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Prajapati MR, Manav A, Singhal P, Sidharthan VK, Sirohi U, Kumar M, Bharti MK, Singh J, Kumar P, Kumar R, Prakash S, Baranwal VK. Complete Genomic RNA Sequence of Tuberose Mild Mosaic Virus and Tuberose Mild Mottle Virus Acquired by High-Throughput Sequencing. Pathogens 2022; 11:pathogens11080861. [PMID: 36014982 PMCID: PMC9412269 DOI: 10.3390/pathogens11080861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/10/2022] Open
Abstract
Tuberose (Polianthes tuberosa) is an ornamental flowering crop of the Amaryllidaceae family. Tuberose mild mosaic virus (TuMMV) and tuberose mild mottle virus (TuMMoV), members of the genus Potyvirus, are ubiquitously distributed in most tuberose growing countries worldwide with low biological incidence. Here, we report the first coding-complete genomic RNA of TuMMV and TuMMoV obtained through high-throughput sequencing (HTS) and further, the presence of both the viruses were confirmed using virus-specific primers in RT-PCR assays. Excluding the poly (A) tail, the coding-complete genomic RNA of TuMMV and TuMMoV was 9485 and 9462 nucleotides (nts) in length, respectively, and contained a single large open reading frame (ORF). Polyprotein encoded by both the viral genomes contained nine putative cleavage sites. BLASTn analysis of TuMMV and TuMMoV genomes showed 72.40–76.80% and 67.95–77% nucleotide sequence similarities, respectively, with the existing potyviral sequences. Phylogenetic analysis based on genome sequences showed that TuMMV and TuMMoV clustered in a distinct clade to other potyviruses. Further studies are required to understand the mechanism of symptom development, distribution, genetic variability, and their possible threat to tuberose production in India.
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Affiliation(s)
- Malyaj R Prajapati
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Aakansha Manav
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Pankhuri Singhal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Venkidusamy K Sidharthan
- Division of Genetics and Tree Improvement, Institute of Forest Biodiversity (ICFRE), Hyderabad 500100, Telangana, India
| | - Ujjwal Sirohi
- College of Agriculture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Mukesh Kumar
- College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Mahesh Kumar Bharti
- College of Veterinary and Animal Science, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Jitender Singh
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Pankaj Kumar
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Ravindra Kumar
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Satya Prakash
- College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, Uttar Pradesh, India
| | - Virendra Kumar Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Prajapati MR, Manav A, Singh J, Kumar P, Kumar A, Kumar R, Prakash S, Baranwal VK. Identification and Characterization of a Garlic Virus E Genome in Garlic ( Allium sativum L.) Using High-Throughput Sequencing from India. PLANTS (BASEL, SWITZERLAND) 2022; 11:224. [PMID: 35050112 PMCID: PMC8780593 DOI: 10.3390/plants11020224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
Garlic (Allium sativum L.) plants exhibiting mosaics, deformation, and yellow stripes symptoms were identified in Meerut City, Uttar Pradesh, India. To investigate the viruses in the garlic samples, the method of high-throughput sequencing (HTS) was used. Complete genome of the garlic virus E (GarV-E) isolate (NCBI accession No. MW925710) was retrieved. The virus complete genome comprises 8450 nucleotides (nts), excluding the poly (A) tail at the 3' terminus, with 5' and 3' untranslated regions (UTRs) of 99 and 384 nts, respectively, and ORFs encoding replicase with a conserved motif for RNA-dependent RNA polymerase (RdRP), TGB1, TGB2, TGB3, serine-rich protein, coat protein, and nucleic acid binding protein (NABP). The sequence homology shared 83.49-90.40% and 87.48-92.87% with those of GarV-E isolates available in NCBI at the nucleotide and amino acid levels, respectively. Phylogenetic analysis showed a close relationship of this isolate from India (MW925710) with GarV-E isolate YH (AJ292230) from Zhejiang, China. The presence of GarV-E was also confirmed by RT-PCR. The present study is the first report of GarV-E in garlic cultivar Yamuna Safed-3 grown in northern India. However, further studies are needed to confirm its role in symptom development, nationwide distribution, genetic diversity, and potential yield loss to the garlic in India.
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Affiliation(s)
- Malyaj R. Prajapati
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, India; (M.R.P.); (A.M.); (P.K.); (A.K.); (R.K.)
| | - Aakansha Manav
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, India; (M.R.P.); (A.M.); (P.K.); (A.K.); (R.K.)
| | - Jitender Singh
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, India; (M.R.P.); (A.M.); (P.K.); (A.K.); (R.K.)
| | - Pankaj Kumar
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, India; (M.R.P.); (A.M.); (P.K.); (A.K.); (R.K.)
| | - Amit Kumar
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, India; (M.R.P.); (A.M.); (P.K.); (A.K.); (R.K.)
| | - Ravindra Kumar
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, India; (M.R.P.); (A.M.); (P.K.); (A.K.); (R.K.)
| | - Satya Prakash
- College of Horticulture, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250110, India;
| | - Virendra Kumar Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
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