Genome evolution in Burkholderia spp

Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization. Results: We performed pan-genome analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. We detected parallel inversions in the second chromosomes of seven B. pseudomallei. Breakpoints of these inversions are formed by genes encoding components of multidrug resistance complex. The membrane components of this system are exposed to the host9s immune system, and hence these inversions may be linked to a phase variation mechanism. We identified 197 genes evolving under positive selection. We found seventeen genes evolving under positive selection on individual branches; most of the positive selection periods map to the branches that are ancestral to species clades. This might indicate rapid adaptation to new ecological niches during species formation. Conclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be possible phase variation mechanism in B. pseudomallei.