Genetic competence drives genome diversity in Bacillus subtilis

Patrícia H Brito, Bastien Chevreux, Cláudia R Serra, Ghislain Schyns, Adriano O Henriques, José B Pereira-Leal

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them.

Original languageEnglish
Pages (from-to)108-124
Number of pages17
JournalGenome Biology And Evolution
Volume10
Issue number1
Early online date20 Dec 2017
DOIs
Publication statusPublished - Jan 2018

Keywords

  • Bacillus subtilis
  • pangenome
  • comparative genomics
  • bacterial genome evolution
  • lateral gene transfer
  • genetic competence

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  • Cite this

    Brito, P. H., Chevreux, B., Serra, C. R., Schyns, G., Henriques, A. O., & Pereira-Leal, J. B. (2018). Genetic competence drives genome diversity in Bacillus subtilis. Genome Biology And Evolution, 10(1), 108-124. https://doi.org/10.1093/gbe/evx270