A comparative phylogenetic approach for dating whole genome duplication events |
| |
Authors: | Chapman Brad A Bowers John E Schulze Stefan R Paterson Andrew H |
| |
Affiliation: | Department of Plant Biology, University of Georgia, Athens, GA 30602, USA. chapmanb@uga.edu |
| |
Abstract: | MOTIVATION: 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. AVAILABILITY: Software and documentation are freely available from http://plantgenome.agtec.uga.edu/bioinformatics/dating/ |
| |
Keywords: | |
本文献已被 PubMed Oxford 等数据库收录! |
|