A comparative phylogenetic approach for dating whole genome duplication events

  • Authors:

  • Brad A. Chapman;John E. Bowers;Stefan R. Schulze;Andrew H. Paterson

  • Affiliations:

  • Department of Plant Biology, University of Georgia, Athens, GA 30602, USA;Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA;Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA;Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA

  • Venue:
  • Bioinformatics
  • Year:
  • 2004

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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/