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Sequence analysis of coat protein and molecular profiling of sunflower necrosis virus (SNV) strains from Indian subcontinent

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Abstract

Sunflower is one of the leading edible oilseed crops of the world and is an important oil-producing crop of India. The sunflower necrosis disease caused by sunflower necrosis virus (SNV) has become a major hurdle for cultivation of sunflower in India. However, there is lack of genetic information and  standard methods for detection and identification of the SNV. To address this issue, we have developed an application using coat protein (CP) to perform molecular profiling of SNV strains. The nucleic acid and amino acid sequence analysis of CP of SNV strains collected from different regions of Maharashtra and Karnataka showed high percent homology (96.89–98.87%). However, 3D structural analysis generated eleven distinct groups of SNV strains.  Comparative bioinformatic analyses of nucleic acid and amino acid sequences with different genera of positive stranded (+) ssRNA viruses established their phylogentic relationship with ~25 (+) ssRNA viruses viz., Ilarvirus, Bromovirus, Cucumovirus, Alfamovirus, Comovirus, Nepovirus, Sequivirus, Potyvirus and Closterovirus. Additionally, the phylogenetic analysis revealed three distinct clusters, wherein major cluster I comprised SNV strains and Tobacco streak virus together showing 99% sequence homology and established closer phylogenetic relationship among all member viruses.

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Abbreviations

SND:

Sunflower necrosis disease

RT-PCR:

Reverse transcriptase–polymerase chain reaction

CP:

Coat protein

SNV:

Sunflower necrosis virus

TSV:

Tobacco streak virus

MP:

Movement protein

ssRNA:

Single-stranded RNA

3D:

Three-dimensional

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Acknowledgement

Authors gratefully acknowledge research funding from Department of Biotechnology, Govt of India (Grant# BT/PR/3900/GBD/27/386/2012) to RLC. Partial funding from SERB (DST), Govt of India (Grant# YSS/2015/000616) to USK is also acknowledged gratefully.

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Authors and Affiliations

  1. Department of Plant Biotechnology, VD College of Agricultural Biotechnology, Nanded Road, Latur, 413512, Maharashtra, India

    R. L. Chavhan, M. K. Verma, V. R. Hinge, U. S. Kadam & S. B. Kokane

  2. Science and Engineering Research Board (DST), Government of India, New Delhi, 110070, India

    U. S. Kadam

  3. Plant Protection Section, Crop Science Division, Indian Council of Agricultural Research, Krishi Bhawan, Dr Rajendra Prasad Road, New Delhi, 110001, India

    Pranjib K. Chakrabarty

Authors
  1. R. L. Chavhan
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  2. M. K. Verma
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  3. V. R. Hinge
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  4. U. S. Kadam
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  5. S. B. Kokane
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  6. Pranjib K. Chakrabarty
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Correspondence to Pranjib K. Chakrabarty.

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Chavhan, R.L., Verma, M.K., Hinge, V.R. et al. Sequence analysis of coat protein and molecular profiling of sunflower necrosis virus (SNV) strains from Indian subcontinent. J. Plant Biochem. Biotechnol. 27, 28–35 (2018). https://doi.org/10.1007/s13562-017-0412-z

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