Draft Genome Sequences of Two Phytoplasma Strains Associated with Sugarcane Grassy Shoot (SCGS) and Bermuda Grass White Leaf (BGWL) Diseases

Kirdat, Kiran; Tiwarekar, Bhavesh; Thorat, Vipool; Narawade, Nitin; Dhotre, Dhiraj; Sathe, Shivaji; Shouche, Yogesh S.; Yadav, Amit

doi:10.1094/mpmi-01-20-0005-a

Cited by 22 publications

(12 citation statements)

References 15 publications

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“…The first complete genome of phytoplasma (onion yellows phytoplasma mild strain (OY-M) was published in 2004 [ 6 ] (data deposited into GenBank in 2003). So far, 47 phytoplasma genomes (35 draft and 12 complete) have been sequenced involving 13 groups and 29 subgroups ( Figure 2 and Table 1 , [ 6 , 7 , 14 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 , 67 , 68 , 69 , 70 , 71 , 72 , 73 , 74 , 75 , 76 , 77 , 78 , 79 , 80 , 81 ]). The size of the complete ge-nomes ranges from 576 to 960 Kb.…”

Section: Phytoplasma Nomenclature: Delineation Of Candidatu...mentioning

confidence: 99%

Phytoplasma Taxonomy: Nomenclature, Classification, and Identification

Wei

Zhao

2022

Biology

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Phytoplasmas are pleomorphic, wall-less intracellular bacteria that can cause devastating diseases in a wide variety of plant species. Rapid diagnosis and precise identification of phytoplasmas responsible for emerging plant diseases are crucial to preventing further spread of the diseases and reducing economic losses. Phytoplasma taxonomy (identification, nomenclature, and classification) has lagged in comparison to culturable bacteria, largely due to lack of axenic phytoplasma culture and consequent inaccessibility of phenotypic characteristics. However, the rapid expansion of molecular techniques and the advent of high throughput genome sequencing have tremendously enhanced the nucleotide sequence-based phytoplasma taxonomy. In this article, the key events and milestones that shaped the current phytoplasma taxonomy are highlighted. In addition, the distinctions and relatedness of two parallel systems of ‘Candidatus phytoplasma’ species/nomenclature system and group/subgroup classification system are clarified. Both systems are indispensable as they serve different purposes. Furthermore, some hot button issues in phytoplasma nomenclature are also discussed, especially those pertinent to the implementation of newly revised guidelines for ‘Candidatus Phytoplasma’ species description. To conclude, the challenges and future perspectives of phytoplasma taxonomy are briefly outlined.

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Section: Phytoplasma Nomenclature: Delineation Of Candidatu...mentioning

confidence: 99%

Phytoplasma Taxonomy: Nomenclature, Classification, and Identification

Wei

Zhao

2022

Biology

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“…Simultaneously, the enriched nucleic acids of SCGS and LW01 were sequenced on the ONT platform. The draft genome sequence of both the phytoplasma strains was obtained as described earlier [51]. The final SCGS assembly contained 29 scaffolds corresponding to 505 173 bp including a putative plasmid of 2976 bp.…”

Section: Full-textmentioning

confidence: 99%

'Candidatus Phytoplasma sacchari’, a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease

Kirdat

Tiwarekar

Thorat

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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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.

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“…All of these weed species except C. sparsiflora have been reported earlier as hosts of different phytoplasma groups (Rao et al 2017). C. bonplandianum has been reported as host of 16SrII and 16SrVI-D subgroup of phytoplasmas in India (Kirdat et al 2020), and we reported another species, C. sparsiflora as Fig. 8 Phylogenetic tree of secY gene sequences constructed by neighbor-joining method and Kimura's three-parameter model, showing the relationships among chickpea phytoplasma isolates, weed isolates and alternate host with reference phytoplasma strains.…”

Section: Discussionmentioning

confidence: 93%

Molecular characterization of chickpea chlorotic dwarf virus and peanut witches’ broom phytoplasma associated with chickpea stunt disease and identification of new host crops and leafhopper vectors in India

2021

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An investigation was carried out to identify and characterize the phytoplasma and viruses associated with the chickpea varieties showing severe stunting, leaf reddening, yellowing and phyllody symptoms during the summer season of 2018–2019 and 2019–2020 in eight states of India. The average disease incidence was recorded from 3 to 32% in different states. The presence of chickpea chlorotic dwarf virus (CpCDV) was confirmed in thirty-seven chickpea samples by amplification of CpCDV coat protein gene and sequence comparison analysis. No record of association of luteovirus, polerovirus and cucumovirus could be detected in any of the symptomatic chickpea samples by RT-PCR assay. Brassica nigra, B. juncea, Lens culinaris, two weeds (Heteropogan contartus, Aeschynomene virginica) and one leafhopper (Amarasca biguttula) were identified as new putative hosts for CpCDV. Association of peanut witches’ broom phytoplasma was confirmed in twenty-eight chickpea samples, Sesamum indicum, five weeds hosts and two leafhopper species (Exitianus indicus, Empoasca motti) using nested PCR assays with primer pairs P1/P7 and R16F2n/R16Rn. The results of phytoplasma association in plants and leafhopper samples were further validated by using five multilocus genes (secA, rp, imp, tuf and secY) specific primers. Sequence comparison, phylogenetic and virtual RFLP analysis of 16S rRNA gene and five multilocus genes confirmed the identity of association of 16SrII-C and 16SrII-D subgroups of phytoplasmas strain with chickpea samples collected from Andhra Pradesh (AP), Telangana, Karnataka, Madhya Pradesh, Uttar Pradesh and New Delhi. Mixed infection of phytoplasma (16SrII-D) and CpCDV was also detected in symptomatic chickpea samples from AP and Telangana. The reports of association of 16SrII-C subgroup phytoplasma in chickpea and 16SrII-D subgroup phytoplasma in C. sparsiflora and C. roseus are the new host records in world and from India, respectively.

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Draft Genome Sequences of Two Phytoplasma Strains Associated with Sugarcane Grassy Shoot (SCGS) and Bermuda Grass White Leaf (BGWL) Diseases

Cited by 22 publications

References 15 publications

Phytoplasma Taxonomy: Nomenclature, Classification, and Identification

Phytoplasma Taxonomy: Nomenclature, Classification, and Identification

'Candidatus Phytoplasma sacchari’, a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease

Molecular characterization of chickpea chlorotic dwarf virus and peanut witches’ broom phytoplasma associated with chickpea stunt disease and identification of new host crops and leafhopper vectors in India

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