烟草脉带花叶病毒、芜菁花叶病毒和马铃薯Y病毒的遗传结构分析
|
摘要
烟草脉带花叶病毒(Tobacco vein banding mosaic virus,TVBMV)、马铃薯Y病毒(Potato virus Y,PVY)和芜菁花叶病毒(Turnip mosaic virus,TuMV)都属于马铃薯Y病毒属(Potyvirus)。TVBMV和PVY是烟草上的重要病毒,在我国烟草上的危害呈上升趋势;TuMV是十字花科植物上的重要病毒。它们侵染作物后造成作物产量和品质的下降。本研究分别分析了TVBMV、TuMV和PVY三种病毒的群体结构。
从中国烟草主产区采集到40个TVBMV分离物,测定了其HC-Pro、P3、6K1和CP基因,通过比较GenBank上其它分离物的相应序列分析了TVBMV的遗传多样性和种群结构。根据不同基因的分析结果,将TVBMV分离物划分为两个(6K1和CP)或三个组(P3和HC-Pro)。中国云南分离物单独成簇,基因交流频繁,但与其它省份分离物之间的基因交流不频繁。TVBMV的4个基因片段都处于负向选择,但不同的基因片段承受的选择压力不同。分析的42个分离物中有13个发生重组。
通过RT-PCR扩增得到中国的56个TuMV萝卜分离物的3′-末端基因组序列,分析其群体变异。中国105个分离物(含GenBank上49个)中,共有12个分离物存在明显重组。系统进化树结果表明,中国TuMV可分为Asian-BR、basal-BR和world-B三个组,有50.5%的分离物位于basal-BR组中。中国basal-BR组分为3个亚组,I和II亚组与日本的basal-BR I、II亚组一致,但是III亚组单独成簇,日本还存在IV亚组。潍坊和泰安的basal-BR分离物是新出现的谱系,处于爆发状态。TuMV每个组或亚组都处于负向(纯化)选择。泰安和潍坊地区的分离物基因交流频繁。
从中国烟草主要种植区采集PVY分离物,接种到苋色藜(Chenopodium amaranticolor)上,经过多次单斑分离获得25个生物纯的分离物。测定了这25个分离物的HC-Pro和CP序列及另外4个分离物的CP序列。25个分离物中有22个能引起烟草叶脉坏死,3个引起烟草花叶或脉明。19个分离物用PVYO CP单克隆抗体检测呈现阳性反应。血清学和分子进化分析表明,25个分离物中有3个为O株系、2个为N株系、2个为NTN株系、16个为N-Wi株系和2个为N-HCO株系。Feixian8和Mengyin60属于N-HCO株系,他们具有类似PVYO株系的HC-Pro与类似PVYN株系的CP基因,但是能引起烟草叶脉坏死,为新的株系。HC-Pro和CP编码区处于负向选择,但是HC-Pro序列的7个氨基酸和CP序列的6个氨基酸处于正向选择。PVY的亚种群不具有寄主特异性,不同亚种群承受的选择压力不同。
马铃薯X病毒(Potato virus X,PVX)是常见的植物病毒之一,主要侵染茄科植物。本研究测得了一株1985年的PVX分离物(PVX-1985)的全基因组序列。PVX-1985不包括Poly(A)尾巴共6 435个核苷酸(nucleotides,nt),含有5个开放阅读框(ORF)。ORF1编码复制酶蛋白,ORF2、3和4为重叠的三联基因块,ORF5编码外壳蛋白。系统进化分析表明,PVX分离物可以分为两个组:欧亚组和美洲组,PVX-1985分离物位于欧亚组。PVX的所有开放阅读框处于负向(纯化)选择,但是依赖于RNA的RNA聚合酶基因(RdRp)中间区域处于正向(多样化)选择。
Tobacco vein banding mosaic virus (TVBMV), Turnip mosaic virus (TuMV) and Potato virus Y (PVY) belong to the genus Potyvirus, the family Potyviridae. TVBMV and PVY infect plants of the family Solanaceae and TuMV infects the family Cruciferae in nature and they cause great economic losses to crop production. The genetic structures of TVBMV, TuMV and PVY were analyzed in this study.
TVBMV is one of the most economically important viruses infecting tobacco in China. In this paper, we determined the HC-Pro, P3, 6K1 and CP gene sequences of 40 TVBMV isolates collected from different tobacco-growing areas in China and compared them with those sequences available to study its genetic diversity and population structure. TVBMV isolates could be divided into two (6K1 and CP) or three (P3 and HC-Pro) groups, depending on which gene was analyzed. The populations from most part of China showed high genetic identities and had frequent gene flow. The population from Yunnan, a southern western province of China, formed a separate group and had frequent gene flow within this region. However, the gene flow between TVBMV isolates from Yunnan and other parts of China was infrequent. TVBMV genes were under strong negative selection, but the pressures were different for different genes. Recombination was common in the evolution of TVBMV isolates. Our data also suggested that the most recent outbreak of TVBMV in China was not due to the emergence of new TVBMV subtype(s).
The 3′- terminal genome of 56 TuMV isolates were determined and analyzed with other Chinese and Japanese isolates available in the GenBank to understand the genetic structure of this virus. Twelve of 105 isolates were clear recombination. Isolates from Radish in China formed three groups: Asian-BR, basal-BR and world B. Group basal-BR consisted of 50.5% isolates and were divided into three subpopulations. Subpopulations I and II were genetical identical with Janpanese subpopulations but subpopulation III was not, while subpopulation IV only existed in Japan. Isolates in the group basal-BR from Tai′an and Weifang were new emergent and in a state of expansion. All populations and subpopulations were under negative pression. Gene flow between Tai′an and Weifang was frequent.
Genetic variability of PVY isolates infecting potato has been characterized, but little is known about genetic diversity of PVY isolates infecting tobacco crops. In this study, PVY isolates were collected from major tobacco-growing areas in China and single-lesion isolates produced by serial inoculation on Chenopodium amaranticolor. Twenty-two of 25 isolates caused systemic veinal necrosis symptoms and three isolates caused mosaic in tobacco. Nineteen of 25 isolates were detected by PVYO CP specific antibodies. Serological and phylogenetic analyses showed that, among the 25 isolates, three isolates belonged to group O, two isolates belonged to group N, two isolates belonged to group NTN, sixteen isolates belonged to group N-Wi and two isolates belonged to group N-HcO. Isolates Feixian8 and Mengyin60 contained a PVYN-like coat protein (CP) and PVYO-like helper component
proteinase (HC-Pro) but caused systemic veinal necrosis symptoms in tobacco, and hence designated as PVYN-HcO recombination. Seven amino acids in HC-Pro and six amino acids in CP were under positive selection. Selection pressures differed between the subpopulations of PVY distinguished by phylogenetic analysis of HC-Pro and CP sequences. When PVY isolates from potato were included, no host-specific clustering of the PVY isolates was observed in phylogenetic and nucleotide diversity analyses. Potato virus X (PVX) is one of the most common plant viruses that cause great economic losses to solanaceous plants. The complete genome of PVX-1985 is 6 435 nucleotides (nt) exinclude Poly (A) and contains five open reading frames (ORFs). ORF1 encodes a protein of 166 kDa that functions as RNA-dependent RNA polymerase (RdRp). The overlapping ORFs 2, 3 and 4 encode triple gene block proteins (TGBp) of 25, 12 and 8 kDa, respectively. ORF 5 encodes the 25 kDa coat protein (CP). The phylogenetic trees of the full genomic sequences and the CP gene demonstrated that PVX isolates were clustered into two groups: Eurasia and America, and PVX-1985 fell within the group Eurasia. All the open reading frames of PVX were under negative (or purifying) selection, but the central region of RdRp was under positive or diversifying selection.
