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2016
M. Tayahi, Gharsallah, C., Khamassy, N., Fakhfakh, H., Djilani-Khouadja, F., Tayahi, M., Gharsallah, C., Khamassy, N., Fakhfakh, H., and Djilani-Khouadja, F., Biological, serological and molecular typing of potato virus Y (PVY) isolates from Tunisia, vol. 15, no. 4, p. -, 2016.
ACKNOWLEDGMENTSResearch supported in part by the Ministry of Higher Education and Scientific Research of Tunisia and the CORUS code “212” France-Tunisia grant. The authors thank Drs. Camille Kerlan and Laurent Glais for providing standard PVY isolates.REFERENCESÁvila AC, Melo PE, Leite LR, Inoue-Nagata AK, et al (2009). Ocorrência de vírus em batata em sete estados do Brasil. Hortic. Bras. 27: 490-497. http://dx.doi.org/10.1590/S0102-05362009000400015 Bandelt HJ, Forster P, Röhl A, et al (1999). Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16: 37-48. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026036 Beczner L, Horvath H, Romhanyi L, Forster H, et al (1984). Etiology of tuber ringspot disease in potato. Potato Res. 27: 339-351. http://dx.doi.org/10.1007/BF02357646 Berger PH, Adams MJ, Barnett OW, et al. (2005). Potyviridae. In: Eighth Report of the International Committee on Taxonomy of Viruses (Fauquet CM, Mayo MA, Maniloff J, Desselberger U and Ball LA, eds). Academic Press Elsevier, UK, 819-41. Blanco-Urgoiti B, Tribodet M, Leclere S, Ponz F, et al (1998). Characterization of potato potyvirus Y (PVY) isolates from seed potato batches. Situation of the NTN, Wilga and Z isolates. Eur. J. Plant Pathol. 104: 811-819. http://dx.doi.org/10.1023/A:1008698719645 Boukhris-Bouhachem S, Djilani-Khouadj F, Fakhfakh H, Glais L, et al (2010). Incidence and Characterization of Potato virus Y in Seed Potatoes in Tunisia. Potato Res. 53: 151-166. http://dx.doi.org/10.1007/s11540-010-9159-9 Chikh Ali M, Maoka T, Natsuaki T, Natsuaki KT, et al (2010). PVYNTN-NW, a novel recombinant strain of Potato virus Y predominating in potato fields in Syria. Plant Pathol. 59: 31-41. http://dx.doi.org/10.1111/j.1365-3059.2009.02174.x Clark MF, Adams AN, et al (1977). Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. J. Gen. Virol. 34: 475-483. http://dx.doi.org/10.1099/0022-1317-34-3-475 Dake Z, Chen J, Deng L, Mao Q, et al (2010). Evolutionary selection associated with the multi-function of overlapping genes in the hepatitis B virus infection. Gen. Evol. 10: 84-88. http://dx.doi.org/10.1016/j.meegid.2009.10.006 Djilani-Khouadja F, Glais L, Tribodet M, Kerlan C, et al (2010). Incidence of potato viruses and characterization of Potato virus Y variability in late season planted potato crops in Northern Tunisia. Eur. J. Pl. Pthol. 126: 479-488. http://dx.doi.org/10.1007/s10658-009-9554-8 Emberger L, et al (1966). Une classification biogéographique des climats. Recherches et Travaux des Laboratoires de Géologie, Botanique et Zoologie. Faculté des Sciences Montpellier 7: 1-43. FAOSTAT Database Results (2014). Agriculture Crops primary. Tunisia production area. Available at [http://apps.fao.org]. Fu YX, Li WH, et al (1993). Statistical tests of neutrality of mutations. Genetics 133: 693-709. García-Arenal F, Fraile A, Malpica JM, et al (2001). Variability and genetic structure of plant virus populations. Annu. Rev. Phytopathol. 39: 157-186. http://dx.doi.org/10.1146/annurev.phyto.39.1.157 Gibbs A, Ohshima K, et al (2010). Potyviruses and the digital revolution. Annu. Rev. Phytopathol. 