Worobey, M., & Holmes, E. C. (1999). Evolutionary aspects of recombination in RNA viruses. Journal of General Virology, 80(10), 2535-2543. doi:10.1099/0022-1317-80-10-2535
Elena, S. F., Bedhomme, S., Carrasco, P., Cuevas, J. M., de la Iglesia, F., Lafforgue, G., … Zwart, M. P. (2011). The Evolutionary Genetics of Emerging Plant RNA Viruses. Molecular Plant-Microbe Interactions, 24(3), 287-293. doi:10.1094/mpmi-09-10-0214
Jones, R. A. C. (2009). Plant virus emergence and evolution: Origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control. Virus Research, 141(2), 113-130. doi:10.1016/j.virusres.2008.07.028
[+]
Worobey, M., & Holmes, E. C. (1999). Evolutionary aspects of recombination in RNA viruses. Journal of General Virology, 80(10), 2535-2543. doi:10.1099/0022-1317-80-10-2535
Elena, S. F., Bedhomme, S., Carrasco, P., Cuevas, J. M., de la Iglesia, F., Lafforgue, G., … Zwart, M. P. (2011). The Evolutionary Genetics of Emerging Plant RNA Viruses. Molecular Plant-Microbe Interactions, 24(3), 287-293. doi:10.1094/mpmi-09-10-0214
Jones, R. A. C. (2009). Plant virus emergence and evolution: Origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control. Virus Research, 141(2), 113-130. doi:10.1016/j.virusres.2008.07.028
Urcuqui-Inchima, S., Haenni, A.-L., & Bernardi, F. (2001). Potyvirus proteins: a wealth of functions. Virus Research, 74(1-2), 157-175. doi:10.1016/s0168-1702(01)00220-9
Chung, B. Y.-W., Miller, W. A., Atkins, J. F., & Firth, A. E. (2008). An overlapping essential gene in the Potyviridae. Proceedings of the National Academy of Sciences, 105(15), 5897-5902. doi:10.1073/pnas.0800468105
Hall, J. S., Adams, B., Parsons, T. J., French, R., Lane, L. C., & Jensen, S. G. (1998). Molecular Cloning, Sequencing, and Phylogenetic Relationships of a New Potyvirus: Sugarcane Streak Mosaic Virus, and a Reevaluation of the Classification of the Potyviridae. Molecular Phylogenetics and Evolution, 10(3), 323-332. doi:10.1006/mpev.1998.0535
Moury, B., Johansen, E., Jacquemond, M., & Morel, C. (2002). Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses. Journal of General Virology, 83(10), 2563-2573. doi:10.1099/0022-1317-83-10-2563
Singh, R. P., Valkonen, J. P. T., Gray, S. M., Boonham, N., Jones, R. A. C., Kerlan, C., & Schubert, J. (2007). Discussion paper: The naming of Potato virus Y strains infecting potato. Archives of Virology, 153(1), 1-13. doi:10.1007/s00705-007-1059-1
Glais, L., Tribodet, M., & Kerlan, C. (2002). Genomic variability in Potato potyvirus Y (PVY): evidence that PVY N W and PVY NTN variants are single to multiple recombinants between PVY O and PVY N isolates. Archives of Virology, 147(2), 363-378. doi:10.1007/s705-002-8325-0
Schubert, J., Fomitcheva, V., & Sztangret-Wiśniewska, J. (2007). Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers. Journal of Virological Methods, 140(1-2), 66-74. doi:10.1016/j.jviromet.2006.10.017
Chare, E. R., & Holmes, E. C. (2005). A phylogenetic survey of recombination frequency in plant RNA viruses. Archives of Virology, 151(5), 933-946. doi:10.1007/s00705-005-0675-x
Ogawa, T., Tomitaka, Y., Nakagawa, A., & 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 Research, 131(2), 199-212. doi:10.1016/j.virusres.2007.09.010
Martin, D. P., Lemey, P., Lott, M., Moulton, V., Posada, D., & Lefeuvre, P. (2010). RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics, 26(19), 2462-2463. doi:10.1093/bioinformatics/btq467
Hu, X., He, C., Xiao, Y., Xiong, X., & Nie, X. (2009). Molecular characterization and detection of recombinant isolates of potato virus Y from China. Archives of Virology, 154(8), 1303-1312. doi:10.1007/s00705-009-0448-z
Chikh Ali, M., Maoka, T., Natsuaki, T., & Natsuaki, K. T. (2010). PVYNTN-NW, a novel recombinant strain ofPotato virus Ypredominating in potato fields in Syria. Plant Pathology, 59(1), 31-41. doi:10.1111/j.1365-3059.2009.02174.x
Dullemans, A. M., Cuperus, C., Verbeek, M., & van der Vlugt, R. A. A. (2010). Complete nucleotide sequence of a potato isolate of strain group C of Potato virus Y from 1938. Archives of Virology, 156(3), 473-477. doi:10.1007/s00705-010-0853-3
