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

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dc.contributor.authorSharma, Parulen
dc.contributor.authorJohnson, Marcela A.en
dc.contributor.authorMazloom, Rezaen
dc.contributor.authorAllen, Caitilynen
dc.contributor.authorHeath, Lenwood S.en
dc.contributor.authorLowe-Power, Tiffany M.en
dc.contributor.authorVinatzer, Boris A.en
dc.date.accessioned2022-07-20T12:33:35Zen
dc.date.available2022-07-20T12:33:35Zen
dc.date.issued2022-03en
dc.description.abstractRalstonia solanacearum 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 (similar to 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 (R. solanacearum, R. pseudosolanacearum, R. syzygii) 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 (egl). 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.en
dc.description.notesFunding to Boris A. Vinatzer, Caitilyn Allen and Lenwood S. Heath was provided by USDA APHIS (contract AP19PPQS and T00C083). Funding to Boris A. Vinatzer and Lenwood S. Heath was also provided by NSF (DBI-2018522). Funding to Boris A. Vinatzer was also provided in part by the Virginia Agricultural Experiment Station and the Hatch Program of USDA NIFA. Caitilyn Allen was funded by U. Wisconsin-Madison College of Agricultural and Life Sciences. Tiffany M. Lowe-Power was funded by USDA NIFA (grant no. 2022-67013-36272) and UC Davis College of Agricultural and Environmental Sciences and Department of Plant Pathology (laboratory start-up funds).en
dc.description.sponsorshipUSDA APHIS [AP19PPQS, T00C083]; NSF [DBI-2018522]; Virginia Agricultural Experiment Station; USDA NIFA; U. Wisconsin-Madison College of Agricultural and Life Sciences; USDA NIFA [2022-67013-36272]; UC Davis College of Agricultural and Environmental Sciences and Department of Plant Pathologyen
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1099/mgen.0.000791en
dc.identifier.issn2057-5858en
dc.identifier.issue3en
dc.identifier.other791en
dc.identifier.pmid35297758en
dc.identifier.urihttp://hdl.handle.net/10919/111304en
dc.identifier.volume8en
dc.language.isoenen
dc.publisherMicrobiology Societyen
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectbacterial wilten
dc.subjectcore genomeen
dc.subjectsequevaren
dc.subjectspecies conceptsen
dc.subjecttaxonomyen
dc.subjectrecombinationen
dc.titleMeta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecologyen
dc.title.serialMicrobial Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten

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