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Author Lin, Chi Ho ♦ Bourque, Guillaume ♦ Tan, Patrick
Source CiteSeerX
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Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Mol Biol Evol ♦ Large-scale Genome Rearrangement ♦ Comparative Synteny Map ♦ Burkholderia Specie ♦ Fine-scale Nucleotide Variation ♦ Functional Diversity ♦ Species-specific Gene ♦ Genome Rearrangement Event ♦ Synteny Block ♦ Insertion Sequence Element ♦ Relative Order ♦ Burkholderia Malleus ♦ Boundary Gene ♦ Boundary Element ♦ Gram-negative Burkholderia Family ♦ Core Set ♦ Genome Rearrangement ♦ Burkholderia Cenocepacia ♦ Burkholderia Thailandensis ♦ Burkholderia Pseudomallei ♦ Related Microbial Specie ♦ Predicted Minimum ♦ Preferential Localization ♦ Common Phenomenon ♦ Molecular Divergence ♦ Breakpoint Location ♦ Boundary Metagenes ♦ Local Fine-scale Nucleotide Alteration ♦ Individual Synteny Block ♦ Enhanced Divergence
Abstract 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.
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