从中国烟草主产区采集到40个TVBMV分离物,测定了其HC-Pro、P3、6K1和CP基因,通过比较GenBank上其它分离物的相应序列分析了TVBMV的遗传多样性和种群结构。根据不同基因的分析结果,将TVBMV分离物划分为两个(6K1和CP)或三个组(P3和HC-Pro)。中国云南分离物单独成簇,基因交流频繁,但与其它省份分离物之间的基因交流不频繁。TVBMV的4个基因片段都处于负向选择,但不同的基因片段承受的选择压力不同。分析的42个分离物中有13个发生重组。
通过RT-PCR扩增得到中国的56个TuMV萝卜分离物的3′-末端基因组序列,分析其群体变异。中国105个分离物(含GenBank上49个)中,共有12个分离物存在明显重组。系统进化树结果表明,中国TuMV可分为Asian-BR、basal-BR和world-B三个组,有50.5%的分离物位于basal-BR组中。中国basal-BR组分为3个亚组,I和II亚组与日本的basal-BR I、II亚组一致,但是III亚组单独成簇,日本还存在IV亚组。潍坊和泰安的basal-BR分离物是新出现的谱系,处于爆发状态。TuMV每个组或亚组都处于负向(纯化)选择。泰安和潍坊地区的分离物基因交流频繁。
从中国烟草主要种植区采集PVY分离物,接种到苋色藜(Chenopodium amaranticolor)上,经过多次单斑分离获得25个生物纯的分离物。测定了这25个分离物的HC-Pro和CP序列及另外4个分离物的CP序列。25个分离物中有22个能引起烟草叶脉坏死,3个引起烟草花叶或脉明。19个分离物用PVYO CP单克隆抗体检测呈现阳性反应。血清学和分子进化分析表明,25个分离物中有3个为O株系、2个为N株系、2个为NTN株系、16个为N-Wi株系和2个为N-HCO株系。Feixian8和Mengyin60属于N-HCO株系,他们具有类似PVYO株系的HC-Pro与类似PVYN株系的CP基因,但是能引起烟草叶脉坏死,为新的株系。HC-Pro和CP编码区处于负向选择,但是HC-Pro序列的7个氨基酸和CP序列的6个氨基酸处于正向选择。PVY的亚种群不具有寄主特异性,不同亚种群承受的选择压力不同。
马铃薯X病毒(Potato virus X,PVX)是常见的植物病毒之一,主要侵染茄科植物。本研究测得了一株1985年的PVX分离物(PVX-1985)的全基因组序列。PVX-1985不包括Poly(A)尾巴共6 435个核苷酸(nucleotides,nt),含有5个开放阅读框(ORF)。ORF1编码复制酶蛋白,ORF2、3和4为重叠的三联基因块,ORF5编码外壳蛋白。系统进化分析表明,PVX分离物可以分为两个组:欧亚组和美洲组,PVX-1985分离物位于欧亚组。PVX的所有开放阅读框处于负向(纯化)选择,但是依赖于RNA的RNA聚合酶基因(RdRp)中间区域处于正向(多样化)选择。
Tobacco vein banding mosaic virus (TVBMV), Turnip mosaic virus (TuMV) and Potato virus Y (PVY) belong to the genus Potyvirus, the family Potyviridae. TVBMV and PVY infect plants of the family Solanaceae and TuMV infects the family Cruciferae in nature and they cause great economic losses to crop production. The genetic structures of TVBMV, TuMV and PVY were analyzed in this study.
TVBMV is one of the most economically important viruses infecting tobacco in China. In this paper, we determined the HC-Pro, P3, 6K1 and CP gene sequences of 40 TVBMV isolates collected from different tobacco-growing areas in China and compared them with those sequences available to study its genetic diversity and population structure. TVBMV isolates could be divided into two (6K1 and CP) or three (P3 and HC-Pro) groups, depending on which gene was analyzed. The populations from most part of China showed high genetic identities and had frequent gene flow. The population from Yunnan, a southern western province of China, formed a separate group and had frequent gene flow within this region. However, the gene flow between TVBMV isolates from Yunnan and other parts of China was infrequent. TVBMV genes were under strong negative selection, but the pressures were different for different genes. Recombination was common in the evolution of TVBMV isolates. Our data also suggested that the most recent outbreak of TVBMV in China was not due to the emergence of new TVBMV subtype(s).
The 3′- terminal genome of 56 TuMV isolates were determined and analyzed with other Chinese and Japanese isolates available in the GenBank to understand the genetic structure of this virus. Twelve of 105 isolates were clear recombination. Isolates from Radish in China formed three groups: Asian-BR, basal-BR and world B. Group basal-BR consisted of 50.5% isolates and were divided into three subpopulations. Subpopulations I and II were genetical identical with Janpanese subpopulations but subpopulation III was not, while subpopulation IV only existed in Japan. Isolates in the group basal-BR from Tai′an and Weifang were new emergent and in a state of expansion. All populations and subpopulations were under negative pression. Gene flow between Tai′an and Weifang was frequent.
Genetic variability of PVY isolates infecting potato has been characterized, but little is known about genetic diversity of PVY isolates infecting tobacco crops. In this study, PVY isolates were collected from major tobacco-growing areas in China and single-lesion isolates produced by serial inoculation on Chenopodium amaranticolor. Twenty-two of 25 isolates caused systemic veinal necrosis symptoms and three isolates caused mosaic in tobacco. Nineteen of 25 isolates were detected by PVYO CP specific antibodies. Serological and phylogenetic analyses showed that, among the 25 isolates, three isolates belonged to group O, two isolates belonged to group N, two isolates belonged to group NTN, sixteen isolates belonged to group N-Wi and two isolates belonged to group N-HcO. Isolates Feixian8 and Mengyin60 contained a PVYN-like coat protein (CP) and PVYO-like helper component
proteinase (HC-Pro) but caused systemic veinal necrosis symptoms in tobacco, and hence designated as PVYN-HcO recombination. Seven amino acids in HC-Pro and six amino acids in CP were under positive selection. Selection pressures differed between the subpopulations of PVY distinguished by phylogenetic analysis of HC-Pro and CP sequences. When PVY isolates from potato were included, no host-specific clustering of the PVY isolates was observed in phylogenetic and nucleotide diversity analyses. Potato virus X (PVX) is one of the most common plant viruses that cause great economic losses to solanaceous plants. The complete genome of PVX-1985 is 6 435 nucleotides (nt) exinclude Poly (A) and contains five open reading frames (ORFs). ORF1 encodes a protein of 166 kDa that functions as RNA-dependent RNA polymerase (RdRp). The overlapping ORFs 2, 3 and 4 encode triple gene block proteins (TGBp) of 25, 12 and 8 kDa, respectively. ORF 5 encodes the 25 kDa coat protein (CP). The phylogenetic trees of the full genomic sequences and the CP gene demonstrated that PVX isolates were clustered into two groups: Eurasia and America, and PVX-1985 fell within the group Eurasia. All the open reading frames of PVX were under negative (or purifying) selection, but the central region of RdRp was under positive or diversifying selection.
