Genetic diversity analyses reveal novel recombination events in Grapevine leafroll-associated virus 3 in China
Tài liệu tham khảo
Adkar-Purushothama, 2011, A sensitive and reliable RT-nested PCR assay for detection of Citrus tristeza virus from naturally infected citrus plants, Current Microbiology, 62, 1455, 10.1007/s00284-011-9883-7
Bertolini, 2003, Multiplex nested reverse-transcription polymerase chain reaction in a single tube for sensitive and simultaneous detection of four RNA viruses and Pseudomonas savastanoi pv. savastanoi in olive trees, Phytopathology, 93, 286, 10.1094/PHYTO.2003.93.3.286
Bester, 2012, Complete nucleotide sequence of a new strain of grapevine leafroll-associated virus 3 in South Africa, Archives of Virology, 157, 1815, 10.1007/s00705-012-1333-8
Callaway, 2001, The multifunctional capsid proteins of plant RNA viruses, Annual Review of Phytopathology, 39, 419, 10.1146/annurev.phyto.39.1.419
Chare, 2004, Selection pressures in the capsid genes of plant RNA viruses reflect mode of transmission, Journal of General Virology, 85, 3149, 10.1099/vir.0.80134-0
Chooi, 2009, Sequence variation in Grapevine leafroll-associated virus 3 (GLRaV-3) New Zealand isolates, 290
Dovas, 2003, A spot nested RT-PCR method for the simultaneous detection of members of the Vitivirus and Foveavirus genera in grapevine, Journal of Virological Methods, 107, 99, 10.1016/S0166-0934(02)00197-0
Engel, 2008, Genome analysis and detection of a Chilean isolate of Grapevine leafroll associated virus-3, Virus Genes, 37, 110, 10.1007/s11262-008-0241-1
Engelbrecht, 1990, Transmission of grapevine leafroll disease and associated closteroviruses by the vine mealybug Planococcus ficus, Phytophylactica, 22, 341
Fajardo, 2007, Variability of the coat protein gene of Grapevine leafroll-associated virus 3 in Brazil, Fitopatologia Brasileira, 32, 335, 10.1590/S0100-41582007000400008
Fu, 1993, Statistical tests of neutrality of mutations, Genetics, 133, 693, 10.1093/genetics/133.3.693
Fuchs, 2009, Survey for the three major leafroll disease-associated viruses in Finger lakes vineyards in New York, Plant Disease, 93, 395, 10.1094/PDIS-93-4-0395
Galetto, 2006, Dissection of a circumscribed recombination hot spot in HIV-1 after a single infectious cycle, Journal of Biological Chemistry, 281, 2711, 10.1074/jbc.M505457200
Gouveia, 2011, Five phylogenetic groups identified in the coat protein gene of grapevine leafroll-associated virus 3 obtained from Portuguese grapevine varieties, Archives of Virology, 156, 413, 10.1007/s00705-010-0878-7
Holmes, 2009
Hong, 2005, Gene cloning of etiological viruses causing grapevine leafroll in China, 89
Jarugula, 2010, 3′-Coterminal subgenomic RNAs and putative cis-acting elements of Grapevine leafroll-associated virus 3 reveals ‘unique’ features of gene expression strategy in the genus Ampelovirus, Virology Journal, 7, 180, 10.1186/1743-422X-7-180
Jooste, 2010, Three genetic Grapevine leafroll-associated virus 3 variants identified from South African vineyards show high variability in their 5′UTR, Archives of Virology, 155, 1997, 10.1007/s00705-010-0793-y
Jukes, 1969, Evolution of protein molecules, 21
Karasev, 2000, Genetic diversity and evolution of closteroviruses, Annual Review of Phytopathology, 38, 293, 10.1146/annurev.phyto.38.1.293
Kelley, 2009, Protein structure prediction on the Web: a case study using the Phyre server, Nature Protocols, 4, 363, 10.1038/nprot.2009.2
Ling, 2004, Complete nucleotide sequence and genome organization of Grapevine leafroll-associated virus 3, type member of the genus Ampelovirus, Journal of General Virology, 85, 2099, 10.1099/vir.0.80007-0
Maree, 2008, Complete nucleotide sequence of a South African isolate of grapevine leafroll-associated virus 3 reveals a 5′ UTR of 737 nucleotides, Archives of Virology, 153, 755, 10.1007/s00705-008-0040-y
Martelli, 2002, The family Closteroviridae revised, Archives of Virology, 147, 2039, 10.1007/s007050200048
Martelli, 2012, Taxonomic revision of the family closteroviridae with special reference to the grapevine leafroll-associated members of the genus ampelovirus and the putative species unassigned to the family, Journal of Plant Pathology, 94, 7
Martin, 2010, RDP3: a flexible and fast computer program for analyzing recombination, Bioinformatics, 26, 2462, 10.1093/bioinformatics/btq467
Maydt, 2006, Recco: recombination analysis using cost optimization, Bioinformatics, 22, 1064, 10.1093/bioinformatics/btl057
Palacio, 1999, Single-strand conformation polymorphism (SSCP) analysis as a tool for viroid characterization, Journal of Virological Methods, 77, 27, 10.1016/S0166-0934(98)00121-9
Rezaian, 1991, Detection of virus-associated dsRNA from leafroll infected grapevines, Journal of Virological Methods, 31, 325, 10.1016/0166-0934(91)90170-5
Roossinck, 1997, Mechanisms of plant virus evolution, Annual Review of Phytopathology, 35, 1953, 10.1146/annurev.phyto.35.1.191
Rozas, 2003, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, 19, 2496, 10.1093/bioinformatics/btg359
Rubio, 2001, Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination, Journal of Virology, 75, 8054, 10.1128/JVI.75.17.8054-8062.2001
Sambrook, 1989
Sharma, 2011, Occurrence of grapevine leafroll-associated virus complex in Napa valley, PLoS ONE, 6, e26227, 10.1371/journal.pone.0026227
Simon, 1994, RNA–RNA recombination and evolution in virus-infected plants, Annual Review of Phytopathology, 32, 337, 10.1146/annurev.py.32.090194.002005
Simon-Loriere, 2011, Why do RNA viruses recombine?, Nature, 6, 617
Tamura, 2011, MEGA5 molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Molecular Biology and Evolution, 28, 2731, 10.1093/molbev/msr121
Thompson, 1997, The CLUSTAL_X windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Research, 25, 4876, 10.1093/nar/25.24.4876
Tsai, 2008, Transmission of Grapevine leafroll-associated virus 3 by the vine mealybug (Planococcus ficus), Phytopathology, 98, 1093, 10.1094/PHYTO-98-10-1093
Turturo, 2005, Genetic variability and population structure of Grapevine leafroll-associated virus 3 isolates, Journal of General Virology, 86, 217, 10.1099/vir.0.80395-0
Walter, 1997, Clonal and sanitary selection of the grapevine, 43
Wang, 2011, Genetic diversity in the 3′ terminal 4.7-kb region of Grapevine leafroll-associated virus 3, Phytopathology, 101, 445, 10.1094/PHYTO-07-10-0173
Worobey, 1999, Evolutionary aspects of recombination in RNA viruses, Journal of General Virology, 80, 2535, 10.1099/0022-1317-80-10-2535
Xu, 2006, Cloning and expression in E. coli of Grapevine leafroll-associated virus 3 RdRp gene, Journal of Fruit Science, 2, 252
Zhang, 1994, Retrovirus recombination depends on the length of sequence identity and is not error prone, Journal of Virology, 68, 2409, 10.1128/JVI.68.4.2409-2414.1994