Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and...
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![Page 1: Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy Junkang Rong, John E. Bowers, Stefan.](https://reader035.fdocuments.in/reader035/viewer/2022062322/5697c0221a28abf838cd339a/html5/thumbnails/1.jpg)
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
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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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Liger (Liger (獅虎獅虎 ) = Lion + ) = Lion + TigerTiger
http://past.people.com.cn
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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 =
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Arabidopsis & Arabidopsis & GossypiumGossypium
http://grs.psc.riken.jp
http://www.kingsnake.com
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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
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ArabidopsisArabidopsis
• Small genome size– 125 Mb
• Complete genetic and physical maps– 5 chromosomes (2001)
• Short life cycle– about 6 weeks
• Few repetitive DNA sequences
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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]
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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
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PolyploidyPolyploidy
• Autopolyploidy– Polyploids created by chromosome
duplication within a species
• Allopolyploidy– Polyploids created by hybridization
between different species
http://www.agri.pref.hokkaido.jp/ http://www.jsafc.net/ http://218.7.20.32/pic/
+ =I’m
小麥
I’m 黑麥 I’m 小黑麥
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Genome DuplicationGenome Duplication
• A: a genome that has 22 genes
• B: a genome duplication
http://biology.plosjournals.org
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Gene LossGene Loss
• C: a genome duplication followed by significant gene losses
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DiploidizationDiploidization
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Gene DivergenceGene Divergence
• The duplication of a region of chromosome containing a (generally functional) gene
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Conserved SyntenyConserved Synteny• A chromosome
pair, one from each of two species that share at least one ortholog
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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
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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.
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Thank You