Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species

Abstract

BackgroundStreptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group.ResultsDespite evidence of extensive recombination, the S. pneumoniae phylogenetic tree revealed six major lineages. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes - genes present in more than one strain but not in all strains - was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant evolutionary process of the core genome of S. pneumoniae. Genetic exchange occurred both within and across the borders of the species, and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with the number of strains and linearly with the number of polymorphic sites of the sampled genomes, suggesting that acquired genes accumulate proportionately to the age of clones. Most genes associated with pathogenicity were shared by all S. pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis, indicating that these genes are not sufficient to determine virulence.ConclusionsGenetic exchange with related species sharing the same ecological niche is the main mechanism of evolution of S. pneumoniae. The open pan-genome guarantees the species a quick and economical response to diverse environments.

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits

“…Owing to recent acquisition and deletion events 21 , the dispensable gene set was more variable than the core gene set. The frequency of SNPs in the core gene set was estimated to be 2.67 sites per Kbp, significantly less than 4.12/Kbp in the dispensable gene set (t-test, P < 0.01).…”

Viral/bacterial respiratory tract co-infections in children

“…Phylogenetic analyses of polymorphisms in the core genome of 44 S. pneumoniae strains have identified six major lineages of genetically related strains (249,250). These clusters generally correlated poorly with capsular serotype, geographic location and disease-or carriage-associated isolates (249,250 (254). STs can be further grouped into clonal complexes based on their similarity to a central allelic profile, with the assumption that they share a recent common ancestor.…”

“…Between strains, isolates share approximately 74% of their core genome, with homologous recombination the driving evolutionary process for diversity (250). Phylogenetic analyses of polymorphisms in the core genome of 44 S. pneumoniae strains have identified six major lineages of genetically related strains (249,250).…”

“…STs can be further grouped into clonal complexes based on their similarity to a central allelic profile, with the assumption that they share a recent common ancestor. Generally, phylogenies inferred from MLST data correlate well with phylogenies inferred from whole genome analysis (250,255). In this project, both MLST and molecular capsular serotyping were used to assess the diversity of a panel of S. pneumoniae strains isolated from children with ARI symptoms.…”

“…The species thus has a set of core genomic sequences shared by all strains, and a set of accessory genome sequences only present in a subset of isolates (together referred to as the pan-genome) (249)(250)(251). Between strains, isolates share approximately 74% of their core genome, with homologous recombination the driving evolutionary process for diversity (250).…”