48: 205-223. http://dx.doi.org/10.1146/annurev-phyto-073009-114404 Galvino-Costa S, Dos Reis Figueira A, Camargos V, Geraldino P, et al (2012). A novel type of Potato virus Y recombinant genome, determined for the genetic strain PVYE. J. Plant Pathol. 61: 388-398. http://dx.doi.org/10.1111/j.1365-3059.2011.02495.x Glais L, Tribodet M, Kerlan C, et al (2005). Specific detection of the PVY(N)-W variant of Potato virus Y. J. Virol. Methods 125: 131-136. http://dx.doi.org/10.1016/j.jviromet.2005.01.007 Goymer P, et al (2007). Synonymous mutations break their silence. Nat. Rev. Genet. 8: 92. Gray S, De Boer S, Lorenzen J, Karasev A, et al (2010). Potato virus Y: an evolving concern for potato crops in the United States and Canada. Plant Dis. 94: 1384-1397. http://dx.doi.org/10.1094/PDIS-02-10-0124 Holsinger KE, Tajima D, Fu FS, Wu H, et al. (2010). Available at [http://darwin.eeb.uconn.edu/eeb348/lecturenotes/mole vol-tajima]. Jukes TH and Cantor CR (1996). Evolution of protein molecules. In: Mammalian protein metabolism (Munro HN, eds.). Academic Press, New York, 21-123. Karasev AV, Hu X, Brown CJ, Kerlan C, et al (2011). Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains. Phytopathology 101: 778-785. http://dx.doi.org/10.1094/PHYTO-10-10-0284 Keese P, Mackenzie A, Gibbs A, et al (1989). Nucleotide sequence of the genome of an Australian isolate of turnip yellow mosaic tymovirus. Virology 172: 536-546. http://dx.doi.org/10.1016/0042-6822(89)90196-7 Kerlan C, Nikolaeva OV, Hu X, Meacham T, et al (2011). Identification of the molecular make-up of the Potato virus Y strain PVY(Z): genetic typing of PVY(Z)-NTN. Phytopathology 101: 1052-1060. http://dx.doi.org/10.1094/PHYTO-11-10-0317 Khamassy N (1999). Contribution à la mise au point d’un système de production de semences de pomme de terre adapté aux contraintes de la culture en Tunisie. Doctoral thesis, National Institute of agronomic Research of Tunis, Tunisia. Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, et al (2007). A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 315: 525-528. http://dx.doi.org/10.1126/science.1135308 Koenig R, Lennefors BL, et al (2000). Molecular analyses of European A, B and P type sources of Beet necrotic yellow vein virus and detection of the rare P type in Kazakhstan. Arch. Virol. 145: 1561-1570. http://dx.doi.org/10.1007/s007050070076 Lévy-Hartmann L, Roussel V, Letourneur Y, Sellos DY, et al (2011). Global and New Caledonian patterns of population genetic variation in the deep-sea splendid alfonsino, Beryx splendens, inferred from mtDNA. Genetica 139: 1349-1365. http://dx.doi.org/10.1007/s10709-012-9628-y Librado P, Rozas J, et al (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452. http://dx.doi.org/10.1093/bioinformatics/btp187 Lopez P, Casane D, Philippe H, et al (2002). Phylogénie et évolution moléculaires. J. Med. Sci. 18: 1146-1154. Mantel N, et al (1967). The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220. Miller MP (1997). Tools for population genetic analysis (TFPGA) 1.3: A Windows program for the analysis of allozyme and molecular population genetic data. Computer software distributed by authors. Mora MS, Lessa EP, Cutrera AP, Kittlein MJ, et al (2007). Phylogeographical structure in the subterranean tuco-tuco Ctenomys talarum (Rodentia: Ctenomyidae): contrasting the demographic consequences of regional and habitat-specific histories. Mol. Ecol. 16: 3453-3465. http://dx.doi.org/10.1111/j.1365-294X.2007.03398.x Nei M, Tajima F, et al (1983). Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics 105: 207-217. Nie X, Singh RP, et al (2002). Probable geographical grouping of PVY(N) and PVY(NTN) based on sequence variation in P1 and 5′-UTR of PVY genome and methods for differentiating North American PVY(NTN). J. Virol. Methods 103: 145-156. http://dx.doi.org/10.1016/S0166-0934(02)00023-X Nolasco G, de Blas C, Torres V, Ponz F, et al (1993). A method combining immunocapture and PCR amplification in a microtiter plate for the detection of plant viruses and subviral pathogens. J. Virol. Methods 45: 201-218. http://dx.doi.org/10.1016/0166-0934(93)90104-Y Ogawa T, Tomitaka Y, Nakagawa A, Ohshima K, et al (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. http://dx.doi.org/10.1016/j.virusres.2007.09.010 Rogers AR, Harpending H, et al (1992). Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9: 552-569. Saitou N, Nei M, et al (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. Schmidt D and Pool J (2002). The effect of population history on the distribution of the Tajima’s D statistic, 1-8. Available at [http://peaple.mbi.ohiostate.edu/dschmidt/TajimasD.pdf]. Singh RP, Valkonen JPT, Gray SM, Boonham N, et al (2008). Discussion paper: The naming of Potato virus Y strains infecting potato. Arch. Virol. 153: 1-13. http://dx.doi.org/10.1007/s00705-007-1059-1 Tajima F, et al (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595. Tamura K, Peterson D, Peterson N, Stecher G, et al (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739. http://dx.doi.org/10.1093/molbev/msr121 Van den Heuvel JFJM, Van der Vlugt RAA, Verbeek M, de Haan PT, et al (1994). Characteristics of a resistance-breaking isolate of potato virus Y causing potato tuber necrotic ringspot disease. Eur. J. Plant Pathol. 100: 347-356. http://dx.doi.org/10.1007/BF01876445    
M. Tayahi, Gharsallah, C., Khamassy, N., Fakhfakh, H., Djilani-Khouadja, F., Tayahi, M., Gharsallah, C., Khamassy, N., Fakhfakh, H., and Djilani-Khouadja, F., Biological, serological and molecular typing of potato virus Y (PVY) isolates from Tunisia, vol. 15, no. 4, p. -, 2016.
ACKNOWLEDGMENTSResearch supported in part by the Ministry of Higher Education and Scientific Research of Tunisia and the CORUS code “212” France-Tunisia grant. The authors thank Drs. Camille Kerlan and Laurent Glais for providing standard PVY isolates.REFERENCESÁvila AC, Melo PE, Leite LR, Inoue-Nagata AK, et al (2009). Ocorrência de vírus em batata em sete estados do Brasil. Hortic. Bras. 27: 490-497. http://dx.doi.org/10.1590/S0102-05362009000400015 Bandelt HJ, Forster P, Röhl A, et al (1999). Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16: 37-48. http://dx.doi.org/10.1093/oxfordjournals.molbev.a026036 Beczner L, Horvath H, Romhanyi L, Forster H, et al (1984). Etiology of tuber ringspot disease in potato. Potato Res. 27: 339-351. http://dx.doi.org/10.1007/BF02357646 Berger PH, Adams MJ, Barnett OW, et al. (2005). Potyviridae. In: Eighth Report of the International Committee on Taxonomy of Viruses (Fauquet CM, Mayo MA, Maniloff J, Desselberger U and Ball LA, eds). Academic Press Elsevier, UK, 819-41. Blanco-Urgoiti B, Tribodet M, Leclere S, Ponz F, et al (1998). Characterization of potato potyvirus Y (PVY) isolates from seed potato batches. Situation of the NTN, Wilga and Z isolates. Eur. J. Plant Pathol. 104: 811-819. http://dx.doi.org/10.1023/A:1008698719645 Boukhris-Bouhachem S, Djilani-Khouadj F, Fakhfakh H, Glais L, et al (2010). Incidence and Characterization of Potato virus Y in Seed Potatoes in Tunisia. Potato Res. 53: 151-166. http://dx.doi.org/10.1007/s11540-010-9159-9 Chikh Ali M, Maoka T, Natsuaki T, Natsuaki KT, et al (2010). PVYNTN-NW, a novel recombinant strain of Potato virus Y predominating in potato fields in Syria. Plant Pathol. 