Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing

G3: Genes, Genomes, Genetics

Volumn 3, Issue 9, 2013, Pages 1809-1818

  Page, Justin T ^a   Huynh, Mark D ^a   Liechty, Zach S ^a   Grupp, Kara ^b   Stelly, David ^c   Hulse, Amanda M ^c   Ashrafi, Hamid ^d   Van Deynze, Allen ^d   Wendel, Jonathan F ^b   Udall, Joshua A ^a  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

^c TEXAS A AND M UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Allopolyploid; Comparative genomics; Cotton fiber; Molecular evolution

Indexed keywords

ALLOPOLYPLOIDY; ARTICLE; COMPARATIVE GENE MAPPING; CONTROLLED STUDY; DIPLOIDY; GENE DELETION; GENE DUPLICATION; GENE SEQUENCE; GOSSYPIUM; GOSSYPIUM ARBOREUM; GOSSYPIUM HERBACEUM; GOSSYPIUM HIRSUTUM; GOSSYPIUM RAIMONDII; NONHUMAN; PLANT EVOLUTION; PLANT GENOME; POLYPLOIDY; SINGLE NUCLEOTIDE POLYMORPHISM; COTTON; EVOLUTION; GENE LOCUS; PLANT CHROMOSOME; PLANT GENETICS;

GOSSYPIUM; GOSSYPIUM ARBOREUM; GOSSYPIUM HERBACEUM; GOSSYPIUM HIRSUTUM; GOSSYPIUM RAIMONDII;

ALLOPOLYPLOID; COMPARATIVE GENOMICS; COTTON FIBER; MOLECULAR EVOLUTION;

DIPLOIDY; EVOLUTION, MOLECULAR; GENOME, PLANT; GOSSYPIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; POLYPLOIDY; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION;

EID: 84885745161     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.113.007229     Document Type: Article

References (40)

