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

被引：309

作者：

Lyons, Eric ^{[1
]}

Pedersen, Brent ^{[1
]}

Kane, Josh ^{[1
]}

Alam, Maqsudul ^{[2
]}

Ming, Ray ^{[3
]}

Tang, Haibao ^{[4
]}

Wang, Xiyin ^{[4
]}

Bowers, John ^{[4
]}

Paterson, Andrew ^{[4
]}

Lisch, Damon ^{[1
]}

Freeling, Michael ^{[1
]}

机构：

[1] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[2] Univ Hawaii, Dept Microbiol, Honolulu, HI 96822 USA

[3] Univ Illinois, Dept Plant Biol, Urbana, IL 61801 USA

[4] Univ Georgia, Ctr Appl Genet Technol, Athens, GA 30602 USA

来源：

PLANT PHYSIOLOGY | 2008年 / 148卷 / 04期

基金：

美国国家科学基金会;

关键词：

D O I：

10.1104/pp.108.124867

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

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 precis of an online tutorial, CoGe with Rosids (http://tinyurl.com/4a23pk), presents sample results graphically.

引用

页码：1772 / 1781

页数：10

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