Sequence diversity studies of papaya ringspot virus isolates in South India reveal higher variability and recombination in the 5′-terminal gene sequences
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.
KeywordsVariability Recombination Papaya ringspot virus Potyvirus
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.
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.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- 2.Aleman-Verdaguer ME, Goudou-Urbino C, Dubern J, Beachy RN, Fauquet C. Analysis of the sequence diversity of the P1, HC, P3, NIb and CP genomic regions of several yam mosaic potyvirus isolates, implications for the intraspecies molecular diversity of potyviruses. J Gen Virol. 1997;78:1253–64.CrossRefPubMedGoogle Scholar
- 9.Hall TA. BioEdit, a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser. 1999;41:95–8.Google Scholar
- 23.Purcifull DE, Edwardson JR, Hiebert E, Gonsalves D. Papaya ringspot virus. In: CMI/AAB descriptions of plant viruses. Wellesbourne, UK: Association of Applied Biologists; 1984. p. 292.Google Scholar
- 24.Silva-Rosales L, Ruiz-Castro S, Teliz-Ortiz D, Noa-Carrazena JC. Coat protein sequence comparison of three Mexican isolates of papaya ringspot virus with other geographical isolates reveal a close relationship to American and Australian isolates. Arch Virol. 2000;145:835–43.CrossRefPubMedGoogle Scholar
- 29.Webb RE, Scott HA. Isolation and identification of Watermelon mosaic viruses 1 and 2. Phytopathology. 1965;55(8):895–900.Google Scholar