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, Michael Freeling

Research output: Contribution to journalArticle

213 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1772-1781
Number of pages10
JournalPlant physiology
Volume148
Issue number4
DOIs
StatePublished - Dec 1 2008

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ASJC Scopus subject areas

  • Physiology
  • Genetics
  • Plant Science

Cite this

Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D., & Freeling, M. (2008). Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape: CoGe with rosids. Plant physiology, 148(4), 1772-1781. https://doi.org/10.1104/pp.108.124867