Genomic delineation and description of species and within-species lineages in the genus Pantoea

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dc.contributor.authorCrosby, Katherine C.en
dc.contributor.authorRojas, Mariahen
dc.contributor.authorSharma, Parulen
dc.contributor.authorJohnson, Marcela A.en
dc.contributor.authorMazloom, Rezaen
dc.contributor.authorKvitko, Brian H.en
dc.contributor.authorSmits, Theo HM M.en
dc.contributor.authorVenter, Stephanus N.en
dc.contributor.authorCoutinho, Teresa A.en
dc.contributor.authorHeath, Lenwood S.en
dc.contributor.authorPalmer, Marikeen
dc.contributor.authorVinatzer, Boris A.en
dc.date.accessioned2024-01-22T18:41:41Zen
dc.date.available2024-01-22T18:41:41Zen
dc.date.issued2023-11-09en
dc.description.abstractAs the name of the genus <i>Pantoea</i> (“of all sorts and sources”) suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.en
dc.description.versionPublished versionen
dc.format.extent23 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifierARTN 1254999 (Article number)en
dc.identifier.doihttps://doi.org/10.3389/fmicb.2023.1254999en
dc.identifier.eissn1664-302Xen
dc.identifier.issn1664-302Xen
dc.identifier.orcidVinatzer, Boris [0000-0003-4612-225X]en
dc.identifier.orcidHeath, Lenwood [0000-0003-1608-431X]en
dc.identifier.otherPMC10665919en
dc.identifier.pmid38029109en
dc.identifier.urihttps://hdl.handle.net/10919/117568en
dc.identifier.volume14en
dc.language.isoenen
dc.publisherFrontiersen
dc.relation.urihttps://www.ncbi.nlm.nih.gov/pubmed/38029109en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectPantoeaen
dc.subjecttaxonomyen
dc.subjectgenomicsen
dc.subjectreverse ecologyen
dc.subjectcore genomeen
dc.subjectpangenome analysisen
dc.titleGenomic delineation and description of species and within-species lineages in the genus <i>Pantoea</i>en
dc.title.serialFrontiers in Microbiologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2023-10-10en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Engineeringen
pubs.organisational-group/Virginia Tech/Engineering/Computer Scienceen
pubs.organisational-group/Virginia Tech/Faculty of Health Sciencesen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Engineering/COE T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/School of Plant and Environmental Sciencesen

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