Suzuki, H., Lefebure, T., Hubisz, M. J., Pavinski Bitar, P., Lang, P., Siepel, A., Stanhope, M. J. (2011) Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol Evol, 3. pp. 168-85. ISSN 1759-6653
Preview |
PDF (Paper)
Siepel Genome Biology and Evolution 2011.pdf - Published Version Download (1MB) | Preview |
Abstract
Comparative genomics of closely related bacterial species with different pathogenesis and host preference can provide a means of identifying the specifics of adaptive differences. Streptococcus dysgalactiae (SD) is comprised of two subspecies: S. dysgalactiae subsp. equisimilis is both a human commensal organism and a human pathogen, and S. dysgalactiae subsp. dysgalactiae is strictly an animal pathogen. Here, we present complete genome sequences for both taxa, with analyses involving other species of Streptococcus but focusing on adaptation in the SD species group. We found little evidence for enrichment in biochemical categories of genes carried by each SD strain, however, differences in the virulence gene repertoire were apparent. Some of the differences could be ascribed to prophage and integrative conjugative elements. We identified approximately 9% of the nonrecombinant core genome to be under positive selection, some of which involved known virulence factors in other bacteria. Analyses of proteomes by pooling data across genes, by biochemical category, clade, or branch, provided evidence for increased rates of evolution in several gene categories, as well as external branches of the tree. Promoters were primarily evolving under purifying selection but with certain categories of genes evolving faster. Many of these fast-evolving categories were the same as those associated with rapid evolution in proteins. Overall, these results suggest that adaptation to changing environments and new hosts in the SD species group has involved the acquisition of key virulence genes along with selection of orthologous protein-coding loci and operon promoters.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Animals Bacterial Proteins/*genetics/metabolism Cattle Cattle Diseases/*microbiology Child *Evolution, Molecular Genome, Bacterial *Genomics Humans Molecular Sequence Data Phylogeny *Promoter Regions, Genetic Streptococcal Infections/*microbiology/*veterinary Streptococcus/chemistry/classification/*genetics/isolation & purification |
| Subjects: | organism description > bacteria bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes > comparative genomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes |
| CSHL Authors: | |
| Communities: | CSHL labs > Siepel lab |
| Depositing User: | Matt Covey |
| Date: | 2011 |
| Date Deposited: | 13 Jan 2015 15:18 |
| Last Modified: | 13 Jan 2015 15:18 |
| PMCID: | PMC3056289 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/31109 |
Actions (login required)
 |
Administrator's edit/view item |