A comparative phylogenetic approach for dating whole genome duplication events.
BACKGROUND
Whole genome duplications have played a major role in determining the structure of eukaryotic genomes. Current evidence revealing large blocks of duplicated chromatin yields new insights into the evolutionary history of species, but also presents a major challenge for researchers attempting to utilize comparative genomics techniques. Understanding the timing of duplication events relative to divergence among taxa is critical to accurate and comprehensive cross-species comparisons.


RESULTS
We describe a large-scale approach to estimate the timing of duplication events in a phylogenetic context. The methodology has been previously utilized for analysis of Arabidopsis and Saccharomyces duplication events. This new implementation provides a more flexible and reusable framework for these analyses. Scripts written in the Python programming language drive a number of freely available bioinformatics programs, creating a no-cost tool for researchers. The usefulness of the approach is demonstrated through genome-scale analysis of Arabidopsis and Oryza (rice) duplications.


BACKGROUND
Software and documentation are freely available from http://plantgenome.agtec.uga.edu/bioinformatics/dating/
Chapman
Brad A
BA
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA. chapmanb@uga.edu
Bowers
John E
JE
Schulze
Stefan R
SR
Paterson
Andrew H
AH
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods; D019143:Evolution, Molecular; D020440:Gene Duplication; D020869:Gene Expression Profiling / Q000379:methods*; D016678:Genome; D016247:Information Storage and Retrieval / Q000379:methods; D012275:Oryza / Q000235:genetics; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software; D013997:Time Factors