Complete genome characterization and population dynamics of potato virus Y-NTN strain from India
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Potato virus Y (PVY) is a major threat to potato cultivation worldwide. PVY exists as biologically and genetically distinct strains and causes varying degrees of pathogenicity and a wide range of symptoms in potato. Knowledge of the nature of PVY strains is essential for breeding PVY resistant cultivars that are durable against a wide range of strains. We report the complete genome of a PVY potato isolate (JK12) characterised from the potato production areas of Jammu and Kashmir, India. Nucleotide sequence comparisons and phylogenetic analysis with known PVY strains revealed that the isolate belongs to the NTN strain of PVY. At the whole genome sequence level, the JK12 isolate shared the highest identity (99.42%) with PVY-NTN strains reported from Germany, followed by those from United Kingdom (99.34%) and Japan (99.33%). Recombination detection analysis identified two recombination break points and JK12 appeared to have originated from a recombination event between a PVY-N strain from Belgium as a major parent and a PVY-O strain from China as the minor parent. Our results suggest possible mutation and recombination could be the basis for the evolution and the subsequent establishment of NTN in this region. Furthermore, a global evolutionary lineage analysis of all the known PVY strains showed relatively low nucleotide diversity among the PVY-NTN strains. Neutrality tests showed that all the genotypes of PVY are undergoing purifying selection suggesting population expansion of PVY. This is the first report of complete genomic characterization of an NTN strain of PVY isolated from commercial potato fields in India. The implications of the emergence of this strain in the Indian context are discussed.
KeywordsPotato virus Y PVY-NTN strain Genome analysis Recombination Virus evolution
This work was supported by the Grant to AH by the University Grants Commission of India, No F. 5-4/2016(IC).
- 3.Carrington JC, Freed DD. Cap-independent enhancement of translation by a plant potyvirus 5′ nontranslated region. J Virol. 1990;64:1590–7.Google Scholar
- 6.Davie K, Holmes R, Pickup J, Lacomme C. Dynamics of PVY strains in field grown potato: impact of strain competition and ability to overcome host resistance mechanisms. Virus Res. 2017; 16:pii: S0168-1702(17)30119-3. https://doi.org/10.1016/j.virusres.2017.06.012.
- 10.Edwardson JR, Christie RG. Potyviruses. In: Florida agricultural experiment station monograph series 18-II—viruses infecting pepper and other solanaceous crops (University of Florida, ed.). 1997; 424–524. Gainesville, FL: University of Florida.Google Scholar
- 13.Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 1997;147(2):915–25.Google Scholar
- 14.Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics. 1993;133(3):693–709.Google Scholar
- 15.Funke CN, Nikolaeva OV, Green KJ, Tran LT, Chikh-Ali M, Quintero-Ferrer A, Cating RA, Frost KE, Hamm PB, Olsen N, Pavek MJ. Strain-specific resistance to Potato virus Y (PVY) in potato and its effect on the relative abundance of PVY strains in commercial potato fields. Plant Dis. 2017;101(1):20–8.CrossRefGoogle Scholar
- 27.Kerlan C. Potato virus Y. AAB/CMI descriptions of plant viruses. 2006; 414. http://www.dpvweb.net/dpv/showdpv.php?dpvno=414.
- 34.Maynard SJ. Analyzing the mosaic structure of genes. J Mol Evol. 1992;34:126–9.Google Scholar
- 37.Nagy PD. Recombination in plant RNA viruses. In book: plant virus evolution. 2008; 133–156. https://doi.org/10.1007/978-3-540-75763-4_8.
- 46.Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123(3):585–95.Google Scholar
- 48.Verchot J, Carrington JC. Evidence that the potyvirus P1 proteinase functions in trans as an accessory factor for genome amplification. J Virol. 1995;69:3668–74.Google Scholar
- 50.Yambao MLM, Yagihashi H, Sekiguchi H, Sekiguchi T, Sasaki T, Sato M, Atsumi G, Takahashi Y, Nakahara KS, Uyeda I. Point mutations in helper component protease of clover yellow vein virus are associated with the attenuation of RNA-silencing suppression activity and symptom expression in broad bean. Arch Virol. 2008;153:105–15.CrossRefGoogle Scholar