Breakpoint graphs and ancestral genome reconstructions
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
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- Received June 30, 2008.
- Accepted January 22, 2009.
- Copyright © 2009, Cold Spring Harbor Laboratory Press