引文
1.常青,周开亚.分子进化研究中系统发生树的重建.生物多样性, 1998. 6(1): 55–62
2.陈瑞泰,韩晓东,史万华,李林森,刘保安,张文丽.五省烟区烟草病毒类型的初步研究.中国烟草科学, 1986.1–4
3.陈瑞泰,朱贤朝.全国16个主产烟省(区)烟草侵染性病害调研报告.中国烟草科学, 1997. (l):34-35
4.陈秀斋,温亮,魏代福,高瑞,袁从阳,李向东.蒙阴烟草病毒种类检测.山东农业科学, 2009. (10): 62–63
5.关国经,高乔婉,范怀忠.贵州省烤烟花叶病主要病毒种类的初步鉴定.华南农学院学报, 1982. 3(4): 64–71
6.郭兴启,朱汉城,吕士恩,王智法,陈瑞泰.酶标记羊抗兔间接法检测烟草马铃薯Y病毒的研究.中国烟草学报, 1998. 4: 38–42
7.韩晓东,陈瑞泰,姜仁杰,石金开,张文丽,陈作义,郑巧兮,沈菊英,朱本明. CMV和PVY复合感染引起的烟草叶脉坏死病.生物化学与生物物理学报, 1983. 15: 279–282
8.纪玲玲.烟草脉带花叶病毒CP基因的原核表达及免疫金标试纸条的研制.硕士学位论文,西北农林科技大学, 2008
9.兰玉菲,刘金亮,高瑞,王红艳,朱天生,竺晓平,李向东.烟草脉带花叶病毒cp基因的原核表达及抗血清制备.植物病理学报, 2007. 37 (5): 461–466
10.李慧琴,冯崇川.陕西省烟草侵染性病害发生种类与分布危害调查研究.西北农业学报, 1994. 3(4): 27–31
11.李向东,李义强,高宝昌,耿建国,王洪刚,王维超,郑全立.河南省郏县襄城两地烟草病毒病大发生的原因及对策.中国烟草学报, 2001. 7: 23–26.
12.李向东,刘金亮,李文法,范在丰,李怀方,王洪刚.潍坊萝卜红心病病原鉴定,植物病理学报, 2005. 35(1): 13–18
13.马占鸿,李怀方,裘维蕃.玉米种子携带MDMV的生物和免疫检测.植物病毒与病毒病防治研究, 1997. (1): 97–102
14.施曼玲,李桂新,陶小荣.芜菁花叶病毒温州分离物HC–Pro基因序列分析.微生物学通报, 2002. 29(1): 26–30
15.施曼玲,周雪平.芜菁花叶病毒两分离物的CP基因及HC-Pro基因的比较.浙江大学学报(农业与生命科学版), 2005. 31(6): 689–693
16.施曼玲.芜菁花叶病毒分离物NBXC的CP和HC-Pro基因克隆与序列分析.科技通报, 2007. 23(1): 41–45
17.宋云枝,李玲玲,朱常香,温孚江,温孚凯.芜菁花叶病毒山东分离物外壳蛋白基因的克隆及序列分析.中国农业科学, 2005. 38(3): 504–510
18.王劲波,王凤龙,钱玉梅,时焦,王从丽,杨德廉,胡明珠,张友诚,刘彩萍.山东烟区主要病毒的株系鉴定中国烟草学报, 1998. 4(1): 24–32
19.王智法,严敦余,张广民,刘开启,陈瑞泰.山东省烟草病毒类型鉴定.山东农业大学学报, 1986. 17: 75–82
20.吴元华.我国烟草上马铃薯Y病毒3个新株系研究.辽宁省首届青年学术年会论文集.东北工学院出版社, 1992. 98–102
21.谢成颂,刘延荣,王智法,张修国.用血清学方法检测山东烟草病毒病流行趋势.中国烟草科学, 1993. 4: 1–5
22.于晓庆.马铃薯X病毒和烟草脉带花叶病毒的分子变异及协生作用.博士学位论文,山东农业大学, 2008
23.张仲恺,李毅.云南植物病毒.科学出版社,北京, 2001. 46–49
24.赵建邦,高林,宋佳.一种基于代谢路径构建系统发生树的有效方法.电子学报, 2009. 37(8): 1633–1638
25.朱贤朝,王彦亭,王智发.中国烟草病害.中国农业出版社, 2002. 191–259
26. Aaziz R, Tepfer M. Recombination in RNA viruses and in virus-resistant transgenic plants. J Gen Virol, 1999. 80(6): 1339–1346
27. Adair T L, Kearney C M. Recombination between a 3-kilobase tobacco mosaic virus transgene and a homologous viral construct in the restoration of viral and nonviral genes. Arch Virol, 2000. 145(9): 1867–1883
28. Adams M J, Antoniw J F. DPVweb: a comprehensive database of plant and fungal virus genes and genomes. Nucleic Acids Res, 2006. 34: D382–D385
29. Alabi O J, Martin R R, Naidu R A. Sequence diversity, population genetics and potential recombination events in grapevine rupestris stem pitting-associated virus in Pacific North-West vineyards. J Gen Virol, 2010. 91: 265–276
30. Alejska M, Kurzyniska-Kokorniak A, Broda M, Kierzek R, Figlerowicz M. How RNA viruses exchange their genetic material. Acta Biochim Pol, 2001. 48(2): 391–407
31. Aleman Verdaguer M E, Goudou U C, Dubern J, Beachy R N, Fauquet C. Analysis of the sequence diversity of the P1, HC, P3, Nlb and CP genomic regions of several yam mosaic potyvirus isolates: implications for the intraspecies molecular diversity of potyviruses. Gen Virol, 1997. 78(6): 1253–1264
32. Aranda M A, Fraile A, Dopazo J, Malpica J M. Contribution of mutation and RNA recombination to the evolution of a plant pathogenic RNA. J Mol Evol, 1997. 44: 81–88
33. Arboleda M, Azzam O. Inter- and intra-site genetic diversity of natural field populations of rice tungro bacilliform virus in the Philippines. Arch Virol, 2000. 145: 275–289
34. Ayme V, Petit-Pierre J, Souche S, Palloix A, Moury B. Molecular dissection of the potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper. J Gen Virol, 2007. 88: 1594–1601
35. Baratova L A, Efimov A V, Dobrov E N, Fedorova N V, Hunt B, Badun G A, Ksenofontov A L, Torrance L, J?rvekülg L. In situ spatial organization of potato virus A coat protein subunits as assessed by tritium bombardment. J Virol, 2001. 75: 9696–9702
36. Barker H, McGeachy K D, Toplak N, Gruden K, Zel J, Browning I. Comparison of genome sequence of PVY isolates with biological properties. Am J Potato Res, 2009. 86: 227–238
37. Bass B L. RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem, 2002. 71(1): 817–846
38. Blanco-Urgoiti B, Sánchez F, Pérez de San Román C, Dopazo J, Ponz F. Potato virus Y group C isolates are a homogeneous pathotype but two different genetic strains. J Gen Virol, 1998a. 79: 2037–2042
39. Boni M F, Posada D, Feldman M W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics, 2007. 176: 1035–1047
40. Bonnet J, Fraile A, Sacristan S, Malpica J M, Garcia-Arenal F. Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus. Virology, 2005. 332 (1): 359–368
41. Boonham N, Walsh K, Hims M, Preston S, North J, Barker I. Biological and sequence comparisons of Potato virus Y isolates associated with potato tuber necrotic ringspot disease. Plant Pathol, 2002. 51: 117–126
42. Bousalem M, Douzery E J P, Fargette D. High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution. J Gen Virol, 2004. 81: 243–255
43. Browning I, Charlet K, Chrzanowska M, Dedic P, Kerlan C, Kryszczuk A, Schubert J, Varveri C, Werkman A, Wolf I. What is PVYNTN? The reaction of potato cultivars to inoculation with a range of PVY isolates. In: Abstracts 12th EAPR Virology Section Meeting, Rennes, France, 2004. 48–50
44. Brunt A, Crabtree K, Dallwitz M, Gibbs A, Watson L. Viruses of Plants: Descriptions and Lists from the VIDE Database. CAB International, Wallingford, UK, 1996
45. Bujarski J J, Kaesberg P. Genetic recombination between RNA components of a multipartite plant virus. Nature, 1986. 321(6069): 528–531
46. Bujarski J J, Nagy P D, Flasinski S. Molecular studies of genetic RNA-RNA recombination in brome mosaic virus. Adv Virus Res, 1994. 43: 275–302
47. Cerovska N, Moravec T, FiligarováM, Petrzik K. Nucleotide sequences of 5′- temrinal parts of coat protein genes of various isolates of NTN strain of potato virus Y. Acta Viorl, 2001. 45(l): 55–59
48. Chang B Y, Huang C R, Yeh S D, Chiang J K, Hung L M, Hu H Y. Nucleotide-sequence of the coat protein-coding region of the potyvirus Tobacco vein-banding mosaic virus. Arch Virol, 1994. 138: 17–25
49. Chare E R, Holmes E C. A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol, 2006. 151: 933–946
50. Chen J, Chen J P, Adams M J. Variation between Turnip mosaic virus isolates in Zhejiang Province, China and evidence for recombination. J Phytopathol, 2002. 150: 142–145
51. Cheng C P, Nagy P D. Mechanism of RNA recombination in carmo- and tombusviruses: evidence for template switching by the RNA-dependent RNA polymerase in vitro. J Virol, 2003. 77(22): 12033–12047
