title: Phylogenomics and the dynamic genome evolution of the genus Streptococcus.
abstract: The genus Streptococcus comprises important pathogens that have a severe impact on human health and are responsible for substantial economic losses to agriculture. Here, we utilize 46 Streptococcus genome sequences (44 species), including eight species sequenced here, to provide the first genomic level insight into the evolutionary history and genetic basis underlying the functional diversity of all major groups of this genus. Gene gain/loss analysis revealed a dynamic pattern of genome evolution characterized by an initial period of gene gain followed by a period of loss, as the major groups within the genus diversified. This was followed by a period of genome expansion associated with the origins of the present extant species. The pattern is concordant with an emerging view that genomes evolve through a dynamic process of expansion and streamlining. A large proportion of the pan-genome has experienced lateral gene transfer (LGT) with causative factors, such as relatedness and shared environment, operating over different evolutionary scales. Multiple gene ontology terms were significantly enriched for each group, and mapping terms onto the phylogeny showed that those corresponding to genes born on branches leading to the major groups represented approximately one-fifth of those enriched. Furthermore, despite the extensive LGT, several biochemical characteristics have been retained since group formation, suggesting genomic cohesiveness through time, and that these characteristics may be fundamental to each group. For example, proteolysis: mitis group; urea metabolism: salivarius group; carbohydrate metabolism: pyogenic group; and transcription regulation: bovis group.
authors.affiliation: Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University.
authors.forename: Vincent P
authors.initials: VP
authors.lastname: Richards
authors.forename: Sara R
authors.initials: SR
authors.lastname: Palmer
authors.forename: Paulina D
authors.initials: PD
authors.lastname: Pavinski Bitar
authors.forename: Xiang
authors.initials: X
authors.lastname: Qin
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Highlander
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Town
authors.forename: Robert A
authors.initials: RA
authors.lastname: Burne
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Stanhope
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000502:physiology*; D016680:Genome, Bacterial / Q000502:physiology*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D013291:Streptococcus / Q000235:genetics*
keywords: comparative genomics; enrichment; gene gain and loss; lateral gene transfer; phylogenetics