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Kirdat K, Tiwarekar B, Thorat V, Sathe S, Shouche Y, Yadav A. 'Candidatus Phytoplasma sacchari', a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease. Int J Syst Evol Microbiol 2020; 71. [PMID: 33289626 DOI: 10.1099/ijsem.0.004591] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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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Affiliation(s)
- Kiran Kirdat
- Department of Microbiology, Tuljaram Chaturchand College, Baramati 413 102, Maharashtra, India
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Bhavesh Tiwarekar
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Vipool Thorat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati 413 102, Maharashtra, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
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Nithya K, Parameswari B, Viswanathan R. Mixed Infection of Sugarcane Yellow Leaf Virus and Grassy Shoot Phytoplasma in Yellow Leaf Affected Indian Sugarcane Cultivars. THE PLANT PATHOLOGY JOURNAL 2020; 36:364-377. [PMID: 32788895 PMCID: PMC7403522 DOI: 10.5423/ppj.oa.06.2020.0092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 02/08/2023]
Abstract
Sugarcane is an important sugar crop contributes more than 80% of world sugar production. Mosaic, leaf fleck, and yellow leaf (YL) are the major viral diseases affecting sugarcane, amongst YL occurrence is widely reported in all the sugarcane growing countries. It is caused by Sugarcane yellow leaf virus (SCYLV) and detailed works were done on complete genome characterization, transmission, and management. However, in countries like Egypt, South Africa, Cuba, Mauritius and Hawaii, the disease was reported to the cause of sugarcane yellow leaf phytoplasma (SCYP) and/or SCYLV as single/combined infections. Hence, we have investigated in detail to identify the exact Candidatus phytoplasma taxon associated in Indian cultivars affected with YL. The sequencing results and the restriction fragment length polymorphism pattern of the PCR products using the universal phytoplasma primers confirmed presence of sugarcane grassy shoot (SCGS) phytoplasma (16SrXI group) in the YL-affected plants. Mixed infection of SCYLV and SCGS phytoplasma was estimated as 32.8% in YL affected plants. Evolutionary genetic relationship between SCYP and SCGS phytoplasma representatively taken from different countries showed that SCYP from South Africa and Cuba were diverged from others and had a highest similarity with SCGS phytoplasma. Although we wanted to identify SCYP from YL affected Indian sugarcane cultivars, the study clearly indicated a clear absence of SCYP in YL affected plants and we found SCYLV as the primary cause for the disease.
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Affiliation(s)
- Kadirvel Nithya
- ICAR-Sugarcane Breeding Institute, Coimbatore 641 007, Tamil Nadu, India
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Kirdat K, Tiwarekar B, Thorat V, Narawade N, Dhotre D, Sathe S, Shouche Y, Yadav A. Draft Genome Sequences of Two Phytoplasma Strains Associated with Sugarcane Grassy Shoot (SCGS) and Bermuda Grass White Leaf (BGWL) Diseases. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:715-717. [PMID: 32040378 DOI: 10.1094/mpmi-01-20-0005-a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
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.
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Affiliation(s)
- Kiran Kirdat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, Maharashtra 413102, India
| | - Bhavesh Tiwarekar
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Vipool Thorat
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Nitin Narawade
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Dhiraj Dhotre
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, Maharashtra 413102, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Amit Yadav
- National Centre for Microbial Resource, National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
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Yadav A, Thorat V, Deokule S, Shouche Y, Prasad DT. New subgroup 16SrXI-F phytoplasma strain associated with sugarcane grassy shoot (SCGS) disease in India. Int J Syst Evol Microbiol 2017; 67:374-378. [DOI: 10.1099/ijsem.0.001635] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Amit Yadav
- Microbial Culture Collection, National Centre for Cell Science, Pashan, Pune 411 021, India
| | - Vipool Thorat
- Microbial Culture Collection, National Centre for Cell Science, Pashan, Pune 411 021, India
| | - Subhash Deokule
- Department of Botany, University of Pune, Ganeshkhind, Pune 411 007, India
| | - Yogesh Shouche
- Microbial Culture Collection, National Centre for Cell Science, Pashan, Pune 411 021, India
| | - D. Theertha Prasad
- Department of Biotechnology, University of Agriculture Sciences, Gandhi Krishi Vigyan Kendra, Bangalore 560 065, India
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Abeysinghe S, Abeysinghe PD, Kanatiwela-de Silva C, Udagama P, Warawichanee K, Aljafar N, Kawicha P, Dickinson M. Refinement of the Taxonomic Structure of 16SrXI and 16SrXIV Phytoplasmas of Gramineous Plants using Multilocus Sequence Typing. PLANT DISEASE 2016; 100:2001-2010. [PMID: 30683016 DOI: 10.1094/pdis-02-16-0244-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytoplasmas that infect gramineous plants, including Napier grass stunt, sugarcane whiteleaf, sugarcane grassy shoot, and Bermuda grass whiteleaf, have been classified into two closely related groups, 16SrXI and 16SrXIV, based on the 16S ribosomal RNA (rRNA) gene. Subsequently, phytoplasmas associated with coconut and Areca palm in southern India and Sri Lanka have been added into the 16SrXI group. However, the 16S rRNA gene gives relatively poor resolution between these phytoplasmas. In this study, a new set of universal phytoplasma primers that amplify approximately 1 kb of the leucyl transfer RNA synthetase (leuS) gene have been validated on a broad range of phytoplasma taxonomic groups. These have been used along with partial sequences of the secA gene to clarify the taxonomic classification of 16SrXI and 16SrXIV phytoplasmas. Based on this data, the sugarcane whiteleaf and grassy shoot phytoplasmas appear to be the same phytoplasma. The Napier grass stunt phytoplasma forms a distinct group from the Bermuda grass whiteleaf and sugarcane phytoplasmas, suggesting that Napier grass stunt should be in its own 'Candidatus Phytoplasma sp.'. The phytoplasmas associated with coconut and arecanut in southern India and Sri Lanka, which are in the same 16SrXI group, appear in different groups based on secA analysis.
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Affiliation(s)
- Saman Abeysinghe
- Department of Botany, Faculty of Science, University of Ruhuna, Matara, Sri Lanka
| | | | | | - Preethi Udagama
- Department of Zoology, Faculty of Science, University of Colombo, Colombo 03, Sri Lanka
| | - Kanjana Warawichanee
- Plant Virology Section, Department of Agriculture, Chatuchak, Bangkok, 10900, Thailand
| | - Naofel Aljafar
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, LE12 5RD, UK
| | - Praphat Kawicha
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, LE12 5RD, UK
| | - Matt Dickinson
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, LE12 5RD, UK
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Molecular Diagnostics and Application of DNA Markers in the Management of Major Diseases of Sugarcane. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Genetic Diversity of Sugarcane Grassy Shoot (SCGS)-Phytoplasmas Causing Grassy Shoot Disease in India. SUGAR TECH 2011. [DOI: 10.1007/s12355-011-0084-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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