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Volume 8, Issue 3

Meta-analysis of the species complex (RSSC) based on comparative evolutionary genomics and reverse ecology Open Access

Abstract

species complex (RSSC) strains are bacteria that colonize plant xylem tissue and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures and physiological traits. To increase our understanding of the evolution, diversity and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4940 genes on average, and a pangenome analysis found that there are 3262 genes in the core genome (~60 % of the mean RSSC genome) with 13 128 genes in the extensive flexible genome. A core genome phylogenetic tree and a whole-genome similarity matrix aligned with the previously named species (, , ) and phylotypes (I–IV). These analyses also highlighted a third unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. We also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene (). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved, cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced RSSC strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bacterial wilt , core genome , recombination , sequevar , species concepts and taxonomy
Funding
This study was supported by the:
  • Directorate for Biological Sciences (Award DBI-2018522)
    • Principle Award Recipient: LenwoodS. Heath
  • Directorate for Biological Sciences (Award DBI-2018522)
    • Principle Award Recipient: BorisA. Vinatzer
  • Animal and Plant Health Inspection Service (Award AP19PPQS&T00C083)
    • Principle Award Recipient: LenwoodS. Heath
  • Animal and Plant Health Inspection Service (Award AP19PPQS&T00C083)
    • Principle Award Recipient: CaitilynAllen
  • Animal and Plant Health Inspection Service (Award AP19PPQS&T00C083)
    • Principle Award Recipient: BorisA. Vinatzer
  • National Institute of Food and Agriculture (Award 2022-67013-36272)
    • Principle Award Recipient: TiffanyM Lowe-Power
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-03-17
2024-04-25
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Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology
M Gen 8, 000791 (2022); https://doi.org/10.1099/mgen.0.000791
/content/journal/mgen/10.1099/mgen.0.000791
/content/journal/mgen/10.1099/mgen.0.000791
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