Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapa

Gene

Volumn 540, Issue 1, 2014, Pages 54-61

  Wu, Ping ^a   Shao, Zhu Qing ^a   Wu, Xun Zong ^a   Wang, Qiang ^a   Wang, Bin ^a   Chen, Jian Qun ^a   Hang, Yue Yu ^b   Xue, Jia Yu ^a,b  

^a NANJING UNIVERSITY   (China)

^b INSTITUTE OF BOTANY   (China)

Author keywords

Evolutionary pattern; Gene loss retention; NBS encoding genes; Polyploidy

Indexed keywords

ARABIDOPSIS THALIANA; ARTICLE; BRASSICA RAPA; CONTROLLED STUDY; EVOLUTIONARY RATE; GENE FUNCTION; GENE IDENTIFICATION; GENE LOCUS; GENE LOSS; GENE SEQUENCE; GENOME ANALYSIS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE BINDING SITE; PHYLOGENY; POLYPLOIDY; PRIORITY JOURNAL;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BRASSICA RAPA;

EVOLUTIONARY PATTERN; GENE LOSS/RETENTION; NBS-ENCODING GENES; POLYPLOIDY;

ARABIDOPSIS; BRASSICA RAPA; DISEASE RESISTANCE; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; PHYLOGENY; PLANT PROTEINS; PLOIDIES; RECOMBINATION, GENETIC; SEQUENCE ANALYSIS, DNA; SYNTENY;

EID: 84895896267     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.01.082     Document Type: Article

References (45)

1. Adams K.L., Wendel J.F. Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 2005, 8:135-141.
2. Ameline-Torregrosa C., et al. Identification and characterization of nucleotide-binding site-leucine-rich repeat genes in the model plant Medicago truncatula. Plant Physiol. 2008, 146:5-21.
3. Blanc G., Wolfe K.H. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell Online 2004, 16:1679-1691.
4. Blomme T., Vandepoele K., De Bodt S., Simillion C., Maere S., Van de Peer Y. The gain and loss of genes during 600millionyears of vertebrate evolution. Genome Biol. 2006, 7:R43.
5. Bowers J.E., Chapman B.A., Rong J., Paterson A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003, 422:433-438.
6. Cárdenas P.D., Gajardo H.A., Huebert T., Parkin I.A., Iniguez-Luy F.L., Federico M.L. Retention of triplicated phytoene synthase (PSY) genes in Brassica napus L. and its diploid progenitors during the evolution of the Brassiceae. Theor. Appl. Genet. 2012, 124:1215-1228.
7. Charon C., Bruggeman Q., Thareau V., Henry Y. Gene duplication within the Green Lineage: the case of TEL genes. J. Exp. Bot. 2012, 63:5061-5077.
8. Chen Q., Han Z., Jiang H., Tian D., Yang S. Strong positive selection drives rapid diversification of R-genes in Arabidopsis relatives. J. Mol. Evol. 2010, 70:137-148.
9. Cheng F., et al. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol. 2011, 11:136.
10. Collier S.M., Moffett P. NB-LRRs work a "bait and switch" on pathogens. Trends Plant Sci. 2009, 14:521-529.
11. Dangl J.L., Jones J.D. Plant pathogens and integrated defence responses to infection. Nature 2001, 411:826-833.
12. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
13. Force A., Lynch M., Pickett F.B., Amores A., Yan Y.-l., Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 1999, 151:1531-1545.
14. Hedrick P. Neutral Theory and Coalescence, Geneics of Populations 2005, chapter 8, 443-449.
15. Huson D.H., Bryant D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 2006, 23:254-267.
16. Li J., et al. Unique evolutionary pattern of numbers of gramineous NBS-LRR genes. Mol. Gen. Genomics. 2010, 283:427-438.
17. Libault M., et al. Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection. Plant Physiol. 2010, 152:541-552.
18. Lisch D. Epigenetic regulation of transposable elements in plants. Annu. Rev. Plant Biol. 2009, 60:43-66.
19. Lou P., Wu J., Cheng F., Cressman L.G., Wang X., McClung C.R. Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell Online 2012, 24:2415-2426.
20. Lupas A., Van Dyke M., Stock J. Predicting coiled coils from protein sequences. Science (New York, NY) 1991, 252:1162.
21. Lynch M., Conery J.S. The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-1155.
22. Lysak M.A., Koch M.A., Pecinka A., Schubert I. Chromosome triplication found across the tribe Brassiceae. Genome Res. 2005, 15:516-525.
23. Lysak M.A., Cheung K., Kitschke M., Bureš P. Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size. Plant Physiol. 2007, 145:402-410.
24. Martin D.P., Lemey P., Lott M., Moulton V., Posada D., Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 2010, 26:2462-2463.
25. Meyers B.C., Kozik A., Griego A., Kuang H., Michelmore R.W. Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell Online 2003, 15:809-834.
26. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3:418-426.
27. Nelson R.T., Shoemaker R. Identification and analysis of gene families from the duplicated genome of soybean using EST sequences. BMC Genomics 2006, 7:204.
28. Proost S., Pattyn P., Gerats T., Van de Peer Y. Journey through the past: 150millionyears of plant genome evolution. Plant J. 2011, 66:58-65.
29. Shoemaker R., et al. Genome duplication in soybean (Glycine subgenus soja). Genetics 1996, 144:329-338.
30. Slotkin R.K., Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 2007, 8:272-285.
31. Soltis D.E., et al. Polyploidy and angiosperm diversification. Am. J. Bot. 2009, 96:336-348.
32. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28:2731-2739.
33. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
34. Town C.D., et al. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell Online 2006, 18:1348-1359.
35. Tuskan G.A., et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 2006, 313:1596-1604.
36. Van de Peer Y., Fawcett J.A., Proost S., Sterck L., Vandepoele K. The flowering world: a tale of duplications. Trends Plant Sci. 2009, 14:680-688.
37. Wang B., Xue J., Li L., Liu Y., Qiu Y.-L. The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Curr. Genet. 2009, 55:601-609.
38. Wang X., et al. The genome of the mesopolyploid crop species Brassica rapa. Nat. Genet. 2011, 43:1035-1039.
39. Wolfe K.H., Shields D.C. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 1997, 387:708-712.
40. Xue J.-Y., Liu Y., Li L., Wang B., Qiu Y.-L. The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Curr. Genet. 2010, 56:53-61.
41. Xue J.-Y., et al. A primary survey on bryophyte species reveals two novel classes of nucleotide-binding site (NBS) genes. PloS One 2012, 7:e36700.
42. Yang Y.-W., Lai K.-N., Tai P.-Y., Li W.-H. Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages. J. Mol. Evol. 1999, 48:597-604.
43. Yang S., et al. Genome-wide investigation on the genetic variations of rice disease resistance genes. Plant Mol. Biol. 2006, 62:181-193.
44. Yang S., Zhang X., Yue J.-X., Tian D., Chen J.-Q. Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol. Gen. Genomics. 2008, 280:187-198.
45. Zhang X., Feng Y., Cheng H., Tian D., Yang S., Chen J.-Q. Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication. Mol. Gen. Genomics. 2011, 285:79-90.