Cargando…

Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India

Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fie...

Descripción completa

Detalles Bibliográficos
Autores principales: Rashid, Shahjahan, Wani, Farhana, Ali, Gowhar, Sofi, Tariq A., Dar, Zahoor Ahmed, Hamid, Aflaq
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9532741/
https://www.ncbi.nlm.nih.gov/pubmed/36212886
http://dx.doi.org/10.3389/fmicb.2022.943382
_version_ 1784802184418820096
author Rashid, Shahjahan
Wani, Farhana
Ali, Gowhar
Sofi, Tariq A.
Dar, Zahoor Ahmed
Hamid, Aflaq
author_facet Rashid, Shahjahan
Wani, Farhana
Ali, Gowhar
Sofi, Tariq A.
Dar, Zahoor Ahmed
Hamid, Aflaq
author_sort Rashid, Shahjahan
collection PubMed
description Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses.
format Online
Article
Text
id pubmed-9532741
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-95327412022-10-06 Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India Rashid, Shahjahan Wani, Farhana Ali, Gowhar Sofi, Tariq A. Dar, Zahoor Ahmed Hamid, Aflaq Front Microbiol Microbiology Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses. Frontiers Media S.A. 2022-09-21 /pmc/articles/PMC9532741/ /pubmed/36212886 http://dx.doi.org/10.3389/fmicb.2022.943382 Text en Copyright © 2022 Rashid, Wani, Ali, Sofi, Dar and Hamid. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Rashid, Shahjahan
Wani, Farhana
Ali, Gowhar
Sofi, Tariq A.
Dar, Zahoor Ahmed
Hamid, Aflaq
Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India
title Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India
title_full Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India
title_fullStr Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India
title_full_unstemmed Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India
title_short Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India
title_sort viral metatranscriptomic approach to study the diversity of virus(es) associated with common bean (phaseolus vulgaris l.) in the north-western himalayan region of india
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9532741/
https://www.ncbi.nlm.nih.gov/pubmed/36212886
http://dx.doi.org/10.3389/fmicb.2022.943382
work_keys_str_mv AT rashidshahjahan viralmetatranscriptomicapproachtostudythediversityofvirusesassociatedwithcommonbeanphaseolusvulgarislinthenorthwesternhimalayanregionofindia
AT wanifarhana viralmetatranscriptomicapproachtostudythediversityofvirusesassociatedwithcommonbeanphaseolusvulgarislinthenorthwesternhimalayanregionofindia
AT aligowhar viralmetatranscriptomicapproachtostudythediversityofvirusesassociatedwithcommonbeanphaseolusvulgarislinthenorthwesternhimalayanregionofindia
AT sofitariqa viralmetatranscriptomicapproachtostudythediversityofvirusesassociatedwithcommonbeanphaseolusvulgarislinthenorthwesternhimalayanregionofindia
AT darzahoorahmed viralmetatranscriptomicapproachtostudythediversityofvirusesassociatedwithcommonbeanphaseolusvulgarislinthenorthwesternhimalayanregionofindia
AT hamidaflaq viralmetatranscriptomicapproachtostudythediversityofvirusesassociatedwithcommonbeanphaseolusvulgarislinthenorthwesternhimalayanregionofindia