Reconstructing the genomic architecture of mammalian ancestors using multispecies comparative maps.

Stephen J O'Brien,William J Murphy,Guillaume Bourque,Pavel Pevzner,Glenn Tesler

doi:10.1186/1479-7364-1-1-30

Stephen J O'Brien, William J Murphy

Open Access

https://doi.org/10.1186/1479-7364-1-1-30

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Abstract

Rapidly developing comparative gene maps in selected mammal species are providing an opportunity to reconstruct the genomic architecture of mammalian ancestors and study rearrangements that transformed this ancestral genome into existing mammalian genomes. Here, the recently developed Multiple Genome Rearrangement (MGR) algorithm is applied to human, mouse, cat and cattle comparative maps (with 311-470 shared markers) to impute the ancestral mammalian genome. Reconstructed ancestors consist of 70-100 conserved segments shared across the genomes that have been exchanged by rearrangement events along the ordinal lineages leading to modern species genomes. Genomic distances between species, dominated by inversions (reversals) and translocations, are presented in a first multispecies attempt using ordered mapping data to reconstruct the evolutionary exchanges that preceded modern placental mammal genomes.

Highlights

IntroductionComparative studies to identify and quantify the extent of conserved segments between two genomes are often based on the breakpoint analysis approach pioneered by Nadeau and Taylor.[17] These early studies of rearrangements between human and mouse genomes considered breakpoints independently, without revealing combinatorial dependencies between related breakpoints
The genomic maps of homologous markers were first compared between human, mouse and cat using the Multiple Genome Rearrangement (MGR) and GRIMM-synteny algorithms
Using multispecies mammalian comparative maps, coupled with new computational tools for multichromosomal rearrangement analysis, we have been able to demonstrate the promise of generating ancestral chromosome architectures from small numbers of taxa and fewer than 500 shared markers

Summary

Introduction

Comparative studies to identify and quantify the extent of conserved segments between two genomes are often based on the breakpoint analysis approach pioneered by Nadeau and Taylor.[17] These early studies of rearrangements between human and mouse genomes considered breakpoints independently, without revealing combinatorial dependencies between related breakpoints. Kececioglu and Sankoff 18 were the first to explore the importance of dependencies between breakpoints, and developed an approximation algorithm for the reversal distance problem (eg studies of rearrangements in unichromosomal genomes). Hannenhalli and Pevzner[19,20] developed a polynomial-time algorithm for the reversal distance problem, which was extended to the genomic distance problem of finding a most parsimonious scenario for multichromosomal genomes under inversions (reversals), translocations, fusions and fissions of chromosomes.[21,22,23]

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