Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy Junkang Rong, John E. Bowers, Stefan.

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Presentation transcript:

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

再繁殖下去呢 Lineage 雄虎 + 雌獅 = 虎獅雄獅 + 雌獅虎 = 獅獅虎雄虎 + 雌獅虎 = 虎獅虎雄獅 + 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)

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

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

Arabidopsis Small genome size 125 Mb Complete genetic and physical maps 5 chromosomes (2001) Short life cycle about 6 weeks Few repetitive DNA sequences Mb = megabases (百萬對nucleotide base pairs )

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 Allopolyploidy 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/

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, PLoS Biol, Vol. 3, No. 10, 2005.

Thank You