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A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions

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Rodrigues Jardim, B., Gambley, C., Tran-Nguyen, L. T. T., Webster, C., Kehoe, M., Kinoti, W. M., Bond, S., Davis, R., Jones, L., Pathania, N., Sharman, M., Chapman, T., Rodoni, B. C. and Constable, F. E. (2024) A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions. Microbial Genomics, 10 (3). ISSN 2057-5858


Article Link: https://doi.org/10.1099/mgen.0.001213

Publisher URL: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001213


In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group (‘Ca. Phytoplasma stylosanthis’; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and ‘Ca. Phytoplasma stylosanthis’. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of ‘Ca. Phytoplasma australasiaticum’ and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics.

Item Type:Article
Corporate Creators:Department of Agriculture and Fisheries, Queensland
Business groups:Horticulture and Forestry Science, Crop and Food Science
Keywords:metagenomic assembled genomes (MAGs) Candidatus Phytoplasma stylosanthis Candidatus Phytoplasma australasiaticum draft genomes ANI unclassified phytoplasmas
Subjects:Science > Botany > Genetics
Science > Microbiology > Microbial ecology
Plant culture > Vegetables
Plant pests and diseases > Plant pathology
Agriculture > By region or country > Australia
Live Archive:12 Mar 2024 01:43
Last Modified:12 Mar 2024 01:43

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