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BIOINFORMATICS

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids^1,[W]

Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (E.L., B.P., J.K., D.L., M.F.); Advanced Studies in Genomics, Proteomics and Bioinformatics, and Department of Microbiology, University of Hawaii, Honolulu, Hawaii 96822 (M.A.); Department of Plant Biology, University of Illinois, Urbana, Illinois 61801 (R.M.); and Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602 (H.T., X.W., J.B., A.P.)

In addition to the genomes of Arabidopsis (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 sum 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 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. This précis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically.

The author responsible for the distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Eric Lyons (elyons{at}nature.berkeley.edu).

^[W] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.108.124867

^* Corresponding author; e-mail elyons{at}nature.berkeley.edu.

Received June 16, 2008; accepted October 19, 2008; published October 24, 2008.

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