Toward Characterizing the Spectrum of Diversity in the Gossypium Genus

  • Andrew H. Paterson
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 3)


Sequencing of the human genome has driven the development of a host of technologies that have rendered DNA as the raw material for revealing and understanding biodiversity, integrating rich histories of phenotypic, genetic and evolutionary information with their molecular basis. The exciting day is foreseeable when we have most if not all of the Gossypium genomes sequenced. How will we then convert the sequence into knowledge, and into application? What will be the path? What will be the cost?


Strong Positive Selection Cotton Fiber Development Cotton Gene Angiosperm Genome Tertiary Gene Pool 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Benton MJ (1993) The fossil record 2. Chapman and Hall. New YorkGoogle Scholar
  2. Comai L, Henikoff S (2006) TILLING: practical single-nucleotide mutation discovery. Plant J 45:684–694PubMedCrossRefGoogle Scholar
  3. Initiative TAG (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  4. Jaillon O, Aury JM, al. e (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature advanced online publication: doi:10.1038/nature06148Google Scholar
  5. Lynch M, Force A (2000) The probability of duplicate gene preservation by subfunctionalization. Genetics 154:459–473PubMedGoogle Scholar
  6. Margulies M, Egholm M, Altman WE, Attiva S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GPI, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, Mcdade KE, Mckenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380PubMedGoogle Scholar
  7. McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiology 123:439–442PubMedCrossRefGoogle Scholar
  8. Ming R, Hou S, Feng Y, Yu QY, Dionne-Laporte A, Saw J, Senin P, Wang W, Salzberg SL, Tang H, Lyons E, Rice D, Riley M, Skelton R, Murray J, Chen C, Eustice M, Tong E, Albert H, Paull RE, Wang ML, Zhu Y, Schatz M, Nagarajan N, Agbayani R, Guan P, Blas A, Wang J, Na JK, Michael T, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang X, Bowers JE, Suzuki J, Tripathi S, Neupane K, Wei H, Singh R, Irikura B, Jiang N, Zhang W, Wall K, Presting G, Gschwend A, Li Y, Windsor AJ, Navajas-Perez R, Torres MJ, Feltus FA, Porter B, Paidi M, Luo MC, Liu L, Christopher D, Moore PH, Sugimura T, dePamphilis C, Jiang J, Schuler M, Mitchell-Olds T, Shippen D, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–997PubMedCrossRefGoogle Scholar
  9. Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929–936PubMedGoogle Scholar
  10. Paterson AH (2006) Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nature Reviews Genetics 7:174–184PubMedCrossRefGoogle Scholar
  11. Paterson AH (2007) Sequencing the cotton genomes. World Cotton Research Conference. International Cotton Advisory Committee. Lubbock TXGoogle Scholar
  12. Paterson AH (2008) Paleopolyploidy and its Impact on the Structure and Function of Modern Plant Genomes. Genome Dynamics 4:1–12PubMedCrossRefGoogle Scholar
  13. Persson S, Wei HR, Milne J, Page GP, Somerville CR (2005) Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets. Proceedings of the National Academy of Sciences of the United States of America 102:8633–8638PubMedCrossRefGoogle Scholar
  14. Rong J, Bowers JE, Schulze SR, Waghmare VN, Rogers CJ, Pierce GJ, Zhang H, Estill JC, Paterson AH (2005) Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy. Genome Research 15:1198–1210PubMedCrossRefGoogle Scholar
  15. Rong JK, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding XL, Garza JJ, Marler BS, Park CH, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao XP, Zhu LH, Paterson AH (2004) A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389–417PubMedCrossRefGoogle Scholar
  16. Shendure J, Porreca GJ, Reppas NB, Lin XX, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309:1728–1732PubMedCrossRefGoogle Scholar
  17. Slade AJ, Fuerstenberg SI, Loeffler D, Steine MN, Facciotti D (2005) A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING. Nature Biotechnology 23:75–81PubMedCrossRefGoogle Scholar
  18. Swanson WJ, Clark AG, Waldrip-Dail HM, Wolfner MF, Aquadro CF (2001a) Evolutionary EST analysis identifies rapidly evolving male reproductive proteins in Drosophila. Proceedings of the National Academy of Sciences of the United States of America 98:7375–7379Google Scholar
  19. Swanson WJ, Zhang ZH, Wolfner MF, Aquadro CF (2001b) Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. Proceedings of the National Academy of Sciences of the United States of America 98:2509–2514Google Scholar
  20. Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE, Henikoff JG, Comai L, Henikoff S (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Research 13:524–530PubMedCrossRefGoogle Scholar
  21. Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15:568–573PubMedGoogle Scholar
  22. Yang Z, Nielsen R, Goldman N, Krabbe Pedersen A (2000a) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155Google Scholar
  23. Yang ZH (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 13:555–556PubMedGoogle Scholar
  24. Yang ZH, Nielsen R, Goldman N, Pedersen AMK (2000b) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449Google Scholar
  25. Z. Jeffrey Chen. Brian E. Scheffler. Elizabeth Dennis. Barbara Triplett. Tianzhen Zhang. Xiaoya Chen. David M. Stelly. Pablo D. Rabinowicz. Christopher Town. Tony Arioli. Curt Brubaker. Roy Cantrell. Jean-Marc Lacape. Mauricio Ulloa. Peng Chee. Alan R. Gingle. Candace H. Haigler. Richard Percy. Sukumar Saha. Thea Wilkins. Robert J. Wright. Allen Van Deynze. Yuxian Zhu. Shuxun Yu. Wangzhen Guo. Ibrokhim Abdurakhmonov. Ishwarappa Katageri. Mehboob-ur-Rahman. Yusuf Zafar. John Z. Yu. Russell J. Kohel. Jonathan Wendel. Paterson AH (2007) Toward sequencing cotton (Gossypium) genomes. . Plant Physiology 145:1303–1310.Google Scholar

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© Springer Science+Business Media, LLC 2009

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  • Andrew H. Paterson

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