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Journal of Genetics

, Volume 95, Issue 1, pp 53–62 | Cite as

Evolution of the defensin-like gene family in grass genomes

  • JIANDONG WU
  • XIAOLEI JIN
  • YANG ZHAO
  • QING DONG
  • HAIYANG JIANG
  • QING MAEmail author
RESEARCH ARTICLE

Abstract

Plant defensins are small, diverse, cysteine-rich peptides, belonging to a group of pathogenesis-related defense mechanism proteins, which can provide a barrier against a broad range of pathogens. In this study, 51 defensin-like (DEFL) genes in Gramineae, including brachypodium, rice, maize and sorghum were identified based on bioinformatics methods. Using the synteny analysis method, we found that 21 DEFL genes formed 30 pairs of duplicated blocks that have undergone large-scale duplication events, mostly occurring between species. In particular, some chromosomal regions are highly conserved in the four grasses. Using mean K s values, we estimated the approximate time of divergence for each pair of duplicated regions and found that these regions generally diverged more than 40 million years ago (Mya). Selection pressure analysis showed that the DEFL gene family is subjected to purifying selection. However, sliding window analysis detected partial regions of duplicated genes under positive selection. The evolutionary patterns within DEFL gene families among grasses can be used to explore the subsequent functional divergence of duplicated genes and to further analyse the antimicrobial effects of defensins during plant development.

Keywords

defensin-like genes Gramineae gene evolution duplicated genes selection pressure 

Notes

Acknowledgements

This work was supported by the National Key Technologies Research and Development Programme of China (2012BAD20B00) and Anhui Provincial Natural Science Foundation (1408085MK L35). We would like to thank members of Key Laboratory of Crop Biology of Anhui province for their assistance in this study.

Supplementary material

12041_2015_601_MOESM1_ESM.pdf (1.1 mb)
(PDF 1.05 MB)

