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

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Rodrigues Jardim, B., Tran-Nguyen, L. T. T., Gambley, C., Al-Sadi, A. M., Al-Subhi, A. M., Foissac, X., Salar, P., Cai, H., Yang, J.-Y., Davis, R., Jones, L., Rodoni, B. and Constable, F. E. (2023) The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation. International Journal of Systematic and Evolutionary Microbiology, 73 (7). ISSN 1466-5034


Article Link: https://doi.org/10.1099/ijsem.0.005977

Publisher URL: https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005977


Within 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.

Item Type:Article
Corporate Creators:Department of Agriculture and Fisheries, Queensland
Business groups:Horticulture and Forestry Science
Keywords:AAI phylogenomics genus phytopathogen ANI peanut witches’-broom group Mollicutes subspecies species delimitation species
Subjects:Science > Microbiology
Science > Microbiology > Microbial ecology
Live Archive:15 Aug 2023 01:53
Last Modified:15 Aug 2023 01:53

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