Analysis of gene gain and loss in the evolution of predatory bacteria.
Predatory bacteria are ubiquitously distributed in nature in including in aquatic environments, sewage, intestinal tracts of animals and humans, rhizophere and, soils. However, our understanding of their evolutionary history is limited. Results of recent studies have shown that acquiring novel genes is a major force driving bacterial evolution. Therefore, to gain a better understanding of the impact of gene gain and loss in the evolution of bacterial predators, this study employed comparative genomic approaches to identify core-set gene families and species-specific gene families, and model gene gain and loss events among 11 genomes that represented diverse lineages. In total, 1977 gene families were classified. Of these 509 (pattern 11111111111) were present all of the 11 species. Among the non-core set gene families, 52 were present only in saltwater bacteria predators and had no ortholog in the other genomes. Similarly 109 and 44 were present only in the genomes of Micavibrio spp. and Bdellovibrio spp., respectively. In this study, the gain loss mapping engine GLOOME was selected to analyze and estimate the expectations and probabilities of both gain and loss events in the predatory bacteria. In total, 354 gene families were involved in significant gene gain events, and 407 gene families were classified into gene loss events with high supported value. Moreover, 18 families from the core set gene family were identified as putative genes under positive selection. The results of this study suggest that acquisition of particular genes that encode functional proteins in metabolism and cellular processes and signaling, especially ABC systems, may help bacterial predators adapt to surrounding environmental changes and present different predation strategies for survival in their habitats.
College of Marine Science and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China; School of the Environment, Florida A&M University, Tallahassee, FL, USA. Electronic address: nan.li@famu.edu.
Nan
N
Li
Institute of Biochemistry and Cell Biology, Shanghai Institute of Biological Science, Chinese Academy of Science, Shanghai, China.
Kai
K
Wang
School of the Environment, Florida A&M University, Tallahassee, FL, USA.
Henry N
HN
Williams
College of Marine Science and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China.
Jun
J
Sun
College of Marine Science and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China.
Changling
C
Ding
College of Marine Science and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China.
Xiaoyun
X
Leng
Department of Biological Sciences, Seoul National University, Seoul 151-742, South Korea.
Ke
K
Dong
D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000472:pathogenicity; D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity*; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics / Q000472:pathogenicity; D001501:Bdellovibrio / Q000145:classification / Q000235:genetics / Q000472:pathogenicity; D002874:Chromosome Mapping; D020564:Deltaproteobacteria / Q000145:classification / Q000235:genetics / Q000472:pathogenicity; D017753:Ecosystem; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D006801:Humans; D005810:Multigene Family; D010802:Phylogeny; D014774:Virulence / Q000235:genetics
BALOs; Bacteriovorax; Bdellovibrio; Comparative genomics; Gene gain and loss; Halobacteriovorax; Micavibrio; Positive selection