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

Utilization of 16Sr RNA and secA genes for molecular discernment of 'Candidatus Phytoplasma australasiaticum' strain associated with linseed germplasm in India

The growing prevalence of phytoplasma associated symptoms on linseed or flax (Linum usitatissimum L.) germplasm at Indian Council of Agricultural Research- National Bureau of Plant Genetic Resources (ICAR-NBPGR) fields was noticed during the 2019-22 growing seasons. The characteristic phytoplasma symptoms of phyllody, stem fasciation, stunting, along with floral and capsule malformations were observed in 41 linseed accessions grown at experimental fields of ICAR-NBPGR, Delhi. During 3 years, the presence of phytoplasma in symptomatic linseed accessions was confirmed by nested-PCR assays utilizing 16S rRNA and secA gene-specific primers. The 16S rRNA and secA gene sequences of linseed phytoplasma strains from the representative symptomatic 41 linseed accessions exhibited 100% sequence identity among themselves and 99.93% and 99.82% sequence homology with reference strain, 'Candidatus Phytoplasma australasiaticum' (GenBank Accession: Y10097). Phylogenetic analysis of 16S rRNA and secA gene sequences clustered the linseed isolates with the peanut witches' broom group belonging to 'Ca. P. australasiaticum' strains. The virtual RFLP analysis of 16S rRNA F2nR2 fragment (~1.2 kb) of linseed phytoplasma strains further classified it into 16Sr group II, subgroup D. Our results suggested confirmation of the association of 'Ca. P. australasiaticum' strain (16SrII-D) in the linseed germplasm accessions from North India, which is the first report from India. The phytoplasma infection also reduced the growth and yield parameters of two linseed accessions (IC0498748 and EC0718851).

'Candidatus Phytoplasma vignae', assigning a species description to a long-known phytoplasma occurring in northern Australia

Gene- and genome-based approaches were used to determine whether Vigna little leaf (ViLL) phytoplasma, which occurs in northern Australia, is a distinct 'Candidatus Phytoplasma' species. The ViLL 16S rRNA gene sequences exhibited the highest known similarity to species in the 16SrXXIX-A and 16SrIX-D subgroups, namely 'Candidatus Phytoplasma omanense' (98.03-98.10%) and 'Candidatus Phytoplasma phoenicium' (96.87-97.20%), respectively. A total of 48 single-copy orthologue genes were identified to be shared among the two draft ViLL phytoplasma genomes, 30 publicly available phytoplasma genomes, and one Acholeplasma laidlawii genome as the outgroup taxon. Phylogenomic assessments using the 48 shared single-copy orthologue genes supported that ViLL and 'Ca. Phytoplasma phoenicium' were closely related yet distinct species. The 16S rRNA gene sequence analysis and phylogenomic assessment indicate that ViLL phytoplasmas are a distinct taxon. As such, a novel species, 'Candidatus Phytoplasma vignae', is proposed. Strain BAWM-336 (genome accession number JAUZLI000000000) detected in Momordica charantia (bitter melon) serves as the reference strain of this species, with infected plant material deposited in the Victorian Plant Pathology Herbarium (VPRI) as VPRI 44369.

Phytoplasma-Associated Diseases in South America: Thirty Years of Research

Phytoplasma-associated diseases are mainly insect-transmitted and are present worldwide. Considering that disease detection is a relevant environmental factor that may elucidate the presence of these diseases, a review reporting the geographic distribution of phytoplasma taxa in geographically consistent areas helps manage diseases appropriately and reduce their spreading. This work summarizes the data available about the identification of the phytoplasma associated with several diverse diseases in South America in the last decades. The insect vectors and putative vectors together with the plant host range of these phytoplasmas are also summarized. Overall, 16 'Candidatus Phytoplasma' species were detected, and those most frequently detected in agricultural-relevant crops such as corn, alfalfa, grapevine, and other horticultural species are 'Ca. P. pruni', 'Ca. P. asteris', and 'Ca. P. fraxini'.

A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions

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.

Complete genome sequence of Candidatus Phytoplasma australasiaticum WF_GM2021, a plant pathogen associated with soybean witches' broom disease in Taiwan

The complete genome sequence of Candidatus Phytoplasma australasiaticum strain WF_GM2021, which consists of one 633,005-bp circular chromosome, is presented in this work. This uncultivated plant-pathogenic bacterium is associated with soybean (Glycine max) witches' broom disease in Wufeng District, Taichung City, Taiwan.