RT Journal Article
SR Electronic
T1 Heterogeneity among estimates of the core genome and pan-genome in different pneumococcal populations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 133991
DO 10.1101/133991
A1 Andries J van Tonder
A1 James E Bray
A1 Keith A Jolley
A1 Sigríður J Quirk
A1 Gunnsteinn Haraldsson
A1 Martin CJ Maiden
A1 Stephen D Bentley
A1 Ásgeir Haraldsson
A1 Helga Erlendsdóttir
A1 Karl G Kristinsson
A1 Angela B Brueggemann
YR 2017
UL http://biorxiv.org/content/early/2017/05/06/133991.abstract
AB Background Understanding the structure of a bacterial population is essential in order to understand bacterial evolution, or which genetic lineages cause disease, or the consequences of perturbations to the bacterial population. Estimating the core genome, the genes common to all or nearly all strains of a species, is an essential component of such analyses. The size and composition of the core genome varies by dataset, but our hypothesis was that variation between different collections of the same bacterial species should be minimal. To test this, the genome sequences of 3,121 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (USA) and Maela (Thailand) were analysed.Results The analyses revealed a ‘supercore’ genome (genes shared by all 3,121 pneumococci) of only 303 genes, although 461 additional core genes were shared by pneumococci from Reykjavik, Southampton and Boston. Overall, the size and composition of the core genomes and pan-genomes among pneumococci recovered in Reykjavik, Southampton and Boston were very similar, but pneumococci from Maela were distinctly different. Inspection of the pan-genome of Maela pneumococci revealed several >25 Kb sequence regions that were homologous to genomic regions found in other bacterial species.Conclusions Some subsets of the global pneumococcal population are highly heterogeneous and thus our hypothesis was rejected. This is an essential point of consideration before generalising the findings from a single dataset to the wider pneumococcal population.