A COMPARATIVE PHYLOGENETIC APPROACH FOR DATING WHOLE GENOME DUPLICATION EVENTS

¹ Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia, 30602, USA

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. We describe a large-scale approach to estimate the timing of duplication events in an 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. Software and documentation are freely available from http://plantgenome.agtec.uga.edu/bioinformatics/dating/