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Genome sequencing of cucumber mosaic virus (CMV) isolates infecting chilli and its interaction with host ferredoxin protein of different host for causing mosaic symptoms

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Abstract

Chilli (Capsicum annuum L.) is an important vegetable crop grown in the Indian sub-continent and is prone to viral infections under field conditions. During the field survey, leaf samples from chilli plants showing typical symptoms of disease caused by cucumber mosaic virus (CMV) such as mild mosaic, mottling and leaf distortion were collected. DAC-ELISA analysis confirmed the presence of CMV in 71 out of 100 samples, indicating its widespread prevalence in the region. Five CMV isolates, named Gu1, Gu2, BA, Ho, and Sal were mechanically inoculated onto cucumber and Nicotiana glutinosa plants to study their virulence. Inoculated plants expressed the characteristic symptoms of CMV such as chlorotic spots followed by mild mosaic and leaf distortion. Complete genomes of the five CMV isolates were amplified, cloned, and sequenced, revealing RNA1, RNA2, and RNA3 sequences with 3358, 3045, and 2220 nucleotides, respectively. Phylogenetic analysis classified the isolates as belonging to the CMV-IB subgroup, distinguishing them from subgroup IA and II CMV isolates. Recombination analysis showed intra and interspecific recombination in all the three RNA segments of these isolates. In silico protein–protein docking approach was used to decipher the mechanism behind the production of mosaic symptoms during the CMV-host interaction in 13 host plants. Analysis revealed that the production of mosaic symptoms could be due to the interaction between the coat protein (CP) of CMV and chloroplast ferredoxin proteins. Further, in silico prediction was validated in 13 host plants of CMV by mechanical sap inoculation. Twelve host plants produced systemic symptoms viz., chlorotic spot, chlorotic ringspot, chlorotic local lesion, mosaic and mild mosaic and one host plant, Solanum lycopersicum produced mosaic followed by shoestring symptoms.

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Data availability

The nucleotide accession IDs (GenBank IDs) of all the five isolates under study are available publicly in NCBI with following accession IDs: RNA1: Gu1 (MN340987), Gu2 (MN340993), BA (MN340990), Sal (MN340998), Ho (MN340996) RNA2: Gu1 (MN340988), Gu2 (MN340994), BA (MN340991), Sal (MN3410000), Ho (MN340997) RNA3: Gu1 (MN340989), Gu2 (MN340995), BA (MN340992), Sal (MN3410001), Ho (MN340998)

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Acknowledgements

This work was carried out with financial support from Department of Science Technology-Science and Engineering Research Board (DST-SERB, Grant no. YSS/2015/001449), Government of India through funding the project entitled “Understanding molecular mechanisms of Capsicum annuum L. and cucumber mosaic virus interaction through transcriptomics” University of Agricultural Sciences, GKVK, Bangalore.

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Authors and Affiliations

  1. Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bangalore, Karnataka, 560065, India

    H. D. Vinaykumar, Shridhar Hiremath, M. Nandan, Mantesh Muttappagol, C. R. Jahir Basha & C. N. Lakshminarayana Reddy

  2. Division of Vegetable Science, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka, 560089, India

    Madhavi Reddy

  3. Division of Plant Protection, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka, 560089, India

    V. Venkataravanappa & M. Krishna Reddy

  4. Department of Plant Pathology, College of Horticulture, University of Horticultural Sciences, Bagalkot, Bengaluru, Karnataka, 560065, India

    K. S. Shankarappa

  5. Centre for Functional Genomics and Bioinformatics, The University of Trans-Disciplinary Health Sciences and Technology, 74/2, Jarakabande Kaval, Post Attur via Yelahanka, Bengaluru, 560064, India

    S. Koti Prasanna

  6. Department of Agricultural Statistics, Applied Mathematics and Computer Science, College of Agriculture, University of Agricultural Sciences, GKVK, Bangalore, Karnataka, 560065, India

    T. L. Mohan Kumar

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Contributions

HDV carried out the overall work, SH, MN, MM helped in conducting the experiments. SH, VV, JCR, PSK and KSS helped in bioinformatics analysis, MR provided the materials for conducting an experiment. CNLR and MKR conceptualized the work, provided the overall guidance and funding.

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Correspondence to M. Krishna Reddy or C. N. Lakshminarayana Reddy.

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Vinaykumar, H.D., Hiremath, S., Nandan, M. et al. Genome sequencing of cucumber mosaic virus (CMV) isolates infecting chilli and its interaction with host ferredoxin protein of different host for causing mosaic symptoms. 3 Biotech 13, 361 (2023). https://doi.org/10.1007/s13205-023-03777-8

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