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The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation

hal.structure.identifierAgriculture Victoria Research, La Trobe University, Australia
hal.structure.identifierAgriculture Victoria Research, Department of Energy, Environment and Climate Action, Agribio
dc.contributor.authorRODRIGUES JARDIM, Bianca
hal.structure.identifierPlant Health Australia [PHA]
dc.contributor.authorTRAN-NGUYEN, Lucy
hal.structure.identifierHorticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility
dc.contributor.authorGAMBLEY, Cherie
hal.structure.identifierDepartment of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University
dc.contributor.authorAL-SADI, Abdullah
hal.structure.identifierDepartment of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University
dc.contributor.authorAL-SUBHI, Ali
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorFOISSAC, Xavier
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorSALAR, Pascal
hal.structure.identifierThe Key Laboratory for Plant Pathology, Yunnan Agricultural University
dc.contributor.authorCAI, Hong
hal.structure.identifierInstitute of Biochemistry, National Chung Hsing University
dc.contributor.authorYANG, Jun-Yi
hal.structure.identifierNorthern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry,
dc.contributor.authorDAVIS, Richard
hal.structure.identifierNorthern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry,
dc.contributor.authorJONES, Lynne
hal.structure.identifierAgriculture Victoria Research, La Trobe University, Australia
hal.structure.identifierAgriculture Victoria Research, Department of Energy, Environment and Climate Action, Agribio
dc.contributor.authorRODONI, Brendan
hal.structure.identifierAgriculture Victoria Research, La Trobe University, Australia
hal.structure.identifierAgriculture Victoria Research, Department of Energy, Environment and Climate Action, Agribio
dc.contributor.authorCONSTABLE, Fiona
dc.date.accessioned2024-08-07T02:03:45Z
dc.date.available2024-08-07T02:03:45Z
dc.date.issued2023-07-24
dc.identifier.issn1466-5026
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/201160
dc.description.abstractEnWithin the 16SrII phytoplasma group, subgroups A–X have been classified based on restriction fragment length polymorphism of their 16S rRNA gene, and two species have been described, namely ‘ Candidatus Phytoplasma aurantifolia’ and ‘ Ca . Phytoplasma australasia’. Strains of 16SrII phytoplasmas are detected across a broad geographic range within Africa, Asia, Australia, Europe and North and South America. Historically, all members of the 16SrII group share ≥97.5 % nucleotide sequence identity of their 16S rRNA gene. In this study, we used whole genome sequences to identify the species boundaries within the 16SrII group. Whole genome analyses were done using 42 phytoplasma strains classified into seven 16SrII subgroups, five 16SrII taxa without official 16Sr subgroup classifications, and one 16SrXXV-A phytoplasma strain used as an outgroup taxon. Based on phylogenomic analyses as well as whole genome average nucleotide and average amino acid identity (ANI and AAI), eight distinct 16SrII taxa equivalent to species were identified, six of which are novel descriptions. Strains within the same species had ANI and AAI values of >97 %, and shared ≥80 % of their genomic segments based on the ANI analysis. Species also had distinct biological and/or ecological features. A 16SrII subgroup often represented a distinct species, e.g., the 16SrII-B subgroup members. Members classified within the 16SrII-A, 16SrII-D, and 16SrII-V subgroups as well as strains classified as sweet potato little leaf phytoplasmas fulfilled criteria to be included as members of a single species, but with subspecies-level relationships with each other. The 16SrXXV-A taxon was also described as a novel phytoplasma species and, based on criteria used for other bacterial families, provided evidence that it could be classified as a distinct genus from the 16SrII phytoplasmas. As more phytoplasma genome sequences become available, the classification system of these bacteria can be further refined at the genus, species, and subspecies taxonomic ranks.
dc.language.isoen
dc.publisherMicrobiology Society
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enAAI
dc.subject.enANI
dc.subject.engenus
dc.subject.enMollicutes
dc.subject.enpeanut witches’-broom group
dc.subject.enphylogenomics
dc.subject.enphytopathogen
dc.subject.enspecies
dc.subject.enspecies delimitation
dc.subject.ensubspecies
dc.title.enThe observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation
dc.typeArticle de revue
dc.identifier.doi10.1099/ijsem.0.005977
dc.subject.halSciences du Vivant [q-bio]/Microbiologie et Parasitologie
dc.subject.halSciences du Vivant [q-bio]/Biodiversité/Systématique, phylogénie et taxonomie
bordeaux.journalInternational Journal of Systematic and Evolutionary Microbiology
bordeaux.volume73
bordeaux.hal.laboratoriesBiologie du Fruit & Pathologie (BFP) - UMR 1332*
bordeaux.issue7
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionINRAE
bordeaux.peerReviewedoui
hal.identifierhal-04668368
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04668368v1
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