52. Chetverin A B, Chetverina H V, Demidenko A A, Ugarov V I. Nonhomologous RNA recombination in a cell-free system: evidence for a transesterification mechanism guided by secondary structure. Cell, 1997. 88(4): 503–513
53. Chikh Ali M C, Maoka T, Natsuaki K T. Whole genome sequence and characterization of a novel isolate of PVY inducing tuber necrotic ringspot in potato and leaf mosaic in tobacco. J Phytopathol, 2008. 155: 409–415
54. Chin W T. A survey of tobacco mosaic viruses in central Taiwan. J Agric Ass China, 1966. 55: 85–88
55. Chrzanowska M. Differentiation of Potato virus Y (PVY) isolates. Phytopathol Polon, 1994. 8: 15–20
56. Chrzanowska M. New isolates of the necrotic strain of potato virus Y (PVYN) found recently in Poland. Potato Res, 1991. 34: 179–182
57. Chung B Y W, Miller W A, Atkins J F, Firth A E. An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA, 2008. 105, 5897–5902
58. De Bokx J A. Waardplanten van het aardappel-YN-virus [Host plants of the potato virus YN (Tobacco veinal necrosis virus). Eur J Plant Pathol, 1961. 67: 273–277
59. Dean C E, Clark F. Vein-banding on tobacco in North Florida. Plant Dis Rep, 1968. 52: 887–889
60. Domingo-Calap P, Jose′M C, Sanjua′n R. The fitness effects of random mutations in single-stranded DNA and RNA Bacteriophages. Plos Genetics, 2009. 5(11): 1–7
61. Drake J W, Charlesworth B, Charlesworth D, Crow J F. Rates of spontaneous mutation. Genetics, 1998. 148: 1667–1686
62. Drake J W, Holland J J. Mutation rates among RNA viruses. Proc Natl Acad Sci USA, 1999. 96: 13910–13913
63. Drake J W. Rates of spontaneous mutation among RNA viruses. Proc Natl Acad Sci USA, 1993. 90:4171–4175
64. Esfandiari N, Kohi-Habibi M, Hohn T, Pooggin M M. Complete genome sequence of an Iranian isolate of Potato virus X from the legume plant Pisum sativum. Virus Genes, 2009. 39: 141–145
65. Excoffier L. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol. 2004. 13: 853–864
66. Fajolu O L, Wen R H, Windham A S, Windham M T, Moulton J K, Hajimorad M R. Genetic variability and phylogenetic analysis of hosta virus X. Arch Virol, 2009. 154: 1909–1916
67. Falk B W, Bruening G. Will transgenic crops generate new viruses and new diseases?. Science, 1994. 263(5152):1395–1396
68. Fan Z, Chen H, Cai S, Deng C, Wang W, Liang X, Li H. Molecular characterization of a distinct potyvirus from whitegrass in China. Arch Virol, 2003. 148: 1219–1224
69. Fauquet C M, Mayo M A, Maniloff J, Desselberger U, Ball L A. Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, CA. 2005
70. Fellers J P, Tremblay D, Handest M F, Lommel S A. The Potato virus Y MSNR NIb-replicase is the elicitor of a veinal necrosis-hypersensitive response in root knot nematode resistant tobacco. Mol Plant Pathol, 2002. 3: 145–152
71. Fields B N, Joklik W K. Isolation and preliminary genetic and biochemical characterization of temperature-sensitive mutants of reovirus. Virology, 1969. 37: 335–342
72. Fraile A, Alonso-Prados J L, Aranda M A, Bernal J J, Malpica J M, García-Arenal F. Genetic exchange by recombination or reassortment is infrequent in natural populations of a tripartite RNA plant virus. J Virol, 1997. 71: 934–940
73. Fraile A, Escriu F, Aranda M A, Malpica J M, Gibbs A J, García-Arenal F. A century of tobamovirus evolution in an Australian population of Nicotiana glauca. J Virol, 1997. 71: 8316–8320
74. Frenkel M J, Ward C W, Shukla D D. The use of 3′noncoding nucleotide sequence in the taxonomy of potyviruses: application to water melon mosaic virus and soybean mosaic virus. J Gen Virol, 1989. 70: 2775–2783
75. Froissart R, Roze D, Uzest M, Galibert L, Blanc S, Michalakis Y. Recombination every day: abundant recombination in a virus during a single multi-cellular host infection. PLoS Biol, 2005. 3(3): 389–395
76. Fu Y X, Li W H. Statistical tests of neutrality of mutations. Genetics, 1993. 133: 693–709
77. Gagarinova A G, Babu M, Str?mvik M V, Wang A. Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes. Virol J, 2008. 5 (143): 1–8
78. Garcia-Arenal F, Fraile A, Malpica J M. Variation and evolution of plant virus populations. Int Microbiol, 2003. 6(4): 225–232
79. García-Arenal F, Fraile A, Malpica J M. Variability and genetic structure of plant virus populations. Annu Rev Phytopathol, 2001b. 39: 157–186
80. Gibbs M J, Armstrong J S, Gibbs A J. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics, 2000. 16: 573–582
81. Gierer A, Mundry K W. Production of mutants of tobacco mosaic virus by chemical alteration of its ribonucleic acid in vitro. Nature, 1958. 182 (4647): 1457–1458
82. Glais L, Kerlan C, Tribodet M, Tordo V M J, Robaglia C, Astier-Manifacier S. Molecular characterization of Potato virus YN isolates by PCR-RFLP. Eur J Plant Pathol, 1996. 102: 655–662
83. Glais L, Tribdet M, Kerlan C. Genomic variability in Potato potyviurs Y (PVY): evidence that PVYNW and PVYNTN variants are single to multiple recombinants between PVYO and PVYN isolates. Arch Virol, 2002. 147: 363–378
84. Glais L, Tribodet M, Gauthier J P, Manifacier S A, Robaglia C, Kerlan C. RFLP mappingof the whole genome of ten viral isolates representative of different biological groups of potato virus Y. Arch Virol, 1998. 143: 2077–2091
85. Glasa M, Palkovics L, Kominek P, Labonne G, Pittnerova S, Kudela O, Candresse T, Subr Z. Geographically and temporally distant natural recombinant isolates of Plum pox virus (PPV) are genetically very similar and form a unique PPV subgroup. J Gen Virol, 2004. 85: 2671–2681
86. Gooding G V, Tolin S A. Strains of potato virus Y affecting flue-cured tobacco in the southeastern United States. Plant Dis Rep, 1973. 57: 200–204
87. Gooding G V. Relationship between strains of potato virus Y and breeding for resistance, cross protection, and interference. Tobacco Sci, 1985. 29: 99–104
88. Grant W S, Bowen B W. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered, 1998. 89: 415–426
89. Gray S M, Lampert E P. Relationship between inoculum density and vector phenology on the incidence of potato virus Y in tobacco. Ann Appl Biol, 1988. 112:303–312
90. Greene A E, Allison R F. Recombination between viral RNA and transgenic plant transcripts. Science, 1994. 263(5152):1423–1425
