Cheng, “A genomic analysis of disease-resistance genes encoding nucleotide binding sites in Sorghum bicolor,” Genetics and Molecular Biology, vol. 33, no. 2, pp. 292–297, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. P. S. Schnable, D. Ware, R. S. Fulton et al., “The B73 maize genome: complexity, diversity, and dynamics,” Science, vol. 326, no. 5956, pp. 1112–1115, 2009. View at Google Scholar
  25. M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and Clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007. View at Publisher · View at Google Scholar · View at Scopus
  26. E. B. Houb, “The arms race is ancient history in Arabidopsis, the wildflower,” Nature Reviews Genetics, vol. 2, no. 7, pp. 516–527, 2001. View at Publisher · View at Google Scholar · View at Scopus
  27. J. J. Campanella, L. Bitincka, and J. Smalley, “MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences,” BMC Bioinformatics, vol. 4, article 29, 2003. View at Publisher · View at Google Scholar · View at Scopus
  28. J. Schultz, F. Milpetz, P. Bork, and C. P. Ponting, “SMART, a simple modular architecture research tool: identification of signaling domains,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 11, pp. 5857–5864, 1998. View at Publisher · View at Google Scholar · View at Scopus
  29. K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, and S. Kumar, “MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods,” Molecular Biology and Evolution, vol. 28, no. 10, pp. 2731–2739, 2011. View at Publisher · View at Google Scholar · View at Scopus
  30. S. Yang, X. Zhang, J.-X. Yue, D. Tian, and J.-Q. Chen, “Recent duplications dominate NBS-encoding gene expansion in two woody species,” Molecular Genetics and Genomics, vol. 280, no. 3, pp. 187–198, 2008. View at Publisher · View at Google Scholar · View at Scopus
  31. Y. Cheng, X. Li, H. Jiang et al., “Systematic analysis and comparison of nucleotide-binding site disease resistance genes in maize,” The FEBS Journal, vol. 279, no. 13, pp. 2431–2443, 2012. View at Publisher · View at Google Scholar · View at Scopus
  32. S. A. Goff, D. Ricke, T. H. Lan et al., “A draft sequence of the rice genome (Oryza sativa L. ssp. japonica),” Science, vol. 296, no. 5565, pp. 92–100, 2002. View at Google Scholar
  33. A. H. Paterson, J. E. Bowers, R. Bruggmann et al., “The Sorghum bicolor genome and the diversification of grasses,” Nature, vol. 457, no. 7229, pp. 551–556, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. D. M. Soanes and N. J. Talbot, “Comparative genome analysis reveals an absence of leucine-rich repeat pattern-recognition receptor proteins in the kingdom fungi,” PLoS ONE, vol. 5, no. 9, Article ID e12725, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. A. Diévart, N. Gilbert, G. Droc et al., “Leucine-Rich repeat receptor kinases are sporadically distributed in eukaryotic genomes,” BMC Evolutionary Biology, vol. 11, no. 1, article 367, 2011. View at Publisher · View at Google Scholar · View at Scopus
  36. X. Sun and G.-L. Wang, “Genome-wide identification, characterization and phylogenetic analysis of the rice LRR-kinases,” PLoS ONE, vol. 6, no. 3, Article ID e16079, 2011. View at Publisher · View at Google Scholar · View at Scopus
  37. S. B. Cannon, H. Zhu, A. M. Baumgarten et al., “Diversity, distribution, and ancient taxonomic relationships within the TIR and non-TIR NBS-LRR resistance gene subfamilies,” Journal of Molecular Evolution, vol. 54, no. 4, pp. 548–562, 2002. View at Publisher · View at Google Scholar · View at Scopus
  38. J. C. Walker and R. Zhang, “Relationship of a putative receptor protein kinase from maize to the S-locus glycoproteins of Brassica,” Nature, vol. 345, no. 6277, pp. 743–746, 1990. View at Publisher · View at Google Scholar · View at Scopus
  39. J. Li, J. Ding, W. Zhang et al., “Unique evolutionary pattern of numbers of gramineous NBS-LRR genes,” Molecular Genetics and Genomics, vol. 283, no. 5, pp. 427–438, 2010. View at Publisher · View at Google Scholar · View at Scopus
  40. B. S. Gaut, “Evolutionary dynamics of grass genomes,” New Phytologist, vol. 154, no. 1, pp. 15–28, 2002. View at Publisher · View at Google Scholar · View at Scopus
  41. Z. Swigoňová, J. Lai, J. Ma et al., “Close split of sorghum and maize genome progenitors,” Genome Research, vol. 14, no. 10, pp. 1916–1923, 2004. View at Publisher · View at Google Scholar · View at Scopus
  42. Q. Pan, J. Wendel, and R. Fluhr, “Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes,” Journal of Molecular Evolution, vol. 50, no. 3, pp. 203–213, 2000. View at Google Scholar · View at Scopus
  43. D. E. K. Tarr and H. M. Alexander, “TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders,” BMC Research Notes, vol. 2, article 197, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. J. Li and J. Chory, “A putative leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction,” Cell, vol. 90, no. 5, pp. 929–938, 1997. View at Publisher · View at Google Scholar · View at Scopus
  45. K. Mueller, P. Bittel, D. Chinchill et al., “Chimeric FLS2 receptors reveal the basis for differential flagellin perception in Arabidopsis and tomato,” Plant Cell, vol. 24, no. 5, pp. 2213–2224, 2012. View at Publisher · View at Google Scholar · View at Scopus
  46. M. Gao, X. Wang, D. Wang et al., “Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis,” Cell Host and Microbe, vol. 6, no. 1, pp. 34–44, 2009. View at Publisher · View at Google Scholar · View at Scopus
  47. K. He, S. Xu, and J. Li, “BAK1 directly regulates brassinosteroid perception and BRI1 activation,” Journal of Integrative Plant Biology, vol. 55, no. 12, pp. 1264–1270, 2013. View at Publisher · View at Google Scholar · View at Scopus
  48. S. Baudino, S. Hansen, R. Brettschneider et al., “Molecular characterisation of two novel maize LRR receptor-like kinases, which belong to the SERK gene family,” Planta, vol. 213, no. 1, pp. 1–10, 2001. View at Publisher · View at Google Scholar · View at Scopus
  49. S. Mantelin, H.-C. Peng, B. Li, H. S. Atamian, F. L. W. Takken, and I. Kaloshian, “The receptor-like kinase SlSERK1 is required for Mi-1-mediated resistance to potato aphids in tomato,” The Plant Journal, vol. 67, no. 3, pp. 459–471, 2011. View at Publisher · View at Google Scholar · View at Scopus
  50. X. Chen, S. Zuo, B. Schwessinger et al., “An XA21-associated kinase (OsSERK2) regulates immunity mediated by the XA21 and XA3 immune receptors,” Molecular Plant, vol. 7, no. 5, pp. 874–892, 2014. View at Publisher · View at Google Scholar · View at Scopus