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Population Analysis of Iranian Potato virus Y Isolates Using Complete Genome Sequence
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  • Journal title : The Plant Pathology Journal
  • Volume 32, Issue 1,  2016, pp.33-46
  • Publisher : Korean Society of Plant Pathology
  • DOI : 10.5423/PPJ.OA.07.2015.0144
 Title & Authors
Population Analysis of Iranian Potato virus Y Isolates Using Complete Genome Sequence
Pourrahim, Reza; Farzadfar, Shirin;
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In this study, the full-length nucleotide sequences of four Iranian PVY isolates belonging to strain were determined. The genome of Iranian PVY isolates were 9,703-9,707 nucleotides long encoding all potyviral cistrons including P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP with coding regions of 825, 1,395, 1,095, 156, 1,902, 156, 564, 732, 1,557 and 801 nucleotides in length, respectively. The length of pipo, embedded in the P3 cistron, was 231 nucleotides. Phylogenetic analysis showed that the Iranian isolates clustered with European recombinant NTN isolates in the N lineage. Recombination analysis demonstrated that Iranian isolates had a typical European genome having three recombinant junctions while and were identified as the parents. We used dN/dS methods to detect candidate amino acid positions for positive selection in viral proteins. The mean ratio differed among different genes. Using model M0, values were 0.267 (P1), 0.085 (HC-Pro), 0.153 (P3), 0.050 (CI), 0.078 (VPg), 0.087 (NIa-pro), 0.079 (NIb) and 0.165 (CP). The analysis showed different sites within P1, P3 and CP were under positive selection pressure, however, the sites varied among PVY populations. To the best of our knowledge, our analysis provides the first demonstration of population structure of strain in mid-Eurasia Iran using complete genome sequences and highlights the importance of recombination and selection pressure in the evolution of PVY.
 Cited by
Adams, M. J., Antoniw, J. F. and Beaudoin, F. 2005. Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Mol. Plant. Pathol. 6:471-487. crossref(new window)

Atreya, P. L., Lopez-Moya, J. J., Chu, M., Atreya, C. D. and Pirone, T. P. 1995. Mutational analysis of the coat protein Nterminal amino acids involved in Potyvirus transmission by aphids. J. Gen. Virol. 76:265-270. crossref(new window)

Ayme, V., Petit-Pierre, J., Souche, S., Palloix, A. and Moury, B. 2007. Molecular dissection of the Potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper. J. Gen. Virol. 88:1594-1601. crossref(new window)

Blanc, S., Lopez-Moya, J. J., Wang, R., Garcia-Lampasona, S., Thornbury, D. W. and Pirone, T. P. 1997. A specific interaction between coat protein and helper component correlates with aphid transmission of a Potyvirus. Virology 231:141- 147. crossref(new window)

Broadbent, L., Burt, P. E. and Heathcote, G. D. 1956. The control of potato virus diseases by insecticides. Ann. Appl. Biol. 44: 256-273. crossref(new window)

Charron, C., Nicola, M., Gallois, J. L., Robaglia, C., Moury, B., Palloix, A. and Caranta, C. 2008. Natural variation and functional analyses provide evidence for coevolution between plant eIF4E and potyviral VPg. Plant J. 54:56-68. crossref(new window)

Choi, S. H., Hagiwara-Komoda, Y., Nakahara, K. S., Atsumi, G., Shimada, R., Hisa, Y., Naito, S. and Uyeda, I. 2013. Quantitative and qualitative involvement of P3N-PIPO in overcoming recessive resistance against Clover yellow vein virus in pea carrying the cyv1 gene. J. Virol. 87:7326-7337. crossref(new window)

Chrzanowska, M. 1991. New isolates of the necrotic strain of Potato virus Y (PVYN) found recently in Poland. Potato Res. 34: 79-182. crossref(new window)

Chung, B. Y.-W., Miller, W. A., Atkins, J. F. and Firth, A. E. 2008. An overlapping essential gene in the Potyviridae. Proc. Nation. Acad. Sci. USA 105:5897-5902. crossref(new window)

De Bokx, J. A. and Huttinga, H. 1981. Potato virus Y: description of plant viruses. Kew, England: Commonwealth Mycology Institute. /Association of Applied Biology.

Dolja, V. V., Haldeman, R., Robertson, N. L., Dougherty, W. G. and Carrington, J. C. 1994. Distinct functions of capsid protein in assembly and movement of tobacco etch potyvirus in plants. EMBO J. 13:1482-1491.