91. Guan H, Simon A E. Polymerization of nontemplate bases before transcription initiation at the 3′ends of templates by an RNA-dependent RNA polymerase: an activity involved in 3′end repair of viral RNAs. Proc Natl Acad Sci USA, 2000. 97(23):12451–12456
92. Habera L F, Berger P H, Reddick B B. Molecular evidence from 3′-terminus sequence-analysis that Tobacco vein-banding mosaic virus is a distinct member of the Potyvirus group. Arch Virol, 1994. 138: 27–38
93. Harpending H, Rogers A. Genetic perspectives on human origins and differentiation. Annual Review of Genomics Human. Genetics, 2000. 1: 361–385
94. Hema M, Gopinath K, Kao C. Repair of the tRNA-like CCA sequence in a multipartite positive-strand RNA virus. J Virol, 2005. 79(3):1417–1427
95. Hewitt G M. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J of Linn Soc, 1996. 58(3): 247–276
96. Hewitt G M. Speciation, hybrid zones and phylogeography or seeing genes in space and time. Mol Ecol, 2001. 10: 537–549
97. Hillman B I, Carrington J C, Morris J. A defective interfering RNA that contains a mosaic of a plant virus genome. Cell, 1987. 51(3): 427–433
98. Hong X Y, Chen J, Shi Y H, Chen J P. The‘6K1’protein of a strain of Soybean mosaicvirus localizes to the cell periphery. Arch Virol, 2007. 152: 1547–1551
99. Hu X J, Meachama T, Ewing L, Gray S M, Karasev A V. A novel recombinant strain of Potato virus Y suggests a new viral genetic determinant of vein necrosis in tobacco. Virus Research, 2009c. 143: 68–76
100.Hu X, He C, Xiao Y, Xiong X, Nie X. Molecular characterization and detection of recombinant isolates of potato virus Y from China. Arch. Virol, 2009a. 154: 1303–1312
101.Hu X, Karasev A V, Brown C J, Lorenzen J H. Sequence characteristics of potato virus Y recombinants. J Gen Virol, 2009b. 90: 3033–3041
102.Hudson R R, Boos D D, Kaplan N L. A statistical test for detecting geographic subdivision. Mol Biol Evol, 1992. 9:138–151
103.Hudson R R. A new statistic for detecting genetic differentiation. Genetics, 2000. 155: 2011–2014
104.Huisman M J, Linthorst H J M, Bol J F, Cornelissen B J C. The complete nucleotide sequence of potato virus X and its homologies at the amino acid level with various plus-stranded RNA viruses. J Gen Virol, 1988. 69: 1789–1798
105.James H S, Strauss E G. Evolution of RNA viruses. Ann Rev Microbiol, 1988. 42(6): 57–83
106.Jenner C E, Tomimura K, Ohshima K, Hughes S L, Walsh J A. Mutations in Turnip mosaic virus P3 and cylindrical inclusion proteins are separately required to overcome two Brassica napus resistance genes. Virology, 2002. 300(1): 50–59
107.Jenner C E, Wang X, Ponz F, Walsh J A. A fitness cost for Turnip mosaic_virus to overcome host resistance. Virus research, 2002. 86: 1–6
108.Jenner C E, Walsh J A. Pathotypic variation in turnip mosaic virus with special reference to European isolates. Plant pathology, 1996. 45:848–856
109.Johansen E, Edwards M C, Hampton R O. Seed transmission of viruses: Current perspectives. Annu Rev Phytopathol, 1994. 32: 363–386
110.Jones R A C. Strain group specific and virus specific hypersensitive reactions to infection with potyvirus in potato cultivars. Ann Appl Biol, 1990. 117: 93–105
111.Jones R, Kumar S, Mackie A. Potato virus Y. Department of agriculture Factsheet, 2003. 2: 1443–7783
112.Kagiwada S, Yamaji Y, Nakabayashi H, Ugaki M, Namba S. The complete nucleotide sequence of Potato virus X strain OS: the first complete sequence of a Japanese isolate. J Gen Plant Pathol, 2002. 68, 94–98
113.Kavanagh T, Goulden M, Cruz S S, Chapman S, Barker I, Baulcombe D. Molecularanalysis of a resistance-breaking strain of potato virus X. Virology, 1992. 189: 609–617
114.Kerlan C, Tribodet M, Glais L, Guillet M. Variability of potato virus Y in potato crops in France. J. Phytopathol, 1999. 147: 643–651
115.Kim M J, Kao C. Factors regulating template switch in vitro by viral RNA dependent RNA polymerases: implications for RNA-RNA recombination. Proc Natl Acad Sci USA, 2001. 98(9): 4972–4977
116.Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol, 1980. 16, 111–120
117.Kimura M. Evolution rate at the molecular level. Nature, 1968. 217:624–626
118.Kimura M. The neutral theory of molecular evolution. Cambridge: Cambridge university press.1983
119.Komatsu K, Kagiwada S, Takahashi S, Mori T, Yamaji Y, Hirata H, Ozeki J, Yoshida A, Suzuki M, Ugaki M, Nambe S. Phylogenetic characteristics, genomic heterogeneity and symptomatic variation of five closely related Japanese strains of Potato virus X. Virus Genes, 2005. 31, 99–105
120.Kumar S, Tamura K, Jakobsen I B. MEGA2: molecular evolutionary genetics analysis sofeware. Bioinformatics Applications note, 2001. 17: 1244–1245
121.Kumar S, Tamura K, Nei M. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform, 2004. 5: 150–163
122.Lai M M. RNA recombination in animal and plant viruses. Microbiol Rev, 1992. 56 (1): 61–79
123.Lapp N A, Gooding G V. Occurrence and sources of inoculums of potato virus Y in tobacco in North Carolina. Plant Dis Rep, 1976. 60:1014–1016
124.Latorre B A, Pe?aloza E, Escaffi O. A severe outbreak of potato virus Y in Chilean tobacco. Plant Dis, 1982. 66: 893–895
125.Le Romancer M, Kerlan C, Nedellec M. Biological characterization of various geographical isolates of potato virus Y inducing superficial necrosis on potato tubers. Plant Pathol, 1994. 43: 138–144
126.Li N, Wang X, Zhou G, Dong J. Molecular variability of the coat protein gene of Potato virus Y from tobacco in China. Acta Virol, 2006. 50:107–113
127.Li W H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol, 1993. 36: 96–99.
128.Li W H. Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics, 1977: 85:331–337
129.Li W H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol, 1993. 36: 96–99
130.Lin H X, Rubio L, Smythe A B, Falk B W. Molecular population genetics of Cucumber Mosaic Virus in California: evidence for founder effects and reassortment. J Virol, 2004. 78: 6666–6675
131.Ling K S, Zhu H Y, Petrovic N, Gonsalves D. Serological detection of Grapevine leafroll virus 2 using an antiserum developed against the recombinant coat protein. J. Phytopathol, 2007. 155: 65–69.
