Comparative genomics of Gossypium and Arabidopsis Unraveling the

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

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

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

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

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

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

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]

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

Polyploidy • Autopolyploidy – Polyploids created by chromosome duplication within a species • Allopolyploidy – Polyploids created by hybridization between different species I’m 小麥 I’m 黑麥 ＋ http: //www. agri. pref. hokkaido. jp/ http: //www. jsafc. net/ = I’m 小 黑麥 http: //218. 7. 20. 32/pic/

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

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

Diploidization

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

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

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: //en. wikipedia. org http: //www. nature. com

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, PLo. S Biol, Vol. 3, No. 10, 2005.

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