Breakpoint graphs and ancestral genome reconstructions

  1. Max Alekseyev and
  2. Pavel A. Pevzner1
  1. University of California, San Diego

Abstract

Recently completed whole genome sequencing projects marked the transition from gene-based phylogenetic studies to phylogenomics analysis of entire genomes. We developed an algorithm, MGRA, for reconstructing ancestral genomes and used it to study the rearrangement history of seven mammalian genomes: human, chimpanzee, macaque, mouse, rat, dog, and opossum. MGRA relies on the notion of the multiple breakpoint graphs to overcome some limitations of the existing approaches to ancestral genome reconstructions. MGRA also generates the rearrangement-based characters guiding the phylogenetic tree reconstruction when the phylogeny is unknown.

Footnotes

    • Received June 30, 2008.
    • Accepted January 22, 2009.

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  1. Published in Advance February 13, 2009, doi: 10.1101/gr.082784.108 Genome Res. gr.082784.108 Copyright © 2009, Cold Spring Harbor Laboratory Press

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