132.Liu Y Y, Yu S L, Lan Y F, Zhang C L, Hou S S, Li X D, Chen X Z, Zhu X P. Molecular variability of five Cucumber mosaic virus isolates from China. Acta Virol, 2009. 53: 89–97
133.Lockhart B E L, Fischer H U. A disease of tobacco in morocco caused by a veinal necrosis isolate of Potato virus Y. Plant Dis Rep, 1976. 60: 114–116
134.Lorenzen J H, Meacham T, Berger P H, Shiel P J, Crosslin J M, Hamm P B, Kopp H. Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada. Arch. Virol, 2006. 151: 1055–1074
135.Lutcke H A, Chow K C, Mickel F S, Moss K A, Kern H F, Scheele G A. Selection of AUG initiation codon differs in plants and animals. EMBO J, 1987. 6: 43–48
136.Makino S, Keck J G, Stohlman S A, Lai M M. High-Frequency RNA Recombination of Murine Coronaviruses. J Virol, 1986. 57(3): 729–737
137.Malcuit I, Jong D W, Baulcombe D C, Shields D C, Kavanagh T A. Acquisition of multiple virulence/avirulence determinants by potato virus X (PVX) has occurred through convergent evolution rather than through recombination. Virus Genes, 2000. 20: 165–172
138.Martin D P, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics, 2005. 21: 260–262
139.Martín S, Sambade A, Rubio L, Vives M C, Moya P, Guerri J, Elena S F, Moreno P. Contribution of recombination and selection to molecular evolution of Citrus tristeza virus. J Gen Virol, 2009. 90: 1527–1538
140.Mayo M A, Robinson D J, Jolly C A, Hyman L. Nucleotide Sequence of Potato Leafroll Luteovirus RNA. J Gen Virol, 1989. 70: 1037–1051
141.McDonald J G, Kristjansson G T. New diseases and epidemics properties of strains of potato virus YN in North America. Plant Dis, 1993. 77: 87–89
142.Mih A M, Atiri G I, Rossel H W. Strain-typing of potato virus Y isolates from potato inNigeria by infectivity tests and ELISA. Afr Crop Sci J, 1995. 3: 99–104
143.Moonan F, Molina J, Mirkov T E. Sugarcane Yellow Leaf Virus: An Emerging Virus That Has Evolved by Recombination between Luteoviral and Poleroviral Ancestors. Virology, 2000. 269(1): 156–171
144.Moreno I M, Malpica J M, Díaz-Pendón J A, Moriones E, FraileA, García-Arenal F. Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain. Virology, 2004. 318: 451–460
145.Moret B M, Roshan U, Warnow T. Sequence length requirements for phylogenetic methods. In: Proc 2nd Int'l Workshop Algs in Bioinformatics, 2002. 2452: 343–356
146.Morozov S Y, Solovyev A G. Triple gene block: modular design of a multifunctional machine for plant virus movement. J Gen Virol. 2003: 84: 1351–1366
147.Moury B, Morel C, Johansen E, Jacquemond M. Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses. J Gen Virol, 2002. 83: 2563–2573
148.Nagy P D, Simon A E. New insights into the mechanisms of RNA recombination. Virology, 1997. 235 (1): 1–9
149.Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol, 1986. 3: 18–426
150.Nei M, Kumar S. Molecular Evolution and Phylogenetics. Oxford University Press, New York, USA, 2000
151.Nie X, Singh R P. Specific differentiation of recombinant PVYN:O and PVYNTN strains by multiplex RT-PCR. J Virol Methods, 2003a. 113: 69–77
152.Nie X, Singh R P, Singh M. Molecular and pathological characterization of N:O isolates of the Potato virus Y from Manitoba, Canada. Can J Plant Pathol, 2004. 26: 573–583
153.Nie X, Singh R P. Evolution of North American PVYNTN strain Tu 660 from local PVYN by mutation rather than recombination. Virus Genes, 2003b. 26 (1): 39–47
154.Nie X, Singh R P. Probable geographical grouping of PVYN and PVYNTN based on sequence variation in P1 and 5′-UTR of PVY genome and methods for differentiating North American PVYNTN. J Virol Methods, 2002. 103(2): 145–156
155.Noguchi S, Tajima T, Yamamoto Y, Ohno T, Kubo T. Deletion of a large genomic segment in tobacco varieties that are resistant to potato virus Y (PVY). Mol Gen Genet, 1999. 262: 822–829
156.Ogawa T, Tomitaka Y, Nakagawa A, Ohshima K. Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison withNorth American and European populations. Virus Res, 2008. 131: 199–212
157.Ohshima K, Tomimura Y, Wood J T, Minematsu Y, Kajiyama H, Tomimura K, Gibbs A J. Patterns of recombination in Turnip mosaic virus genomic sequences indicate hotspots of recombination. J Gen Virol, 2007, 88: 298–315
158.Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh J A, Fletcher J, Chen J, Gera A, Gibbs A. Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol, 2002. 83:1511–1521
159.Ohta T, Kimura M. Behavior of neutral mutants influenced by associated overdominant loci in finite populations. Genetics, 1971. 69: 247–260
160.Orman B E, Celnik R M, Mandel A M, Torres H N, Mentaberry A N. Complete cDNA sequence of a South American isolate of potato virus X. Virus Res, 1990. 16(3): 293–305
161.Page R D M, Holmes E C. Molecular evolution: a phylogenetic approach. Blackwell Science Ltd, a Blackwell publishing company, 1998. 1–7
162.Pamilo P, Bianchi N O. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol, 1993. 10: 271–281
163.Pennington R E, Melcher U. In planta deletion of DNA inserts from the large intergenic region of Califlower mosaic virus DNA. Virology, 1993. 192: 188–196
164.Piche L M, Singh R P, Nie X, Gudmestad N C. Diversity among Potato virus Y isolates obtained from potatoes grown in the United States. Phytopathology, 2004. 94: 1368–1375
165.Pilar D C, Jose′M C, Sanjua′n R. The Fitness Effects of Random Mutations in Single-Stranded DNA and RNA Bacteriophages. Plos genet, 2009: 5 (11): 1–7
166.Plisson C, Drucker M, Blanc S, German-Retana S, Le Gall O, Thomas D, Bron P. Structural characterization of HC-Pro, a plant virus multifunctional protein. J Biol Chem, 2003. 278: 23753–23761
167.Posada D, Crandall K A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA, 2001. 98: 13757–13762
168.Pringle C R. Genetic characteristics of conditional lethal mutants of vesicular stomatitis virus induced by 5-fluorouracil, 5-azacytidine, and ethyl methane sulfonate. J Virol, 1970. 5(5): 559–567
169.Rao A L, Hall T C. Recombination and polymerase error facilitate restoration of infectivity in brome mosaic virus. J Virol, 1993. 67(2): 969–979
170.Ramos J D A, Teo S M A, Ou K L, Tsai L C, Lee B W, Cheong N, Chua K Y. Comparative allergenicity studies of native and recombinant Blomia ttropicalisparamyosin (Blot 11). Allergy, 2003. 58(5): 412–419
171.Reddick B B, Collins-Shepard M H, Christie R G, Gooding G V. A new virus-disease in North-America caused by Tobacco vein-banding mosaic virus. Plant Dis, 1992. 76: 856–859
