title: The underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach.
abstract: The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach. Genetic variations have occurred throughout the whole evolutionary history of the Corynebacteriaceae. Gene loss has been the primary force causing genetic changes, not only in terms of the number of protein families affected, but also because of its continuity on the time series. The variation in metabolism caused by these genetic changes mainly occurred for membrane transporters, two-component systems, and metabolism related to amino acids and carbohydrates. Interestingly, horizontal gene transfer (HGT) not only caused changes related to pathogenicity, but also triggered the acquisition of antimicrobial resistance. The Darwinian theory of evolution did not adequately explain the effects of dispersive HGT and/or gene loss in the evolution of the Corynebacteriaceae. These findings provide new insight into the evolution and speciation of Corynebacteriaceae and advance our understanding of the genetic innovation in microbial populations.
authors.affiliation: Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China; State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: xyzhi@ynu.edu.cn.
authors.forename: Xiao-Yang
authors.initials: XY
authors.lastname: Zhi
authors.affiliation: Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China.
authors.forename: Zhao
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Huang
mesh_terms: D000192:Actinomycetales / Q000145:classification* / Q000235:genetics*; D000818:Animals; D022761:Gene Transfer, Horizontal; D049810:Genetic Speciation; D014644:Genetic Variation; D016680:Genome, Bacterial; D023281:Genomics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D010802:Phylogeny
keywords: Corynebacteriaceae; Gene loss; Genetic innovation; Horizontal gene transfer; Phylogenomics; Speciation