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Complete genomic characterization and evolutionary analysis of CMV isolate associated with Ocimum gratissimum

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Abstract

Cucumber mosaic virus (CMV) is among the most devastating plant viruses, which infects more than 1200 plant species and has shown its potential prevalence on medicinal and aromatic plants during the last few years. Genomic sequence of a virus can be used to analyze evolutionary history, mechanism of evolution, host-virus interactions and the development of sustainable management strategies. In this study, the complete genomic characterization of the isolate CMV SS1, isolated from Ocimum gratissimum (February 2017 from Lucknow India), was carried out by designing overlapping primers which were specific to each RNA segment. The genome of CMV consists of tripartite RNA, viz. RNA1, RNA2 and RNA3. The nucleotide sequences of RNA1 (MT877004), RNA2 (MT877005), RNA3 (MK239129) were compared with other known isolates of CMV (subgroup IA, IB and II) and found to be closely related with subgroup IB of CMV. The RNA1, 2, and 3 shared identities of 91–93%, 92–96%, 93–98% with the isolates of subgroup IB: 89–90%, 90% and 89–93% with the sub group IA while the identities were 76%, 73%, and 75–76% with CMV isolates of subgroup II. Multiple amino-acid sequence alignment showed maximum unique substitutions in 1a protein followed by MP, 2b and CP. CP was found to be the most conserved among all five proteins, suggesting its functional importance in the development of disease.

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Data Availability

The datasets generated during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

Authors are thankful to the Director, CSIR-CIMAP, Lucknow for providing necessary research facilities and DST-New Delhi for INSPIRE-SRF to Soumya Sinha

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Authors and Affiliations

  1. Plant Pathology Department, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015, India

    Soumya Sinha & Abdul Samad

  2. Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India

    Soumya Sinha & Abdul Samad

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  1. Soumya Sinha
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  2. Abdul Samad
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Correspondence to Abdul Samad.

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Sinha, S., Samad, A. Complete genomic characterization and evolutionary analysis of CMV isolate associated with Ocimum gratissimum. Eur J Plant Pathol 166, 1–7 (2023). https://doi.org/10.1007/s10658-023-02638-7

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  • DOI: https://doi.org/10.1007/s10658-023-02638-7

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