172.Revers F, Gall O L, Candresse T, Romancer M L, Dunez J. Frequent occurrence of recombinant potyvirus isolates. J Gen Virol, 1996. 77: 1953–1965
173.Riechmann J L, Lain S, García J A. Highlights and prospects of potyvirus molecular biology. J Gen Virol, 1992. 73: 1–16
174.Rochon D M. Rapid de novo generation of defective interfering RNA by cucumber necrosis virus mutants that do not express the 20-kDa nonstructural protein. Proc Natl Acad Sci USA, 1991. 88(24): 11153–11157
175.Rogers A R, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biological Evology, 1992. 9: 552–569
176.Romero A, Blanco-Urgoiti B, Soto M J, Fereres A, Ponz F. Characterization of typical pepper-isolates of PVY reveals multiple pathotypes within a single genetic strain. Virus Res, 2001. 79: 71–80
177.Roossinck M J. Evolutionary History of Cucumber Mosaic Virus deduced by phylogenetic analyses. J Virol, 2002. 76(7): 3382–3387
178.Roossinck M J. Mechanisms of plant virus evolution. Annual Review of Phytopathology 1997. 35: 191–209
179.Roossinck M J. Plant RNA virus evolution. Curr Opin Microbiol, 2003. 6(4): 406–409
180.Rozas J, Sanchez-DelBarrio J C, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 2003. 19: 2496–2497
181.Rubio L, Ayllon M A, Kong P, Fernandez A, Polek M, Guerri J, Moreno P, Falk B W. Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination. J Virol, 2001. 75(17): 8054–8062
182.Saitou N, Nei M. The Neighbor-joining Method: A New Method for reconstructing phylogenetic trees. Mol Biol Evol, 1987. 4(4): 406–425
183.Sako N, Ogata K. Different helper factors associated with aphid transmission of some potyviurses. Viorlogy, 1981. 112: 762–765
184.Salminen M O, Carr J K, Burke D S, McCutchan F E. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by Bootscanning. AIDS Res Hum Retrov, 1995. 11: 1423–1425
185.Sawyer S A. Geneconv: a computer package for the statistical detection of geneconversion. Distributed by the Author. Department of Mathematics. Washington University in St. Louis, available at http://www.math.wustl.edu/~sawyer, 1999
186.Schalk H J, Matzeit V, Schiller B, Schell J, Gronenborn B. Wheat dwarf virus, a geminivirus of graminaceous plants needs splicing for replication. EMBO J, 1989. 8 (2): 359–364
187.Schneider S, Excoffier L. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites.: Application to human mitochondrial DNA. Genetics, 1999. 152: 1079–1089
188.Scholthof H, Wu F C, Richins R D, Shepherd R J. A naturally occurring deletion mutant of Figwort mosaic virus (caulimovirus) is generated by RNA splicing. Virology, 1991. 184: 290–298
189.Schubert J, Fomitcheva V, Sztangret–Wisniewska J. Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers. J Virol Methods, 2007. 140: 66–74
190.Seo J K, Ohshima K, Lee H G, Son M, Choi H S, Lee S H, Sohn S H, Kim K H. Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences. Virology, 2009. 393: 91–103
191.Shukla D D, Strike P M, Tracy S L, Gough K H, Ward C W. The N and C termini of the coat protein of potyviruses are surface-located and N terminus contains the major virus-specific epitopes. J Gen Virol, 1988. 69: 1497–1508
192.Shukla D D, Ward C W. Identifiecation and classification of potyviurses on the basis of coat protein sequence data and serology. Arch of Virol, 1989a. 106: 171–200
193.Shukla D D, Ward C W. Structure of potyvirus coat proteins and its action in the taxonomy of the potyvirus group. Advances in Virus Reserch, 1989b. 36: 273–314
194.Shukla D D, Ward C W, Brunt A A. The Potyviridae. Cambridge University Press, Cambridge. 1994
195.Sievert R C. Effect of potato virus Y on cultivars and hybrids of burley tobacco. Phytopathology, 1978. 68: 974–978
196.Sievert R C. Effect of time of inoculation with potato virus Y on yield and quality of burley tobacco. Phytopathology, 1971. 61: 588–589
197.Singh R P. 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. Can Plant Dis Survey, 1992. 72: 113–119
198.Singh R P, Valkonen J P T, Gray S M, Boonham N, Jones R A C, Kerlan C, Schubert J. The naming of Potato virus Y strains infecting potato. Arch Virol, 2008. 153: 1–13
199.Skryabin K G, Kraev A S, Morozov S Y, Rozanov M N, Chernov B K, Lukasheva L I, Atabekov J G. Nucleic Acids Res, 1988. 16: 10929–10930
200.Slatkin M, Hudson R R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populayions. Genetics, 1991. 129: 555–562
201.Smith J M. Analyzing the mosaic structure of genes. J Mol Evol, 1992. 34: 126–129
202.Smith K M. On the composite nature of certain potato virus diseases of the mosaic group as revealed by the use of plant indicators and selective methods of transmission. Proc Royal Soc B, 1931. 109: 251–267
203.Soto M J, Luis Artega M, Fereres A, Ponz F. Limited degree of serological variability in pepper strains of potato virus Y as revealed by analysis with monoclonal antibodies. Ann Appl Biol, 1994. 124: 37–43
204.Stenseth N C, Mysterud A, Ottersen G. Ecological effects of climate fluctuations. Science, 2002. 297: 1292–1296
205.Sudarsono, Woloshuk S L, Xiong Z, Hellmann G M, Wernsman E A, Weissinger A K, Lommel S A. Nucleotide sequence of the capsid protein cistrons from six potato virus Y (PVY) isolates infecting tobacco. Arch Virol, 1993. 132: 161–170
206.Sudhir K, Sudhindra R, Gadagkar. Efficiency of the Neighbor-Joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies. J Mol Evol, 2000. 51: 544–553
207.Swanson W J, Yang Z, Wolfner M F, Aquadro C F. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. PNAS, 2001. 98: 2509–2514
208.Swofford D L. PAUP*: Phylogenetic analysis using parsimony(*and other methods)4.0 beta. http://paup.csit.fsu.edu/
209.Taberlet P, Fumagalli L, Wust-Saucy A G, Cosson J F. Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol, 1998. 7: 453–464
210.Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 1989. 123: 585–595
211.Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol, 2007. 24(8): 1596–1599
212.Tan Z Y, Wada Y, Chen J, Ohshima K. Inter- and intralineage recombinants are commonin natural populations of Turnip mosaic virus. J Gen Virol, 2004. 85: 2683–2696
213.Tan Z, Gibbs A J, Tomitaka Y, Sánchez F, Ponz F, Ohshima K. Mutation in Turnip mosaic virus genomes that have adapted to Raphanus sativus. J Gen Virol, 2005. 86:501–510
214.Thompson J D, Higgins D G, Gibson T J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res, 1994. 22: 4673–4680
215.Thomson A D, Wright D S C. Incidence and some effects of potato virus Y on New Zealand flue-cured tobacco. New Zealand J Agric Res, 1966. 9: 886–893
