TY - JOUR
T1 - Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar, and grape
T2 - CoGe with rosids
AU - Lyons, Eric
AU - Pedersen, Brent
AU - Kane, Josh
AU - Alam, Maqsudul
AU - Ming, Ray
AU - Tang, Haibao
AU - Wang, Xiyin
AU - Bowers, John
AU - Paterson, Andrew
AU - Lisch, Damon
AU - Freeling, Michael
PY - 2008/12
Y1 - 2008/12
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=57149089296&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=57149089296&partnerID=8YFLogxK
U2 - 10.1104/pp.108.124867
DO - 10.1104/pp.108.124867
M3 - Article
C2 - 18952863
AN - SCOPUS:57149089296
SN - 0032-0889
VL - 148
SP - 1772
EP - 1781
JO - Plant physiology
JF - Plant physiology
IS - 4
ER -