|其他摘要||The genus Streptococcus is the most aboundant group in the phylum Firmicute, which composes diverse and significant zoonotic pathogens. They are responsible for serious infections to human and animals, and substantial economic losses to agriculture. Genus Streptococcus has gone through considerable taxonomic revision and the majority of streptococci were placed into “species groups” due to increasing improvements of systematic bacteriology. The taxonomy of Streptococcus is still not very clear, and its evolutionary mechanism is still not well resolved. Additionally, understanding of species groups remains on phenotypic traits and their evolutionary implications are not clear presently. Besides, previous studies mainly focused on comparative genomic analyses of a single species or several species, lacking of evolutionary process and virulence studies at genus level. As streptococcal genomes are increasingly sequenced and reported, which may provide new insights into Streptococcus genetic evolutionary and biodiversity researches, contributing to the deeply thought through Streptococcus diseases of human and animals. In view of threat and harm of Streptococcus to animal husbandry and public health, it is necessary to understand Streptococcus genome evolution and virulence and antiboitic resistance features.
In this research, comparative genomic approaches were used to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. The major results were summarized as follows:
(1) Genome dynamics analyses indicated that the changing trends of sizes of pan-genome, core genome and unique genes at the species group level were respectively consistent with the ones at the genus level. The change trend of pan-genome size meets a increasing compound fountion: ; the change trend of core genome size meets a decreasing fountion: . These analyses theoretically verified the open status of Streptococcus pan-genome. Also, those results illustrated that pan-genome was underestimated, new genes appears with more streptococcal strains sequenced and more species discovered. Core genome played an important part in homologous clusters; as well, Streptococcus-specific genes might provide clues for adaptative evolution.
(2) Population structure inferenced from genomic data suggested that there were two distinct lineages within the genus, closing to the nature relationships of Streptococcus populations. One included Pyogenic, Bovis, Mutans and Salivarius groups; and the other included Mitis, Anginosus and Unknown groups. The phylogenetic dendrograms also revealed two main clades, which were in accordance with population structure analyses, and species within the same species group clustered together. Due to horizontal gene transfer, Mutans group had a split lineage and contained two clades. The polyphyly profiles also were evidenced by the hybridazation of population structure.
(3) During the scanning of streptococcal genomes, an abundant of virulence factors and antibiotic resistence related genes were detected. Adhesin, immune evasion and stress protein virulence factors accounted for a large proportion; distribution of streptococcal virulence factors has no obvious patterns among the species groups. And evolution of some common virulence factors, e.g., pavA, srtA, slrA, plr/gapA, eno, htrA/degP, tig/ropA, was congruous with the evolution of species groups, according to phylogenetic inference. Additonally, all the strains had bacA and pbp2x gene, and most of the strains had pmrA gene. Streptococcal speices groups possess group-specific antibiotic resistance genes, almost all of strains of Mutans group have bcrA gene while most strains of Pyogenic group have vanug gene. And virulence of GNO1 mutant and URE1 mutant of Streptococcus was reduced obviouly, on the basis of analyses of pathogen host interaction
In this study, the proposed streptococcal species groups were reasonable, which played significant roles in evolution from the viewpoints of comparative genomics. The small genome size and open pan-genome of Streptococcus imply frequently gene exchanges to benefit their novel habits and colonization. Evolution of genus Streptococcus is congruent with the individual evolutionary trajectories of different species groups. Evolutionary trajectories are congruent between genus Streptococcus and individuals of species groups. S. suis was unassigned for phenotypic difference, but it might originated from the same lineage with species of Anginosus group. The results and conclusions will help to understand of streptococcal genome dynamic change and its evolution process, also provide theoretical basis for the prevention and control of Streptococus disease. Furthermore, this study will provide useful data for analyzing large-scale genomes of pathgenic bacteria. With development of research, the evolution details of Streptococus will be clear and be benefit to clinical control and monitoring in the near future.|