Fanigliulo, A., Comes, S., Pacella, R., Harrach, B., Martin, D. P., & Crescenzi, A. (2004). Characterisation of Potato virus Y nnp strain inducing veinal necrosis in pepper: a naturally occurring recombinant strain of PVY. Archives of Virology, 150(4), 709-720. doi:10.1007/s00705-004-0449-x
Fellers, J. P., Tremblay, D., Handest, M. F., & Lommel, S. A. (2002). The Potato virus Y MSNR NIb-replicase is the elicitor of a veinal necrosis-hypersensitive response in root knot nematode resistant tobacco. Molecular Plant Pathology, 3(3), 145-152. doi:10.1046/j.1364-3703.2002.00106.x
Pagán, I., del Carmen Córdoba-Sellés, M., Martínez-Priego, L., Fraile, A., Malpica, J. M., Jordá, C., & García-Arenal, F. (2006). Genetic Structure of the Population of Pepino mosaic virus Infecting Tomato Crops in Spain. Phytopathology, 96(3), 274-279. doi:10.1094/phyto-96-0274
TOMITAKA, Y., & OHSHIMA, K. (2006). A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an ‘emergent’ lineage in Japan. Molecular Ecology, 15(14), 4437-4457. doi:10.1111/j.1365-294x.2006.03094.x
Parker, J., Rambaut, A., & Pybus, O. G. (2008). Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty. Infection, Genetics and Evolution, 8(3), 239-246. doi:10.1016/j.meegid.2007.08.001
Delatte, H., Holota, H., Moury, B., Reynaud, B., Lett, J.-M., & Peterschmitt, M. (2007). Evidence for a Founder Effect After Introduction of Tomato Yellow Leaf Curl Virus–Mild in an Insular Environment. Journal of Molecular Evolution, 65(1), 112-118. doi:10.1007/s00239-007-0005-x
Kosakovsky Pond, S. L., Frost, S. D. W., Grossman, Z., Gravenor, M. B., Richman, D. D., & Brown, A. J. L. (2006). Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses. PLoS Computational Biology, 2(6), e62. doi:10.1371/journal.pcbi.0020062
Kosakovsky Pond, S. L., & Frost, S. D. W. (2005). Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection. Molecular Biology and Evolution, 22(5), 1208-1222. doi:10.1093/molbev/msi105
García-Arenal, F., Fraile, A., & Malpica, J. M. (2001). VARIABILITY ANDGENETICSTRUCTURE OFPLANTVIRUSPOPULATIONS. Annual Review of Phytopathology, 39(1), 157-186. doi:10.1146/annurev.phyto.39.1.157
Fares, M. A., & Travers, S. A. A. (2006). A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses. Genetics, 173(1), 9-23. doi:10.1534/genetics.105.053249
Torres-Puente, M., Cuevas, J. M., Jiménez-Hernández, N., Bracho, M. A., García-Robles, I., Wrobel, B., … González-Candelas, F. (2008). Using evolutionary tools to refine the new hypervariable region 3 within the envelope 2 protein of hepatitis C virus. Infection, Genetics and Evolution, 8(1), 74-82. doi:10.1016/j.meegid.2007.10.005
Lin, L., Luo, Z., Yan, F., Lu, Y., Zheng, H., & Chen, J. (2011). Interaction between potyvirus P3 and ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) of host plants. Virus Genes, 43(1), 90-92. doi:10.1007/s11262-011-0596-6
Wei, T., Zhang, C., Hong, J., Xiong, R., Kasschau, K. D., Zhou, X., … Wang, A. (2010). Formation of Complexes at Plasmodesmata for Potyvirus Intercellular Movement Is Mediated by the Viral Protein P3N-PIPO. PLoS Pathogens, 6(6), e1000962. doi:10.1371/journal.ppat.1000962
Wen, R.-H., & Hajimorad, M. R. (2010). Mutational analysis of the putative pipo of soybean mosaic virus suggests disruption of PIPO protein impedes movement. Virology, 400(1), 1-7. doi:10.1016/j.virol.2010.01.022
Feki, S., Loukili, M. J., Triki-Marrakchi, R., Karimova, G., Old, I., Ounouna, H., … Elgaaied, A. B. A. (2005). Interaction between tobacco Ribulose-l,5-biphosphate Carboxylase/Oxygenase large subunit (RubisCO-LSU) and the PVY Coat Protein (PVY-CP). European Journal of Plant Pathology, 112(3), 221-234. doi:10.1007/s10658-004-6807-4
Jin, Y., Ma, D., Dong, J., Li, D., Deng, C., Jin, J., & Wang, T. (2007). The HC-Pro Protein ofPotato Virus YInteracts with NtMinD of Tobacco. Molecular Plant-Microbe Interactions, 20(12), 1505-1511. doi:10.1094/mpmi-20-12-1505
Jiménez, I., López, L., Alamillo, J. M., Valli, A., & García, J. A. (2006). Identification of a Plum pox virus CI-Interacting Protein from Chloroplast That Has a Negative Effect in Virus Infection. Molecular Plant-Microbe Interactions, 19(3), 350-358. doi:10.1094/mpmi-19-0350