Dolja, V. V., Haldeman-Cahill, R., Montgomery, A. E., Vandenbosch, K. A. and Carrington, J. C. 1995. Capsid protein determinants involved in cell-to-cell and long distance movement of tobacco etch potyvirus. Virology 206:1007-1016. crossref(new window)

Edwardson, J. R. and Christie, R. G. 1997. Potyviruses. In: Florida Agricultural Experiment Station Monograph Series 18-II-Viruses infecting pepper and other solanaceous crops. Gainesville (FL): University of Florida. p. 424-524.

FAO. 2013. FAOSTAT Database results from FAO website. Food and Agriculture Organization of the United Nations.

Farzadfar, S., Pourrahim, R. and Ebrahimi, H. 2014. A phylogeographical study of the Cauliflower mosaic virus population in mid-Eurasia Iran using complete genome analysis. Arch. Virol. 159:1329-1340. crossref(new window)

Froissart, R., Roze, D., Uzest, M., Galibert, L. and Blanc, S. 2005. Recombination every day: abundant recombination in a virus during a single multi-cellular host infection. PLoS Biol. 3:389-395. crossref(new window)

Garcia-Arenal, F. and Palukaitis, F. 2008. Cucumber Mosaic Virus. In: Mahy B.W.J. and van Regenmortel M.H.V. Encyclopedia of VIROLOGY, THIRD EDITION. Academic Press is an imprint of Elsevier, p. 614-619.

Gibbs, M. J., Armstrong, J. S. and Gibbs, A. J. 2000. Sisterscanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16:573-582. crossref(new window)

Hall, T. A. 1999. BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nuc. Acids Sym. Seri. 41:95-98.

Hofius, D., Maier, A. T., Dietrich, C., Jungkunz, I., Bornke, F., Maiss, E. and Sonnewald, U. 2007. Capsid protein-mediated recruitment of host DnaJ-like proteins is required for Potato virus Y infection in tobacco plants. J. Virol. 81:11870-11880. crossref(new window)

Hosseini, A., Massumi, M., Heydarnejad, J., Hosseini Pour, A. and Varsani, A. 2011. Characterisation of Potato virus Y isolates from Iran. Virus Genes 42:128-140. crossref(new window)

Hu, X., Karasev, A. V., Brown, C. J. and Lorenzen, J. H. 2009. Sequence characteristics of Potato virus Y recombinants. J. Gen. Virol. 90:3033-3041. crossref(new window)

Karasev, A. V., Hu, X., Brown, C. J., Kerlan, C., Nikolaeva, O. V., Crosslin, J. M. and Gray, S. M. 2011. Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains. Phytopathology 101:778-785. crossref(new window)

Lorenzen, J. H., Meacham, T., Berger, P. H., Shiel, P. J., Crosslin, J. M., Hamm, P. B. and Kopp, H. 2006. Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada. Arch. Virol. 151:1055-1074. crossref(new window)

Martin, D. P., Lemey, P., Lott, M., Moulton, V. and Posada, D. 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462-2463. crossref(new window)

Moury, B. and Simon, V. 2011. dN/dS-based methods detect positive selection linked to trade-offs between different fitness traits in the coat protein of Potato virus Y. Mol. Biol. Evol. 28:2707-2717. crossref(new window)

Moury, B., Morel, C., Johansen, E. and Jacquemond, M. 2002. Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses. J. Gen. Virol. 83:2563- 2573. crossref(new window)

Moury, B., Morel, C., Johansen, E., Guilbaud, L., Souche, S., Ayme, V., Caranta, C., Palloix, A. and Jacquemond, M. 2004. Mutations in Potato virus Y genome-linked protein determine virulence toward recessive resistances in Capsicum annuum and Lycopersicon hirsutum. Mol. Plant-Microbe Interact. 17: 322-329. crossref(new window)

Ogawa, T., Tomitaka, Y., Nakagawa, A. and Ohshima, K. 2008. Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison with North American and European populations. Virus Res. 131:199-212. crossref(new window)

Pourrahim, R., Farzadfar, Sh., Golnaraghi, A. R. and Ahoonmanesh, A. 2007. Incidence and distribution of important viral pathogens in some Iranian potato fields. Plant Dis. 91:609-615. crossref(new window)

Pruss, G., Ge, X., Shi, X. M., Carrington, J. C. and Vance, V. B. 1997. Plant viral synergism: the potyviral genome encodes a broad-range pathogenicity enhancer that transactivates replication of heterologous viruses. Plant Cell 9:859-868. crossref(new window)

Ramirez-Rodriguez, V. R., Avina-Padilla, K., Frias-Trevino, G., Silva-Rosales, L. and Martinez-Soriano, P. 2006. Presence of necrotic strains of Potato virus Y in Mexican. Virol. J. 48:1- 7.