59: 31-41. http://dx.doi.org/10.1111/j.1365-3059.2009.02174.x Clark MF, Adams AN, et al (1977). Characteristics of the microplate method of enzyme-linked immunosorbent assay for the detection of plant viruses. J. Gen. Virol. 34: 475-483. http://dx.doi.org/10.1099/0022-1317-34-3-475 Dake Z, Chen J, Deng L, Mao Q, et al (2010). Evolutionary selection associated with the multi-function of overlapping genes in the hepatitis B virus infection. Gen. Evol. 10: 84-88. http://dx.doi.org/10.1016/j.meegid.2009.10.006 Djilani-Khouadja F, Glais L, Tribodet M, Kerlan C, et al (2010). Incidence of potato viruses and characterization of Potato virus Y variability in late season planted potato crops in Northern Tunisia. Eur. J. Pl. Pthol. 126: 479-488. http://dx.doi.org/10.1007/s10658-009-9554-8 Emberger L, et al (1966). Une classification biogéographique des climats. Recherches et Travaux des Laboratoires de Géologie, Botanique et Zoologie. Faculté des Sciences Montpellier 7: 1-43. FAOSTAT Database Results (2014). Agriculture Crops primary. Tunisia production area. Available at [http://apps.fao.org]. Fu YX, Li WH, et al (1993). Statistical tests of neutrality of mutations. Genetics 133: 693-709. García-Arenal F, Fraile A, Malpica JM, et al (2001). Variability and genetic structure of plant virus populations. Annu. Rev. Phytopathol. 39: 157-186. http://dx.doi.org/10.1146/annurev.phyto.39.1.157 Gibbs A, Ohshima K, et al (2010). Potyviruses and the digital revolution. Annu. Rev. Phytopathol. 48: 205-223. http://dx.doi.org/10.1146/annurev-phyto-073009-114404 Galvino-Costa S, Dos Reis Figueira A, Camargos V, Geraldino P, et al (2012). A novel type of Potato virus Y recombinant genome, determined for the genetic strain PVYE. J. Plant Pathol. 61: 388-398. http://dx.doi.org/10.1111/j.1365-3059.2011.02495.x Glais L, Tribodet M, Kerlan C, et al (2005). Specific detection of the PVY(N)-W variant of Potato virus Y. J. Virol. Methods 125: 131-136. http://dx.doi.org/10.1016/j.jviromet.2005.01.007 Goymer P, et al (2007). Synonymous mutations break their silence. Nat. Rev. Genet. 8: 92. Gray S, De Boer S, Lorenzen J, Karasev A, et al (2010). Potato virus Y: an evolving concern for potato crops in the United States and Canada. Plant Dis. 94: 1384-1397. http://dx.doi.org/10.1094/PDIS-02-10-0124 Holsinger KE, Tajima D, Fu FS, Wu H, et al. (2010). Available at [http://darwin.eeb.uconn.edu/eeb348/lecturenotes/mole vol-tajima]. Jukes TH and Cantor CR (1996). Evolution of protein molecules. In: Mammalian protein metabolism (Munro HN, eds.). Academic Press, New York, 21-123. Karasev AV, Hu X, Brown CJ, Kerlan C, et al (2011). Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains. Phytopathology 101: 778-785. http://dx.doi.org/10.1094/PHYTO-10-10-0284 Keese P, Mackenzie A, Gibbs A, et al (1989). Nucleotide sequence of the genome of an Australian isolate of turnip yellow mosaic tymovirus. Virology 172: 536-546. http://dx.doi.org/10.1016/0042-6822(89)90196-7 Kerlan C, Nikolaeva OV, Hu X, Meacham T, et al (2011). Identification of the molecular make-up of the Potato virus Y strain PVY(Z): genetic typing of PVY(Z)-NTN. Phytopathology 101: 1052-1060. http://dx.doi.org/10.1094/PHYTO-11-10-0317 Khamassy N (1999). Contribution à la mise au point d’un système de production de semences de pomme de terre adapté aux contraintes de la culture en Tunisie. Doctoral thesis, National Institute of agronomic Research of Tunis, Tunisia. Kimchi-Sarfaty C, Oh JM, Kim IW, Sauna ZE, et al (2007). A “silent” polymorphism in the MDR1 gene changes substrate specificity. Science 315: 525-528. http://dx.doi.org/10.1126/science.1135308 Koenig R, Lennefors BL, et al (2000). Molecular analyses of European A, B and P type sources of Beet necrotic yellow vein virus and detection of the rare P type in Kazakhstan. Arch. Virol. 