1. Brubaker, C. L., A. H. Paterson, and J. F. Wendel, 1999 Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome 42: 184-203.
2. Byers, R. L., D. B. Harker, S. M. Yourstone, P. J. Maughan, and J. A. Udall, 2012 Development and mapping of SNP assays in allotetraploid cotton. Theor. Appl. Genet. 124: 1201-1214.
3. Chaohua, C., W. Xiyuan, and N. I. Xiyuan, 2005 Observation of fiber ultrastructure of Ligon lintless mutant in upland cotton during fiber elongation. Chin. Sci. Bull. 50: 126-130.
4. Chen, J.-M., D. N. Cooper, N. Chuzhanova, C. Férec, and G. P. Patrinos, 2007 Gene conversion: mechanisms, evolution and human disease. Nat. Rev. Genet. 8: 762-775.
5. Chia, J.-M., C. Song, P. J. Bradbury, D. Costich, N. de Leon et al., 2012 Maize HapMap2 identifies extant variation from a genome in flux. Nat. Genet. 44: 803-807.
6. Conesa, A., S. Gotz, J. M. Garcia-Gomez, J. Terol, M. Talon et al., 2005 Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676.
7. Drouin, G., 2002 Characterization of the gene conversions between the multigene family members of the yeast genome. J. Mol. Evol. 55: 14-23.
8. Felsenstein, J., 1989 PHYLIP-Phylogeny Inference Package (version 3.2). Cladistics 5: 163-166.
9. Flagel, L. E., J. F. Wendel, and J. A. Udall, 2012 Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton. BMC Genomics 13: 302.
10. Grover, C. E., and J. F. Wendel, 2010 Recent insights into mechanisms of genome size change in plants. J. Bot. 2010: 1-8.
11. Grover, C. E., K. K. Grupp, R. J. Wanzek, and J. F. Wendel, 2012 Assessing the monophyly of polyploid Gossypium species. Plant Syst. Evol. 298: 1177-1183.
12. Han, F., G. Fedak, W. Guo, and B. Liu, 2005 Rapid and repeatable elimination of a parental genome-specific DNA repeat (pGc1R-1a) in newly synthesized wheat allopolyploids. Genetics 170: 1239-1245.
13. Han, M. V., and C. M. Zmasek, 2009 phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10: 356.
14. Hawkins, J. S., H. Kim, J. D. Nason, R. A. Wing, and J. F. Wendel, 2006 Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res. 16: 1252-1261.
15. Hawkins, J. S., S. R. Proulx, R. A. Rapp, and J. F. Wendel, 2009 Rapid DNA loss as a counterbalance to genome expansion through retrotransposon proliferation in plants. Proc. Natl. Acad. Sci. USA 106: 17811-17816.
16. Hsu, C.-H., Y. Zhang, R. C. Hardison, E. D. Green, and W. Miller, 2010 An effective method for detecting gene conversion events in whole genomes. J. Comput. Biol. 17: 1281-1297.
17. Jacquemin, J., C. Chaparro, M. Laudie, A. Berger, F. Gavory et al., 2011 Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species. Mol. Biol. Evol. 28: 3139-3150.
18. Krzywinski, M., J. Schein, İ. Birol, J. Connors, R. Gascoyne et al., 2009 Circos: an information aesthetic for comparative genomics. Genome Res. 19: 1639-1645.
19. Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., 2009 The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078- 2079.
20. Mondragon-Palomino, M., and B. S. Gaut, 2005 Gene conversion and the evolution of three leucine-rich repeat gene families in Arabidopsis thaliana. Mol. Biol. Evol. 22: 2444-2456.
21. Ozkan, H., 2003 Nonadditive changes in genome size during allopolyploidization in the wheat (Aegilops-triticum) group. J. Hered. 94: 260-264.
22. Page, J. T., A. R. Gingle, and J. A. Udall, 2013 PolyCat: A resource for genome categorization of sequencing reads from allopolyploid organisms. G3 (Bethesda) 3: 517-525.
23. Paterson, A. H., J. F. Wendel, H. Gundlach, H. Guo, J. Jenkins et al., 2012 Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492: 423-427.
24. Quinlan, A. R., and I. M. Hall, 2010 BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
25. Salmon, A., L. Flagel, B. Ying, J. A. Udall, and J. F. Wendel, 2010 Homoeologous nonreciprocal recombination in polyploid cotton. New Phytol. 186: 123-134.
26. Senchina, D. S., I. Alverez, R. C. Cronn, B. Liu, J. Rong et al., 2003 Rate variation among nuclear genes and the age of polyploidy in gossypium. Mol. Biol. Evol. 20: 633-643.
27. Shaked, H., K. Kashkush, H. Ozkan, M. Feldman, and A. A. Levy, 2001 Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13: 1749-1759.
28. Szostak, J. W., T. L. Orr-Weaver, R. J. Rothstein, and F. W. Stahl, 1983 The double-strand-break repair model for recombination. Cell 33: 25-35.
29. Tate, J. A., P. Joshi, K. A. Soltis, P. S. Soltis, and D. E. Soltis, 2009 On the road to diploidization? Homoeolog loss in independently formed populations of the allopolyploid Tragopogon miscellus (Asteraceae). BMC Plant Biol. 9: 80.
30. Udall, J. A., 2006 A global assembly of cotton ESTs. Genome Res. 16: 441- 450.
31. Van Deynze, A., K. Stoffel, M. Lee, T. A. Wilkins, A. Kozik et al., 2009 Sampling nucleotide diversity in cotton. BMC Plant Biol. 9: 125.
32. Wang, X., H. Tang, J. E. Bowers, and A. H. Paterson, 2009 Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization. Genome Res. 19: 1026- 1032.
33. Wendel, J. F., 1989 New World tetraploid cottons contain Old World cytoplasm. Proc. Natl. Acad. Sci. USA 86: 4132-4136.
34. Wendel, J. F., and Cronn, R. C., 2003 Polyploidy and the evolutionary history of cotton, pp. 139-186 in Advances in Agronomy, ed. D. Sparks, Elsevier, New York, NY.
35. Wendel, J. F., L. E. Flagel, and K. L. Adams, 2012 Jeans, genes, and genomes: cotton as a model for studying polyploidy, pp. 181-207 in Polyploidy and Genome Evolution, edited by P. S. Soltis, and D. E. Soltis. Springer, New York.
36. Wendel, J. F., and P. D. Olson, and J. McD. Stewart, 1989 Genetic diversity, introgression, and independent domestication of old world cultivated cottons. Am. J. Bot. 76: 1795-1806.
37. Wu, T. D., and S. Nacu, 2010 Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26: 873-881.
38. Xu, S., T. Clark, H. Zheng, S. Vang, R. Li et al., 2008 Gene conversion in the rice genome. BMC Genomics 9: 93.
39. Yong-Ling Ruan, P. S. C., 1998 A fiberless seed mutation in cotton is associated with lack of fiber cell initiation in ovule epidermis and alterations in sucrose synthase expression and carbon partitioning in developing seeds. Plant Physiol. 118: 399.
40. Zhang, Y., T. Liu, C. A. Meyer, J. Eeckhoute, D. S. Johnson et al., 2008 Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9: R137.