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Genome Res. 2009 May;19(5):943-57. doi: 10.1101/gr.082784.108. Epub 2009 Feb 13.

Breakpoint graphs and ancestral genome reconstructions.

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  • 1Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA 92093-0404, USA.


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.

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