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MBE Advance Access published online on December 27, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm282
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© 2007 The Authors
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Research Article

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

Chi Ho Lin1, Guillaume Bourque1,* and Patrick Tan1,2,*

1 Genome Institute of Singapore, 60 Biopolis Street, #02-01, Genome, Singapore 138672
2 Duke-NUS Graduate Medical School, 2 Jalan Bukit Merah, Singapore 169547

* Corresponding Authors, E-mail : bourque{at}gis.a-star.edu.sg and tanbop{at}gis.a-star.edu.sg, Tel : 65-6-478-8000, Fax : 65-6-478-9058

Received for publication August 27, 2007. Revision received December 17, 2007. 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 four members of the Gram-negative Burkholderia family (B. pseudomallei, B. mallei, B. thailandensis and B. cenocepacia) and identified a core set of 2590 orthologs present in all four 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 to metagenes within blocks, suggesting an association between breakpoint locations and local fine-scale nucleotide alterations. This phenomenon, referred to as Boundary Element Associated Divergence (BEAD), 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 (IS) 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.


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