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

Junkang Rong, John E. Bowers, Stefan R. Schulze, Vijay N. Waghmare,Carl J. Rogers, Gary J. Pierce, Hua Zhang, James C. Estill, andAndrew H. Paterson

Department of Computer Science and Department of Computer Science and Information Engineering, National Taiwan Information Engineering, National Taiwan UniversityUniversity

Pi-Cheng HsiuPi-Cheng Hsiu

Huge GapHuge Gap

OutlineOutline• What research the paper What research the paper

diddid• Why do this researchWhy do this research• Which problems the Which problems the

research suffers fromresearch suffers from• How to do this researchHow to do this research

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LineageLineage

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

• 雄獅 + 雌虎 = 獅虎• 雄虎 + 雌獅 = 虎獅

( 獅 | 虎 )*(獅虎 |虎獅 )

• 雄獅 + 雌獅虎 =

Arabidopsis & Arabidopsis & GossypiumGossypium

http://grs.psc.riken.jp

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Framework of This Framework of This PaperPaper

http://ncbg.unc.eduhttp://www.fmnh.helsinki.fihttp://www.vermeirsch.behttp://www.forestryimages.org

Common Ancestor

GossypiumsGossypiums Arabidopsis

ArabidopsisArabidopsis

• Small genome size– 125 Mb

• Complete genetic and physical maps– 5 chromosomes (2001)

• Short life cycle– about 6 weeks

• Few repetitive DNA sequences

GossypiumGossypium

• 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]

PaleopolyploidizationPaleopolyploidization• 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.htmlhttp://www.nwhc.usgs.gov http://www.dartmouth.edu http://www.chinafarm.com.cn

http://www.fishvetsociety.org.ukhttp://www.uiowa.edu

PolyploidyPolyploidy

• Autopolyploidy– Polyploids created by chromosome

duplication within a species

• Allopolyploidy– Polyploids created by hybridization

between different species

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小麥

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Genome DuplicationGenome Duplication

• A: a genome that has 22 genes

• B: a genome duplication

http://biology.plosjournals.org

Gene LossGene Loss

• C: a genome duplication followed by significant gene losses

DiploidizationDiploidization

Gene DivergenceGene Divergence

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

Conserved SyntenyConserved 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 AnalysisArabidopsis Genome Analysishttp://nucleus.cshl.org/protarab/

• wikipediawikipediahttp://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