Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids | Zendy

Eric Lyons | Zendy; Brent S. Pedersen | Zendy; Josh Kane | Zendy; M. Shahid Alam | Zendy; Ray Ming | Zendy; Haibao Tang | Zendy; Xiyin Wang | Zendy; John Bowers | Zendy; Andrew H. Paterson | Zendy; Damon Lisch | Zendy; Michael Freeling | Zendy

AI Assistant Blog Pricing

Home ZAIA Blog

Open Access

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

Author(s) -

Eric Lyons,

Brent S. Pedersen,

Josh Kane,

M. Shahid Alam,

Ray Ming,

Haibao Tang,

Xiyin Wang,

John Bowers,

Andrew H. Paterson,

Damon Lisch,

Michael Freeling

Publication year - 2008

Publication title -

plant physiology

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.554

H-Index - 312

eISSN - 1532-2548

pISSN - 0032-0889

DOI - 10.1104/pp.108.124867

Subject(s) - genome , synteny , biology , arabidopsis thaliana , arabidopsis , genetics , carica , phylogenetic tree , computational biology , whole genome sequencing , context (archaeology) , subfunctionalization , gene , botany , gene family , paleontology , mutant

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 content you want is available to Zendy users.

Already have an account? Click here to sign in.

Having issues? You can contact us here

Accelerating Research