Identification of Recombination and Positively Selected Genes in Brucella

Abstract

Brucella is a facultative intracellular bacterium belongs to the class alpha proteobacteria. It causes zoonotic disease brucellosis to wide range of animals. Brucella species are highly conserved in nucleotide level. Here, we employed a comparative genomics approach to examine the role of homologous recombination and positive selection in the evolution of Brucella. For the analysis, we have selected 19 complete genomes from 8 species of Brucella. Among the 1599 core genome predicted, 24 genes were showing signals of recombination but no significant breakpoint was found. The analysis revealed that recombination events are less frequent and the impact of recombination occurred is negligible on the evolution of Brucella. This leads to the view that Brucella is clonally evolved. On other hand, 56 genes (3.5 % of core genome) were showing signals of positive selection. Results suggest that natural selection plays an important role in the evolution of Brucella. Some of the genes that are responsible for the pathogenesis of Brucella were found positively selected, presumably due to their role in avoidance of the host immune system.

Keywords: Brucella; Evolution; Positive selection; Recombination.

Fig. 1

Clonal genealogy of Brucella (a) Chromosome I (b) Chromosome II. Phylogenetic tree generated by ClonalFrame using the core genome of Brucella chromosome I and chromosome II extracted from whole genome alignment

Fig. 2

COG classification of genes under positive selection in Brucella genomes. Percent representation was calculated as number of positively selected genes involved in a given COG/number of all genes under positive selection. The COGs categories are coded as follows: E, amino acid transport and metabolism; R, general functional prediction only; K, transcription; S, function-unassigned conserved proteins; T, signal transduction; F, nucleotide transport and metabolism; J, translation; M, cell wall/membrane biogenesis; P, inorganic ion transport and metabolism; C, energy production and conversion; G, carbohydrate transport and metabolism; I, lipid metabolism; L, DNA replication, recombination and repair; D, cell division and chromosome partitioning; H, coenzyme metabolism; O, posttranslational modification, protein turnover and chaperones; Q, secondary metabolites biosynthesis, transport and catabolism; V, defence mechanisms