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Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of ancient and recent polyploidy

This paper explores the comparative genomics of Gossypium and Arabidopsis to understand the effects of polyploidy. It discusses the research done, the problems faced, and the methodology used.

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Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of ancient and recent polyploidy

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  1. Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy Junkang Rong, John E. Bowers, Stefan R. Schulze, Vijay N. Waghmare, Carl J. Rogers, Gary J. Pierce, Hua Zhang, James C. Estill, and Andrew H. Paterson Huge Gap Pi-Cheng Hsiu Department of Computer Science and Information Engineering, National Taiwan University

  2. Outline • What research the paper did • Why do this research • Which problems the research suffers from • How to do this research

  3. Liger (獅虎) = Lion + Tiger http://past.people.com.cn

  4. Lineage • 雄獅+雌虎=獅虎 • 雄虎+雌獅=虎獅 再繁殖下去呢 • 雄獅+雌獅虎= 獅獅虎 • 雄虎+雌獅虎=虎獅虎 • 雄獅+雌虎獅=獅虎獅 • 雄虎+雌虎獅=虎虎獅 (獅|虎)*(獅虎|虎獅)

  5. Arabidopsis & Gossypium http://grs.psc.riken.jp http://www.kingsnake.com

  6. Framework of This Paper Common Ancestor Arabidopsis Gossypiums http://www.forestryimages.org http://www.vermeirsch.be http://www.fmnh.helsinki.fi http://ncbg.unc.edu

  7. Arabidopsis • Small genome size • 125 Mb • Complete genetic and physical maps • 5 chromosomes (2001) • Short life cycle • about 6 weeks • Few repetitive DNA sequences

  8. Gossypium • An appropriate system for studying paleopolyploids • Monoploid (13 chromosomes) • Diploid (e.g., G. trilobum and G. raimondii) • Tetraploid (e.g., G. hirsutum) • Octaploid [Wendel et. al., 2003]

  9. Paleopolyploidization • Whole genome duplication events occurred in the history of evolution • An important evolutionary mechanism (S. Ohno, 1970) • Some evidence • Yeast: 108 years ago • Vertebrates: 2×108 years ago • Plants : particularly prevalent http://www.nap.edu/html/biomems/sohno.html http://www.uiowa.edu http://www.fishvetsociety.org.uk http://www.nwhc.usgs.gov http://www.dartmouth.edu http://www.chinafarm.com.cn

  10. Polyploidy • Autopolyploidy • Polyploids created by chromosome duplication within a species • Allopolyploidy • Polyploids created by hybridization between different species I’m 小黑麥 I’m 黑麥 I’m 小麥 ＋ = http://www.agri.pref.hokkaido.jp/ http://www.jsafc.net/ http://218.7.20.32/pic/

  11. Genome Duplication • A: a genome that has 22 genes • B: a genome duplication http://biology.plosjournals.org

  12. Gene Loss • C: a genome duplication followed by significant gene losses

  13. Diploidization

  14. Gene Divergence • The duplication of a region of chromosome containing a (generally functional) gene

  15. Conserved Synteny • A chromosome pair, one from each of two species that share at least one ortholog

  16. Keys to Infer • Inference of conserved synteny in pre-duplicated genome • What was the original order of blocks? • Nature of post-duplication rearrangements events • How many rearrangements have occurred since the duplication occurred? • Statistics of gene loss versus gene divergence http://www.nature.com http://en.wikipedia.org

  17. Reference • Arabidopsis Genome Analysis http://nucleus.cshl.org/protarab/ • wikipedia http://www.wikipedia.org/ • Wolfe, KH and D. Shields, Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387:708-713, 1997. • P. Dehal and J. L. Boore, Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate, PLoS Biol, Vol. 3, No. 10, 2005.

  18. Thank You

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