Phytoplasmas have been found associated with 129 plant species in India including vegetables, legumes, spices, medicinal plants and ornamental plants, cash and oil crops, palms, fruit trees and weeds, where ten 16Sr groups of phytoplasmas have been identified so far. Sesame phyllody, brinjal little leaf, sugarcane grassy shoot, sandal spike, coconut root wilt, areca nut yellow leaf and many diseases in ornamental plants are causing the most severe economic losses in the country. Identified phytoplasmas are related to ‘Candidatus Phytoplasma asteris’, ‘Ca. P. pruni’, ‘Ca. P. ziziphi’, ‘Ca. P. trifolii’, ‘Ca. P. solani’, ‘Ca. P. cynodontis’, ‘Ca. P. oryzae’, ‘Ca. P. phoenicium’, ‘Ca. P. australasia’ and ‘Ca. P. pini’. Among them ‘Ca. P. asteris’-related strains (aster yellows, 16SrI group) are the prevalent phytoplasmas identified associated with 62 diseases followed by phytoplasmas classified in 16SrII, 16SrVI, 16SrXIV and 16SrXI groups. At least seven insect vectors, belonging to leafhoppers and planthoppers species, have been reported as putative or natural vectors for important phytoplasma diseases. The majority of phytoplasma disease reports are from north and south part of India. Little attempt has been made to genomics, epidemiology, host phytoplasma interaction and management aspects of these diseases. Presently the suggested effective management practices in India are growing resistant varieties, control of insect vectors, weed species as alternative hosts and use of healthy planting materials.

Phytoplasma taxonomy has been a topic of discussion for the last two and half decades. Since the Japanese scientists discovered the phytoplasma bodies in 1967, the phytoplasma taxonomy was limited to disease symptomology for a long time. The advances in DNA-based markers and sequencing improved phytoplasma classification. In 2004, the International Research Programme on Comparative Mycoplasmology (IRPCM)- Phytoplasma/Spiroplasma Working Team – Phytoplasma taxonomy group provided the description of the provisional genus ‘Candidatus Phytoplasma’ with guidelines to describe the new provisional phytoplasma species. The unintentional consequences of these guidelines led to the description of many phytoplasma species where species characterization was restricted to a partial sequence of the 16S rRNA gene alone. Additionally, the lack of a complete set of housekeeping gene sequences or genome sequences, as well as the heterogeneity among closely related phytoplasmas limited the development of a comprehensive Multi-Locus Sequence Typing (MLST) system. To address these issues, researchers tried deducing the definition of phytoplasma species using phytoplasmas genome sequences and the average nucleotide identity (ANI). In another attempts, a new phytoplasma species were described based on the Overall Genome relatedness Values (OGRI) values fetched from the genome sequences. These studies align with the attempts to standardize the classification and nomenclature of ‘Candidatus’ bacteria. With a brief historical account of phytoplasma taxonomy and recent developments, this review highlights the current issues and provides recommendations for a comprehensive system for phytoplasma taxonomy until phytoplasma retains ‘Candidatus’ status.

Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with ‘Ca. Phytoplasma cynodontis’ strain BGWL-C1 followed by 97.65 % similarity with ‘Ca. P. oryzae’ strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to ‘Ca. P. cynodontis’, were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon ‘Candidatus Phytoplasma sacchari’ is proposed.

We performed whole-genome sequencing of two phytoplasmas associated with sugarcane grassy shoot (SCGS) and Bermuda grass white leaf diseases. These are the first draft genomes of SCGS phytoplasma (strain SCGS) and ‘Candidatus Phytoplasma cynodontis’ (strain LW01) and may help to delineate these phytoplasmas at a finer taxonomic level.

Parthenium weed (Parthenium hysterophorus, Asteraceae) is a common, invasive weed found throughout the Indian subcontinent, Africa, America and Australia. The observed disease, Parthenium Witches’ Broom (PWB), characterised by phylloidy, stunting and prolific branching was observed during a field survey conducted between September 2014 to June 2015. PWB phytoplasma was detected in all symptomatic plant samples and in the previously reported insect vector, Orosius albicinctus belonging to family Cicadellidae (subfamily Deltocephalinae) and other Hemipteran insect samples by amplifying its 16S rRNA gene. To our knowledge, this is the first report of a ‘Ca. Phytoplasma aurantifolia’- related strains associated with witches’ broom disease of P. hysterophorus and insect vector Orosius albicinctus.

The disease symptoms characterised by little leaf, phyllody, stunting and branch proliferation were observed during a field survey conducted from June 2015 to January 2016 on common invasive weeds Cleome viscosa (tick weed), Trichodesma zeylanicum (cattle bush) and Tephrosia perpurea (wild indigo), which were found infected with peanut witches’ broom phytoplasmas (16SrII group) strains. Phylogenetically similar phytoplasma strains were also detected in symptomatic samples of Sesamum indicum (sesame), Vigna unguiculata (cow pea), Phaseolus vulgaris (French bean), Dendrocalamus strictus (bamboo) and Carica papaya (papaya) from the same or adjacent fields. This is the first report of 16SrII-D group phytoplasmas (‘Candidatus Phytoplasma aurantifolia’-related strains) associated with witches’ broom disease of C. viscosa, D. strictus and yellow stunting disease of C. papaya. The association of 16SrII-C group phytoplasmas with witches’ broom disease of T. zeylanicum and T. purpurea is also reported for the first time. From the obtained results, it can be inferred that the weed hosts harbors 16SrII group phytoplasma strains associated with little leaf and witches’ broom diseases of economically important grain legume crop species like S. indicum, V. unguiculata and P. vulgaris.