SHI, Y., CHEN, J., HONG, X., CHEN, J., & ADAMS, M. J. (2007). A potyvirus P1 protein interacts with the Rieske Fe/S protein of its host. Molecular Plant Pathology, 8(6), 785-790. doi:10.1111/j.1364-3703.2007.00426.x
Verchot, J., Herndon, K. L., & Carrington, J. C. (1992). Mutational analysis of the tobacco etch potyviral 35-kDa proteinase: Identification of essential residues and requirements for autoproteolysis. Virology, 190(1), 298-306. doi:10.1016/0042-6822(92)91216-h
Ayme, V., Petit-Pierre, J., Souche, S., Palloix, A., & Moury, B. (2007). Molecular dissection of the potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper. Journal of General Virology, 88(5), 1594-1601. doi:10.1099/vir.0.82702-0
Ayme, V., Souche, S., Caranta, C., Jacquemond, M., Chadœuf, J., Palloix, A., & Moury, B. (2006). Different Mutations in the Genome-Linked Protein VPg of Potato virus Y Confer Virulence on the pvr23 Resistance in Pepper. Molecular Plant-Microbe Interactions, 19(5), 557-563. doi:10.1094/mpmi-19-0557
Ruffel, S., Dussault, M.-H., Palloix, A., Moury, B., Bendahmane, A., Robaglia, C., & Caranta, C. (2002). A natural recessive resistance gene against potato virus Y in pepper corresponds to the eukaryotic initiation factor 4E (eIF4E). The Plant Journal, 32(6), 1067-1075. doi:10.1046/j.1365-313x.2002.01499.x
Moury, B., Morel, C., Johansen, E., Guilbaud, L., Souche, S., Ayme, V., … Jacquemond, M. (2004). Mutations inPotato virus YGenome-Linked Protein Determine Virulence Toward Recessive Resistances inCapsicum annuumandLycopersicon hirsutum. Molecular Plant-Microbe Interactions, 17(3), 322-329. doi:10.1094/mpmi.2004.17.3.322
Robaglia, C., & Caranta, C. (2006). Translation initiation factors: a weak link in plant RNA virus infection. Trends in Plant Science, 11(1), 40-45. doi:10.1016/j.tplants.2005.11.004
Peng, Y. H., Wang, Y., Gal-On, A., Huet, H., Kadoury, D., & Raccah, B. (1998). Mutations in the HC-Pro gene of zucchini yellow mosaic potyvirus: effects on aphid transmission and binding to purified virions. Journal of General Virology, 79(4), 897-904. doi:10.1099/0022-1317-79-4-897
Andersen, K., & Johansen, I. E. (1998). A Single Conserved Amino Acid in the Coat Protein Gene of Pea Seed-Borne Mosaic Potyvirus Modulates the Ability of the Virus to Move Systemically inChenopodium quinoa. Virology, 241(2), 304-311. doi:10.1006/viro.1997.8967
López-Moya, J. J., & Pirone, T. P. (1998). Charge changes near the N terminus of the coat protein of two potyviruses affect virus movement. Journal of General Virology, 79(1), 161-165. doi:10.1099/0022-1317-79-1-161
Valli, A., Lopez-Moya, J. J., & Garcia, J. A. (2007). Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. Journal of General Virology, 88(3), 1016-1028. doi:10.1099/vir.0.82402-0
Edgar, R. C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32(5), 1792-1797. doi:10.1093/nar/gkh340
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28(10), 2731-2739. doi:10.1093/molbev/msr121
Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7(1), 214. doi:10.1186/1471-2148-7-214
Wang, T. H., Donaldson, Y. K., Brettle, R. P., Bell, J. E., & Simmonds, P. (2001). Identification of Shared Populations of Human Immunodeficiency Virus Type 1 Infecting Microglia and Tissue Macrophages outside the Central Nervous System. Journal of Virology, 75(23), 11686-11699. doi:10.1128/jvi.75.23.11686-11699.2001
Librado, P., & Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11), 1451-1452. doi:10.1093/bioinformatics/btp187
Yang, Z. (2007). PAML 4: Phylogenetic Analysis by Maximum Likelihood. Molecular Biology and Evolution, 24(8), 1586-1591. doi:10.1093/molbev/msm088
Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6), 716-723. doi:10.1109/tac.1974.1100705
Fares, M. A. (2004). SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics, 20(16), 2867-2868. doi:10.1093/bioinformatics/bth303
Li, W.-H. (1993). Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution, 36(1), 96-99. doi:10.1007/bf02407308
KORBER, B., & MYERS, G. (1992). Signature Pattern Analysis: A Method for Assessing Viral Sequence Relatedness. AIDS Research and Human Retroviruses, 8(9), 1549-1560. doi:10.1089/aid.1992.8.1549
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