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Evidence of novel genetic variants of Grapevine rupestris stem pitting-associated virus and intra-host diversity in Indian grapevine cultivars

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Abstract

Grapevine rupestris stem pitting-associated virus (GRSPaV) is a member of the genus Foveavirus in the family Betaflexiviridae exhibiting high genetic variability. In the present study, a total of eleven full length coat protein gene sequences of GRSPaV were characterized from wine grape cultivars grown in the state of Maharashtra (Nashik and Pune) and Imphal (Manipur). Their molecular diversity was compared with corresponding sequences reported from other grape-growing regions globally. In pairwise sequence comparisons, the coat protein (CP) sequences of Indian GRSPaV isolates exhibited the identity in the range of 81–98% at nucleotide level when compared to respective CP sequences of GRSPaV isolates reported across the globe. A maximum likelihood phylogenetic analysis based on CP with the global isolates revealed six major phylogenetic clusters and two putative new clusters. Nine Indian GRSPaV isolates clustered in previously recognized three major lineages (groups II, III, and IV), while two of the isolates GRSPaV-RG14 and -B2 shared the recently identified putative group VIII. Our study also revealed the intra-host diversity exhibiting the presence of genetically distinct variants in the single host and inconsistencies in the placements was observed in their CP-based phylogenetic tree. This study also analyzed the population genetic parameters of GRSPaV isolates that showed the CP sequences were more variable within the isolates of group III (GRSPaV-BS) cluster (π =0.054), while various other factors including Tajima values (D) for group VIII appeared to be deviating from the trend for other GRSPaV lineages.

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Fig. 1

Data availability

The datasets generated during and/or analyzed the current study are available in the GenBank repository (Accessions are the following: MW401834, MW401835, MW401836, MW401837, MW401838, MW401839, MW401840, MW401841 MW401842, MW401843, and MW401844).

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Funding

This work was supported by ICAR-Outreach program New Delhi (project code 02).

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Authors and Affiliations

  1. Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Richa Rai, P. Vignesh Kumar & Virendra Kumar Baranwal

  2. ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat, Imphal, 795004, India

    Susheel Kumar Sharma

Authors
  1. Richa Rai
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  2. Susheel Kumar Sharma
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  3. P. Vignesh Kumar
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  4. Virendra Kumar Baranwal
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Contributions

Dr. Virendra Kumar Baranwal supervised and conceptualized the whole research project, also along with Dr. Susheel Kumar Sharma edited the manuscript. Dr. Richa Rai conducted the experiments and has written the manuscript. Dr. P. Vignesh Kumar contributed in survey and sample collection.

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Correspondence to Virendra Kumar Baranwal.

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Rai, R., Sharma, S.K., Kumar, P.V. et al. Evidence of novel genetic variants of Grapevine rupestris stem pitting-associated virus and intra-host diversity in Indian grapevine cultivars. Trop. plant pathol. 46, 576–580 (2021). https://doi.org/10.1007/s40858-021-00450-4

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  • DOI: https://doi.org/10.1007/s40858-021-00450-4

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