Rohozkoa, J. and Navratil, M. 2011. P1 peptidase a mysterious protein of family Potyviridae. J. Biosci. 36:189-200. crossref(new window)

Rojas, M. R., Zerbini, F. M., Allison, R. F., Gilbertson, R. L. and Lucas, W. J. 1997. Capsid protein and helper component-proteinase function as Potyvirus cell-to-cell movement proteins. Virology 237:283-295. crossref(new window)

Rozas, J., Sanchez-DeIBarrio, J. C., Messeguer, X. and Rozas, R. 2003. dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497. crossref(new window)

Shukla, D., Ward, C. W. and Brunt, A. A. 1994. The Potyviridae, CAB International, Wallingford.

Singh, R. P., Valkonen, J. P. T., Gray, S. M., Boonham, N., Jones, R. A. C., Kerlan, C. and Schubert, J. 2008. Discussion paper: The naming of Potato virus Y strains infecting potato. Arch. Virol. 153:1-13. crossref(new window)

Singh, R. P. 1992. Incidence of the tobacco veinal necrotic strain of Potato virus Y (PVYN) in Canada in 1990 and 1991 and scientific basis for eradication of the disease. Canadian Plant Dis. Sur. 72:113-119.

Tamura, K., Dudley, J., Nei, M. and Kumar, S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599. crossref(new window)

Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739. crossref(new window)

Thresh, J. M. 1976. Gradiants of plant virus diseases. Ann. Appl. Biol. 82:381-406. crossref(new window)

Tian, Y. P., Liu, J. L., Zhang, C. L., Liu, Y. Y., Wang, B., Li, X. D., Guo, Z. K. and Valkonen, J. P. T. 2011. Genetic diversity of Potato virus Y infecting tobacco crops in China. Phytopathology 101:377-387. crossref(new window)

Tomitaka, Y. and Ohshima, K. 2006. Phylogeographical study of the Turnip mosaic virus population in East Asia reveals an 'emergent' lineage in Japan. Mol. Ecol. 5:4437-4457.

Urcuqui-Inchima, S., Haenni, A. L. and Bernardi, F. 2001. Potyvirus proteins: a wealth of functions. Virus Res. 74:157-175. crossref(new window)

Valli, A., Lopez-Moya, J. J. and Garcia, J. A. 2007. Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J. Gen. Virol. 88: 1016-1028. crossref(new window)

Valli, A., Martin-Hernandez, A. M., Lopez-Moya, J. J. and Garcia, J. A. 2006. RNA silencing suppression by a second copy of the P1 serine protease of Cucumber vein yellowing ipomovirus (CVYV), a member of the family Potyviridae that lacks the cysteine protease HCPro. J. Virol. 80:10055-10063. crossref(new window)

Verchot, J. and Carrington, J. C. 1995. Evidence that the Potyvirus P1 proteinase functions in trans as an accessory factor for genome amplification. J. Virol. 69:3668-3674.

Vijayapalani, P., Maeshima, M., Nagasaki-Takekuchi, N. and Miller, W. A. 2012. Interaction of the trans-frame Potyvirus protein P3NPIPO with host protein PCaP1 facilitates Potyvirus movement. PLoS Path. 8:e1002639. crossref(new window)

Weiller, G. F. 1998. Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol. Biol. Evol. 15:326-335. crossref(new window)

Wen, R. H. and Hajimorad, M. R. 2010. Mutational analysis of the putative pipo of Soybean mosaic virus suggests disruption of PIPO protein impedes movement. Virology 400:107.

Wong, W. S. W., Yang, Z., Goldman, N. and Nielsen, R. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051. crossref(new window)

Yang, Z. 2007. PAML4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24:1586-1591. crossref(new window)

Yang, Z., Nielsen, R., Goldman, N. and Pedersen, A. K. 2000. Codon substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.

Yang, Z., Wong, W. S. W. and Nielsen, R. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22:1107-1118. crossref(new window)