References

  1. Aerts A. M., François I. E. J. A., Cammue B. P. A. and Thevissen K. 2008 The mode of antifungal action of plant, insect and human defensins. Cell Mol. Life Sci. 65, 2069–2079.CrossRefPubMedGoogle Scholar
  2. Bennetzen J. L. 2000 Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12, 1021–1029.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Bertioli D. J., Moretzsohn M. C., Madsen L. H., Sandal N., Leal-Bertioli S. C., Guimarães P. M. et al. 2009 An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics 10, 45.CrossRefPubMedPubMedCentralGoogle Scholar
  4. Blanc G. and Wolfe K. H. 2004 Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16, 1667–1678.CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bowers J. E., Chapman B. A, Rong J. and Paterson A. H. 2003 Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422, 433–438.CrossRefPubMedGoogle Scholar
  6. Carvalho Ade O. and Gomes V. M. 2009 Plant defensins—prospects for the biological functions and biotechnological properties. Peptides 30, 1007–1020.CrossRefPubMedGoogle Scholar
  7. Devos K. M. and Gale M. D. 2000 Genome relationships: the grass model in current research. Plant Cell 12, 637–646.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Gale M. D. and Devos K. M. 1998 Plant comparative genetics after 10 years. Science 282, 656–659.CrossRefPubMedGoogle Scholar
  9. Gaut B. S., Morton B. R., McCaig B. C. and Clegg M. T. 1996 Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL. Proc. Natl. Acad. Sci. USA 93, 10274–10279.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Gaut B. S. and Doebley J. F. 1997 DNA sequence evidence for the segmental allotetraploid origin of maize. Proc. Natl. Acad. Sci. USA 94, 6809–6814.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Giacomelli L., Nanni V., Lenzi L., Zhuang J., Serra M. D., Banfield M. J. et al. 2012 Identification and characterization of the defensin-like gene family of grapevine. Mol. Plant Microbe Interact. 25, 1118–1131.CrossRefPubMedGoogle Scholar
  12. Graham M. A., Silverstein K. A., Cannon S. B. and VandenBosch K. A. 2004 Computational identification and characterization of novel genes from legumes. Plant Physiol. 135, 1179–1197.CrossRefPubMedPubMedCentralGoogle Scholar
  13. Keller B. and Feuillet C. 2000 Colinearity and gene density in grass genomes. Trends Plant Sci. 5, 246–251.CrossRefPubMedGoogle Scholar
  14. Kellogg E. A. 2001 Evolutionary history of the grasses. Plant Physiol. 125, 1198–1205.CrossRefPubMedPubMedCentralGoogle Scholar
  15. Lawton-Rauh A. 2003 Evolutionary dynamics of duplicated genes in plants. Mol. Phylogenet. Evol. 29, 396–409.CrossRefPubMedGoogle Scholar
  16. Lay F. T. and Anderson M. A. 2005 Defensins—components of the innate immune system in plants. Curr. Protein Pept. Sci. 6, 85–101.CrossRefPubMedGoogle Scholar
  17. Li Z., Jiang H., Zhou L., Deng L., Lin Y., Peng X. et al. 2014 Molecular evolution of the HD-ZIP I gene family in legume genomes. Gene 533, 218–228.CrossRefPubMedGoogle Scholar
  18. Librado P. and Rozas J. 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451–1452.CrossRefPubMedGoogle Scholar
  19. Maher C, Stein L. and Ware D. 2006 Evolution of Arabidopsis microRNA families through duplication events. Genome Res. 16, 510–519.CrossRefPubMedPubMedCentralGoogle Scholar
  20. Meyer B., Houlne G., Pozueta-Romero J., Schantz M. L. and Schantz R. 1996 Fruit-specific expression of a defensin-type gene family in bell pepper. Upregulation during ripening and upon wounding. Plant Physiol. 112, 615–622.CrossRefPubMedPubMedCentralGoogle Scholar
  21. Muthamilarasan M. R., Khandelwal C. B., Yadav V. S., Bonthala Y. Khan and Prasad M. 2014 Identification and molecular characterization of MYB transcription factor superfamily in C4 model plant foxtail millet (Setaria italica L.) PLoS One 9, e109920.CrossRefPubMedPubMedCentralGoogle Scholar
  22. Nei M. and Gojobori T 1986 Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418–426.PubMedGoogle Scholar
  23. Paterson A. H., Bowers J. E., Burow M. D., Draye X., Elsik C. G., Jiang C. X. et al. 2000 Comparative genomics of plant chromosomes. Plant Cell 12, 1523–1540.CrossRefPubMedPubMedCentralGoogle Scholar
  24. Paterson A. H., Bowers J. E. and Chapman B. A. 2004 Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc. Natl. Acad. Sci. USA 101, 9903–9908.CrossRefPubMedPubMedCentralGoogle Scholar
  25. Prema G. and Pruthvi T. 2012 Antifungal plant defensins. Curr. Biotica 6, 254–270.Google Scholar
  26. SanMiguel P., Gaut B. S., Tikhonov A., Nakajima Y. and Bennetzen J. L. 1998 The paleontology of intergene retrotransposons of maize. Nat. Genet. 20, 43–50.CrossRefPubMedGoogle Scholar
  27. Sato S., Nakamura Y., Kaneko T., Asamizu E., Kato T., Nakao M. et al. 2008 Genome structure of the legume, Lotus japonicus . DNA Res. 15, 227–239.CrossRefPubMedPubMedCentralGoogle Scholar
  28. Silverstein K. A., Graham M. A., Paape T. D. and VandenBosch K. A. 2005 Genome organization of more than 300 defensin-like genes in Arabidopsis. Plant Physiol.. 138, 600–610.CrossRefPubMedPubMedCentralGoogle Scholar
  29. Silverstein K. A., Moskal W. A. Jr., Wu H. C., Underwood B. A., Graham M. A. et al. 2007 Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants. Plant J. 51, 262–280.CrossRefPubMedGoogle Scholar
  30. Stotz H. U, Thomson J. G. and Wang Y 2009 Plant defensins: defense, development and application. Plant Signal Behav. 4, 1010–1012.CrossRefPubMedPubMedCentralGoogle Scholar
  31. Swigonova Z., Lai J. S., Ma J. X., Ramakrishna W., Llaca V., Bennetzen J. L. and Messing J. 2004 Close split of sorghum and maize genome progenitors. Genome Res. 14 1916–1923.Google Scholar
  32. Tamura K., Dudley J., Nei M. and Kumar S. 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599.CrossRefPubMedGoogle Scholar
  33. Thomma B. P, Cammue B. P. and Thevissen K. 2002 Plant defensins. Planta 216, 193–202.CrossRefPubMedGoogle Scholar
  34. Thompson J. D, Gibson T. J. and Higgins D. G. 2002 Multiple sequence alignment using ClustalW and ClustalX.Curr. Protoc. Bioinformatics 2–3.Google Scholar
  35. Vision T. J, Brown D. G. and Tanksley S. D. 2000 The origins of genomic duplications in Arabidopsis. Science 290, 2114–2117.CrossRefPubMedGoogle Scholar
  36. Wang X., Shi X., Hao B., Ge S. and Luo J. 2005 Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol. 165 937–946.Google Scholar
  37. Wei F., Coe E. D., Nelson W., Bharti A. K., Engler F., Beetler E. and Fuks G. 2007 Physical and genetic structure of the maize genome reflects its complex evolutionary history. PLoS Genet. 3, e123.Google Scholar
  38. Yang D., Biragyn A., Hoover D. M., Lubkowski J. and Oppenheim J. J. 2004 Multiple roles of antimicrobial defensins, cathelicidins, and eosinophil-derived neurotoxin in host defense. Annu. Rev. Immunol. 22, 181–215.Google Scholar

Copyright information

© Indian Academy of Sciences 2016

Authors and Affiliations

  • JIANDONG WU
    • 1
  • XIAOLEI JIN
    • 1
  • YANG ZHAO
    • 1
  • QING DONG
    • 1
  • HAIYANG JIANG
    • 1
  • QING MA
    • 1
    Email author
  1. 1.Key Laboratory of Crop Biology of Anhui Province, School of Life SciencesAnhui Agricultural UniversityHefeiPeople’s Republic of China

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