Plant Physiol.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

First published online October 24, 2008; 10.1104/pp.108.124867

Plant Physiology 148:1772-1781 (2008)
© 2008 American Society of Plant Biologists

This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supplemental Data
Right arrow All Versions of this Article:
148/4/1772    most recent
pp.108.124867v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via Web of Science (1)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Lyons, E.
Right arrow Articles by Freeling, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lyons, E.
Right arrow Articles by Freeling, M.
Agricola
Right arrow Articles by Lyons, E.
Right arrow Articles by Freeling, M.
BIOINFORMATICS

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids1,[W]

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

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.

1 This work was supported by the National Science Foundation (NSF; grant nos. DBI 034937 and DBI 0701871 to M.F. [CoGe] and grant nos. MCB–0450260 and DBI–0553417 to A.P. [Cp-4At list of five syntenic genes/positions]); the University of Hawaii and the U.S. Department of Defense (grant no. W81XWH0520013 to M.A. [papaya sequence]); Maui High Performance Computing Center (grant to M.A.); and the Hawaii Agriculture Research Center (grant to R.M. and coworkers).

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.

HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
ASPB Publications PLANT PHYSIOLOGY® THE PLANT CELL
Copyright © 2008 by the American Society of Plant Biologists