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Published on October 24, 2008; 10.1104/pp.108.124867

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Received June 16, 2008
Accepted October 19, 2008

Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids

Eric Lyons *, Brent Pedersen , Josh Kane , Maqsudul Alam , Ray Ming , Haibao Tang , Xiyin Wang , John Bowers , Andrew Paterson , Damon Lisch , and Michael Freeling

Department Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Advanced Studies in Genomics, Proteomics and Bioinformatics, and Department of Microbiology, University of Hawaii, Honolulu, HI 96822, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA

* Corresponding author; email: elyons{at}nature.berkeley.edu.

In addition to the genomes of Arabidopsis thaliana and poplar (Populus trichocarpa), two near-complete rosid genome sequences, grape (Vitis vinifera) and papaya (Carica papaya), have been recently released. The phylogenetic relationship among these four genomes, and the placement of their three independent, fractionated tetraploidies, sums to a powerful comparative genomic system. CoGe, a platform of multiple whole or near-complete genome sequences, provides an integrative web-based system to find and align syntenic chromosomal regions and visualize the output in an intuitive and interactive manner. CoGe has been customized to specifically support comparisons among the rosids. Crucial facts and definitions are presented in order to clearly describe the sorts of biological questions that might be answered in part using CoGe, including patterns of DNA conservation, accuracy of annotation, transposability of individual genes, subfunctionalization and/or fractionation of syntenic gene sets, and conserved noncoding sequence content. A precis of an online tutorial "CoGe with rosids" (http://tinyurl.com/4a23pk) presents sample results graphically.




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Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales
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[Abstract] [Full Text] [PDF]


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