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MBE Advance Access originally published online on December 27, 2007
Molecular Biology and Evolution 2008 25(3):549-558; doi:10.1093/molbev/msm282
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© The Author 2007. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

A Comparative Synteny Map of Burkholderia Species Links Large-Scale Genome Rearrangements to Fine-Scale Nucleotide Variation in Prokaryotes

Chi Ho Lin*, Guillaume Bourque* and Patrick Tan*,{dagger}

* Genome Institute of Singapore, Singapore
{dagger} Duke-NUS Graduate Medical School, Singapore

E-mail: bourque{at}gis.a-star.edu.sg; tanbop{at}gis.a-star.edu.sg.

Accepted for publication December 18, 2007.

Genome rearrangement events, including inversions and translocations, are frequently observed across related microbial species, but the impact of such events on functional diversity is unclear. To clarify this relationship, we compared 4 members of the Gram-negative Burkholderia family (Burkholderia pseudomallei, Burkholderia mallei, Burkholderia thailandensis, and Burkholderia cenocepacia) and identified a core set of 2,590 orthologs present in all 4 species (metagenes). The metagenes were organized into 255 synteny blocks whose relative order has been altered by a predicted minimum of 242 genome rearrangement events. Functionally, metagenes within individual synteny blocks were often related. The molecular divergence of metagenes adjacent to synteny breakpoints (boundary metagenes) was significantly greater compared with metagenes within blocks, suggesting an association between breakpoint locations and local fine-scale nucleotide alterations. This phenomenon, referred to as boundary element associated divergence, was also observed in Pseudomonas and Shigella, suggesting that this is a common phenomenon in prokaryotes. We also observed preferential localization of species-specific genes and insertion sequence element to synteny breakpoints in Burkholderia. Our results suggest that in prokaryotes, genome rearrangements may influence functional diversity through the enhanced divergence of boundary genes and the creation of foci for acquiring and deleting species-specific genes.

Key Words: infectious disease • microbial genomics • melioidosis

Jennifer Wernegreen, Associate Editor


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