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Sequence diversity studies of papaya ringspot virus isolates in South India reveal higher variability and recombination in the 5′-terminal gene sequences

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Abstract

Papaya ringspot virus (PRSV) is one of the most devastating viruses which causes huge damage to papaya plantations across the globe. PRSV is a positive sense RNA virus encoding for a polyprotein that is processed into ten proteins. In this study for the first time we analyzed the variability for 15 PRSV isolates from a selected geographical region of a South Indian state Karnataka, which is under intensive papaya cultivation. Variability studies were done for two genes at the 5′ end of the viral genome, namely P1 and helper component proteinase (Hc-Pro) and towards the 3′ end, a 788 nt overlapping region of nuclear inclusion B (NIb, 692 nt) and of capsid protein (CP, 96 nt), referred as NIb-CP. Our studies indicate that the P1 is most variable region with a wider range of sequence identity, followed by Hc-Pro, while the 788 nt of NIb-CP was most conserved. P1 also showed maximum recombination events followed by Hc-Pro, whereas NIb-CP did not show any recombination. Further, the pattern and number of phylogenetic clusters was variable for each of the three genomic regions of PRSV isolates. Estimation of selection pressure for all the three PRSV genomic regions indicated negative and purifying selection.

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Acknowledgements

We acknowledge the financial support from ICAR’s Network Project on Transgenics in Crops (NPTC) and ICAR-NRCPB. RM acknowledges the post-doctoral fellowship from DST-SERB.

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Authors and Affiliations

  1. ICAR-National Research Centre on Plant Biotechnology, IARI Campus, Pusa, New Delhi, 110012, India

    Ritesh Mishra & Basavaprabhu L. Patil

  2. University of Agricultural Sciences, Raichur, Karnataka, India

    Sharana Patil & Ayyanagouda Patil

  3. ICAR-Indian Institute of Horticultural Research, Bengaluru, 560089, India

    Basavaprabhu L. Patil

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  1. Ritesh Mishra
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  2. Sharana Patil
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  3. Ayyanagouda Patil
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  4. Basavaprabhu L. Patil
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Contributions

BLP designed and monitored all the experiments, SP and AP collected the leaf samples, RM and SP cloned the PRSV fragments, RM helped in sequence analyses and BLP interpreted the results and wrote the manuscript. All the authors read and approved the final manuscript.

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Correspondence to Basavaprabhu L. Patil.

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Electronic supplementary material

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13337_2019_512_MOESM1_ESM.jpg

Symptoms of the entire 15 Papaya ringspot virus (PRSV) affected papaya leaf samples from Karnataka state (India) used in this study. Details of the abbreviations used for each of the PRSV isolates are given in Supplementary Table 2. (JPEG 305 kb)

13337_2019_512_MOESM2_ESM.jpg

Map of Karnataka state (India) showing eleven locations from where the Papaya ringspot virus (PRSV) infected papaya leaf samples were collected and the locations of other PRSV isolates used for sequence analysis are also depicted on the map of India. (JPEG 119 kb)

13337_2019_512_MOESM3_ESM.jpg

Genome organization of Papaya ringspot virus (PRSV) depicting the relative positions of the genomic regions that were cloned and their sequences analysed in this study. (JPEG 30 kb)

13337_2019_512_MOESM4_ESM.jpg

The amino acids of the conserved motifs of (A) P1, (B) Hc-Pro and (C) NIb-CP sequences of all the 15 Papaya ringspot virus (PRSV) isolates from Karnataka are highlighted with yellow colour. Details of the abbreviations used for each of the PRSV isolates are given in Supplementary Table 2. (JPEG 293 kb)

Supplementary material 5 (DOCX 39 kb)

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Mishra, R., Patil, S., Patil, A. et al. Sequence diversity studies of papaya ringspot virus isolates in South India reveal higher variability and recombination in the 5′-terminal gene sequences. VirusDis. 30, 261–268 (2019). https://doi.org/10.1007/s13337-019-00512-x

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  • DOI: https://doi.org/10.1007/s13337-019-00512-x

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