145: 1561-1570. http://dx.doi.org/10.1007/s007050070076 Lévy-Hartmann L, Roussel V, Letourneur Y, Sellos DY, et al (2011). Global and New Caledonian patterns of population genetic variation in the deep-sea splendid alfonsino, Beryx splendens, inferred from mtDNA. Genetica 139: 1349-1365. http://dx.doi.org/10.1007/s10709-012-9628-y Librado P, Rozas J, et al (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452. http://dx.doi.org/10.1093/bioinformatics/btp187 Lopez P, Casane D, Philippe H, et al (2002). Phylogénie et évolution moléculaires. J. Med. Sci. 18: 1146-1154. Mantel N, et al (1967). The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220. Miller MP (1997). Tools for population genetic analysis (TFPGA) 1.3: A Windows program for the analysis of allozyme and molecular population genetic data. Computer software distributed by authors. Mora MS, Lessa EP, Cutrera AP, Kittlein MJ, et al (2007). Phylogeographical structure in the subterranean tuco-tuco Ctenomys talarum (Rodentia: Ctenomyidae): contrasting the demographic consequences of regional and habitat-specific histories. Mol. Ecol. 16: 3453-3465. http://dx.doi.org/10.1111/j.1365-294X.2007.03398.x Nei M, Tajima F, et al (1983). Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics 105: 207-217. Nie X, Singh RP, et al (2002). Probable geographical grouping of PVY(N) and PVY(NTN) based on sequence variation in P1 and 5′-UTR of PVY genome and methods for differentiating North American PVY(NTN). J. Virol. Methods 103: 145-156. http://dx.doi.org/10.1016/S0166-0934(02)00023-X Nolasco G, de Blas C, Torres V, Ponz F, et al (1993). A method combining immunocapture and PCR amplification in a microtiter plate for the detection of plant viruses and subviral pathogens. J. Virol. Methods 45: 201-218. http://dx.doi.org/10.1016/0166-0934(93)90104-Y Ogawa T, Tomitaka Y, Nakagawa A, Ohshima K, et al (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. http://dx.doi.org/10.1016/j.virusres.2007.09.010 Rogers AR, Harpending H, et al (1992). Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9: 552-569. Saitou N, Nei M, et al (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425. Schmidt D and Pool J (2002). The effect of population history on the distribution of the Tajima’s D statistic, 1-8. Available at [http://peaple.mbi.ohiostate.edu/dschmidt/TajimasD.pdf]. Singh RP, Valkonen JPT, Gray SM, Boonham N, et al (2008). Discussion paper: The naming of Potato virus Y strains infecting potato. Arch. Virol. 153: 1-13. http://dx.doi.org/10.1007/s00705-007-1059-1 Tajima F, et al (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595. Tamura K, Peterson D, Peterson N, Stecher G, et al (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739. http://dx.doi.org/10.1093/molbev/msr121 Van den Heuvel JFJM, Van der Vlugt RAA, Verbeek M, de Haan PT, et al (1994). Characteristics of a resistance-breaking isolate of potato virus Y causing potato tuber necrotic ringspot disease. Eur. J. Plant Pathol. 100: 347-356. http://dx.doi.org/10.1007/BF01876445