title: Phylogenomics and evolutionary dynamics of the family Actinomycetaceae.
abstract: The family Actinomycetaceae comprises several important pathogens that impose serious threat to human health and cause substantial infections of economically important animals. However, the phylogeny and evolutionary dynamic of this family are poorly characterized. Here, we provide detailed description of the genome characteristics of Trueperella pyogenes, a prevalent opportunistic bacterium that belongs to the family Actinomycetaceae, and the results of comparative genomics analyses suggested that T. pyogenes was a more versatile pathogen than Arcanobacterium haemolyticum in adapting various environments. We then performed phylogenetic analyses at the genomic level and showed that, on the whole, the established members of the family Actinomycetaceae were clearly separated with high bootstrap values but confused with the dominant genus Actinomyces, because the species of genus Actinomyces were divided into three main groups with different G+C content. Although T. pyogenes and A. haemolyticum were found to share the same branch as previously determined, our results of single nucleotide polymorphism tree and genome clustering as well as predicted intercellular metabolic analyses provide evidence that they are phylogenetic neighbors. Finally, we found that the gene gain/loss events occurring in each species may play an important role during the evolution of Actinomycetaceae from free-living to a specific lifestyle.
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China bsyue@scu.edu.cn min.wu@med.und.edu.
authors.forename: Kelei
authors.initials: K
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China bsyue@scu.edu.cn min.wu@med.und.edu.
authors.forename: Wujiao
authors.initials: W
authors.lastname: Li
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China.
authors.forename: Chunlan
authors.initials: C
authors.lastname: Kang
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China.
authors.forename: Lianming
authors.initials: L
authors.lastname: Du
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China.
authors.forename: Ting
authors.initials: T
authors.lastname: Huang
authors.affiliation: Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China.
authors.forename: Xiuyue
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Basic Sciences, School of Medicine and Health Sciences, University of North Dakota bsyue@scu.edu.cn min.wu@med.und.edu.
authors.forename: Min
authors.initials: M
authors.lastname: Wu
authors.affiliation: Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China bsyue@scu.edu.cn min.wu@med.und.edu.
authors.forename: Bisong
authors.initials: B
authors.lastname: Yue
mesh_terms: D000191:Actinomycetaceae / Q000145:classification / Q000235:genetics*; D005075:Biological Evolution; D010802:Phylogeny
keywords: Actinomycetaceae; Trueperella pyogenes; comparative genomics; gene gain/loss; phylogeny