Tracing <i>Brucella</i> evolutionary dynamics in expanding host ranges through nucleotide, codon and amino acid usages in genomes

The host range of <i>Brucella</i> organisms has expanded from terrestrial and marine mammals to fish and amphibians. The high homology genomes of different <i>Brucella</i> organisms promote us to investigate evolutionary patterns for nucleotide, codon and amino acid usage patterns at gene levels among <i>Brucella</i> species. Although the similar patterns for nucleotide and synonymous codon usages exist in gene population, GC composition at the first codon position has significant correlations to that of the second and third codon positions, respectively, suggesting that nucleotide usages surrounding one codon influence synonymous codon usage patterns. Evolutionary patterns represented by synonymous codon and amino acid usages reflect host factor impacting <i>Brucella</i> speciation. As for genetic variations of important virulent factors involved with different biological functions, genes encoding lipoplysaccharides (LPSs) display more distinctive codon adaptation to <i>Brucella</i> than those of the BvrR/BvrS system and type IV secretion system. By Bayesian analysis, the polygenetic constructions for these genes of virulent factors shared by <i>Brucella</i> species display the purifying/positive selections and partially host factor in mediating genetic variations of these genes. The systemic analyses for nucleotide, synonymous codon and amino acid usages at gene level and genetic variations of important virulent factor genes display that host limitation influences either genetic characterizations at gene level or a particular gene involved in virulent factors of <i>Brucella</i>. Communicated by Ramaswamy H. Sarma