Comparative Genomics in the Genus Burkholderia
Pimlapas Leekitcharoenphon, Gregory S. Buzard and David W. Ussery
from: Burkholderia: From Genomes to Function (Edited by: Tom Coenye and Eshwar Mahenthiralingam). Caister Academic Press, U.K. (2014)
Abstract
The Burkholderia genus contains over 60 species that have colonized a wide diversity of biological niches, including those as animal, human and plant pathogens. We have collected the publicly available whole genome sequences of Burkholderia spp. to explore the genomic diversity within this genus, and we report here on the comparison of 110 Burkholderia genomes. We have constructed three types of phylogenetic trees, based on different sets of genetic information (16S rRNA genes, multiple locus sequence tags [MLST] and pan-genome sequences), as alternate ways to display taxonomic groupings and evolutionary relationships. We have found, among the more than 35,000 gene families that are represented in the Burkholderia pan-genome, a set of 717 core gene families that are conserved across all the Burkholderia genomes we studied. We have also identified the species-unique core genes for each species. Our findings can be used to find new signature sequences for the rapid and accurate detection of the different Burkholderia species. We have also constructed a BLAST atlas that compares the B. pseudomallei and B. mallei genomes which helps visualize gene homologies and shows the fraction of genes found in common in pair-wise comparison and reveals the duplication of genes within their genomes. The B. mallei genome is known to be significantly smaller in size than that of B. pseudomallei; this is also obvious from our analysis that demonstrates that almost all of the B. mallei proteome is present in B. pseudomallei read more ...
