Coat protein gene-based identification and characterization of garlic virus B associated with garlic (Allium sativum L.) in northern India Manav Aakansha1, Prajapati Malyaj R1, Tiwari Ajay Kumar2, Singh Jitender1,*, Kumar Pankaj1, Baranwal V. K.3 1College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India 2UPCSR-Sugarcane Research and Seed Multiplication Center, Khiri, India 3Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India *Corresponding Author : jeets80@gmail.com
Online published on 2 February, 2024. Abstract During mid-January 2018, the garlic cultivar, Yamuna Safed-3 (G-282) with mild mosaic-like symptoms was observed in Horticulture Research Center, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, India. The presence of virus was revealed using high-throughput sequencing (HTS). A total of 32,135,377 reads were generated and contigs were generated using de novo assembly. The sequence mapping coverage of Allexiviruses: GarV-A (14%), GarV-B (5%), GarV-D (36%), GarV-E (18%) and GarV-X (27%) were obtained. BlastX analysis resulted in the identification of five contigs of Garlic virus B, ranging in length from 258 to 1405 nucleotides. The presence of GarV-B in the samples was confirmed with RT-PCR using primers specific to Allexivirus genus and complete coat protein gene. BlastN analysis of the sequences revealed that the complete coat protein gene sequence (MW925694) shared 85.17 percent to 93.61 percent nucleotide identities (nts) and at amino-acids (aa) level sequence shared 90.60 to 93.40 percent identity with other GarV-B sequences reported globally. In Phylogenetic analysis sequence clustered in the same clade with the other GarV-B sequences reported from Poland, China, India, Brazil and Australia. Such study may also play a significant role in developing GarV-B disease management strategies. Top Keywords Garlic virus B, High-throughput sequencing, RT-PCR, Northern India. Top |