216.Tian Y P, Liu J L, Yu X Q, Lei L P, Zhu X P, Valkonen J P T, Li X D. Molecular diversity of tobacco vein banding mosaic virus. Arch Virol, 2007. 152: 1911–1915
217.Tomimura K, Gibbs A J, Jenner C E, Walsh J A, Ohshima K. The phylogeny of Turnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent 'emergence' in East Asia. Mol Ecol. 2003. 12: 2099–2111
218.Tomimura K, ?pak J, Katis N, Jenner C E, Walsh J A, Gibbs A J, Ohshima K. Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Euroasia. Virology, 2004, 330: 408–423
219.Tomitaka Y, Ohshima K. A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an‘emergent’lineage in Japan. Mol Ecol, 2006. 15: 4437–4457
220.Tomitaka Y, Yamashita T, Ohshima K. The genetic structure of populations of Turnip mosaic virus in Kyushu and central Honshu, Japan. J Gen Plant Pathol, 2007. 73: 197–208
221.Tordo V M, Chaehulska A M, Fakhfakh H, Romancer M L, Robaglia C, Astier-Manifacier S. Sequence Polymorphism in the 5’NTR and in the P1 coding region of potato virus Y genomic RNA . Gen Virol, 1995. 76(4): 939–949
222.Tribodet M, Glais L, Kerlan C, Jacquot E. Characterization of Potato virus Y (PVY) molecular determinants involved in the vein necrosis symptom induced by PVYN isolates in infected Nicotiana tabacum cv. Xanthi. J Gen Virol, 2005. 86: 2101–2105
223.Valkonen J P T, Slack S A, Plaisted R L. Use of the virus strain group concept to characterize the resistance to PVX and to PVYO in the potato cv. Allegany. Amer Potato J, 1994. 60: 507–516
224.Valli A, López-Myoya J J, García J A. Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J Gen Virol, 2007. 88: 1016–1028
225.Van der Vlugt R A, Leunissen J, Goldbach R. Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteinsand 3′nontranslated regions. Arch Virol, 1993. 131: 361–375
226.Van der Vlugt R, Allefs S, DeHaan P T, Goldback R W. Nucleotide sequence of the 3'- terminal region of potato virus Y N RNA. J Gen Virol, 1989. 70: 229–233
227.Verbeek M, Piron P G M, Dullemans A M, Cuperus C, van der Vlugt R A A. Determination of aphid transmission efficiencies for N, NTN and Wilga strains of Potato virus Y. Ann Appl Biol, 2010. 156: 39–49
228.Verchot-Lubicz J. A new cell-to-cell transport model for potexviruses. Mol Plabt Microbe Interact, 2005. 8: 283–290
229.Wang H Y, Liu J L, Gao R, Chen J, Shao Y H, Li X D. Complete genomic sequence analyses of Turnip mosaic virus basal-BR isolates from China. Virus Genes, 2009. 38: 421–428
230.Wang H Y, Zhu T S, Cui T T, Hou S S, Yin X, Li X D, Lei L P, Zhu X P. Complete genome sequence of a tobacco isolate of the tobacco vein banding mosaic virus strain prevailing in China. Arch Virol, 2010. 155: 293–295
231.Wei T Y, Yang J G, Liao F L, Gao F L, Lu L M, Zhang X T, Li F, Wu Z J, Lin Q Y, Xie L H, Lin H X. Genetic diversity and population structure of rice stripe virus in China. J Gen Virol, 2009. 90: 1025–1034
232.Weiller G F. Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol, 1998. 15: 326–335
233.White K A, Morris T J. Defective and defective interfering RNAs of monopartite plus-strand RNA plant viruses. Curr Top Microbiol Immunol, 1999. 239: 1–17
234.White K A, Morris T J. RNA determinants of junction site selection in RNA virus recom binants and defective interfering RNAs. RNA, 1995. 1(10): 1029–1040
235.White K A, Nagy P D. Advances in the molecular biology of tombusviruses: gene expression, genome replication, and recombination. Prog Nucleic Acid Res Mol Biol, 2004. 78: 187–226
236.William R, Pearson, Robins G, Zhang T. Generalized Neighbor-Joining: More Reliable Phylogenetic Tree Reconstruction. Mol Biol Evol, 1999. 16(6): 806–816
237.Worobey M, Holmes E C. Evolutionary aspects of recombination in RNA viruses. J Gen Virol, 1999. 80(10): 2535–2543
238.Yang Z, Bielawski J P. Statistical methods for detecting molecular adaptation. Trends Ecol Evol, 2000. 15: 496–503
239.Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol, 2002. 19: 908–917
240.Yang Z, Wong W S W, Nielsen R. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol, 2005. 22: 1107–1118
241.Yang Z. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007. 24: 1586–1591
242.Yu X Q, Lan Y F, Wang H Y, Liu J L, Zhu X P, Valkonen J P T, Li X D.The complete genomic sequence of Tobacco vein banding mosaic virus and its similarities with other potyviruses. Virus Genes, 2007. 35: 801–806
243.Yu X Q, Lan Y, Wang H, Liu J, Zhu X, Valkonen J, Li X D. The complete genomic sequence of Tobacco vein banding mosaic virus and its similarities with other potyviruses. Virus Genes, 2007. 35: 801–806
244.Yu X Q, Wang H Y, Lan Y F, Zhu X P, Li X D, Fan Z F, Li H F, Wang Y Y. J Phytopathol. 2008, 156: 346–351
245.Zimmern. Evolution of RNA viruses. In: Domingo JJHE, Ahlquist P (eds) RNA genetics, vol II CRC, Boca Raton, 1988. pp 211–240
2.陈瑞泰,韩晓东,史万华,李林森,刘保安,张文丽.五省烟区烟草病毒类型的初步研究.中国烟草科学, 1986.1–4
3.陈瑞泰,朱贤朝.全国16个主产烟省(区)烟草侵染性病害调研报告.中国烟草科学, 1997. (l):34-35
4.陈秀斋,温亮,魏代福,高瑞,袁从阳,李向东.蒙阴烟草病毒种类检测.山东农业科学, 2009. (10): 62–63
5.关国经,高乔婉,范怀忠.贵州省烤烟花叶病主要病毒种类的初步鉴定.华南农学院学报, 1982. 3(4): 64–71
6.郭兴启,朱汉城,吕士恩,王智法,陈瑞泰.酶标记羊抗兔间接法检测烟草马铃薯Y病毒的研究.中国烟草学报, 1998. 4: 38–42
7.韩晓东,陈瑞泰,姜仁杰,石金开,张文丽,陈作义,郑巧兮,沈菊英,朱本明. CMV和PVY复合感染引起的烟草叶脉坏死病.生物化学与生物物理学报, 1983. 15: 279–282
8.纪玲玲.烟草脉带花叶病毒CP基因的原核表达及免疫金标试纸条的研制.硕士学位论文,西北农林科技大学, 2008
9.兰玉菲,刘金亮,高瑞,王红艳,朱天生,竺晓平,李向东.烟草脉带花叶病毒cp基因的原核表达及抗血清制备.植物病理学报, 2007. 37 (5): 461–466
10.李慧琴,冯崇川.陕西省烟草侵染性病害发生种类与分布危害调查研究.西北农业学报, 1994. 3(4): 27–31
11.李向东,李义强,高宝昌,耿建国,王洪刚,王维超,郑全立.河南省郏县襄城两地烟草病毒病大发生的原因及对策.中国烟草学报, 2001. 7: 23–26.
12.李向东,刘金亮,李文法,范在丰,李怀方,王洪刚.潍坊萝卜红心病病原鉴定,植物病理学报, 2005. 35(1): 13–18
13.马占鸿,李怀方,裘维蕃.玉米种子携带MDMV的生物和免疫检测.植物病毒与病毒病防治研究, 1997. (1): 97–102
14.施曼玲,李桂新,陶小荣.芜菁花叶病毒温州分离物HC–Pro基因序列分析.微生物学通报, 2002. 29(1): 26–30
15.施曼玲,周雪平.芜菁花叶病毒两分离物的CP基因及HC-Pro基因的比较.浙江大学学报(农业与生命科学版), 2005. 31(6): 689–693
16.施曼玲.芜菁花叶病毒分离物NBXC的CP和HC-Pro基因克隆与序列分析.科技通报, 2007. 23(1): 41–45
17.宋云枝,李玲玲,朱常香,温孚江,温孚凯.芜菁花叶病毒山东分离物外壳蛋白基因的克隆及序列分析.中国农业科学, 2005. 38(3): 504–510
18.王劲波,王凤龙,钱玉梅,时焦,王从丽,杨德廉,胡明珠,张友诚,刘彩萍.山东烟区主要病毒的株系鉴定中国烟草学报, 1998. 4(1): 24–32
19.王智法,严敦余,张广民,刘开启,陈瑞泰.山东省烟草病毒类型鉴定.山东农业大学学报, 1986. 17: 75–82
20.吴元华.我国烟草上马铃薯Y病毒3个新株系研究.辽宁省首届青年学术年会论文集.东北工学院出版社, 1992. 98–102
21.谢成颂,刘延荣,王智法,张修国.用血清学方法检测山东烟草病毒病流行趋势.中国烟草科学, 1993. 4: 1–5
22.于晓庆.马铃薯X病毒和烟草脉带花叶病毒的分子变异及协生作用.博士学位论文,山东农业大学, 2008
23.张仲恺,李毅.云南植物病毒.科学出版社,北京, 2001. 46–49
24.赵建邦,高林,宋佳.一种基于代谢路径构建系统发生树的有效方法.电子学报, 2009. 37(8): 1633–1638
25.朱贤朝,王彦亭,王智发.中国烟草病害.中国农业出版社, 2002. 191–259
26. Aaziz R, Tepfer M. Recombination in RNA viruses and in virus-resistant transgenic plants. J Gen Virol, 1999. 80(6): 1339–1346
27. Adair T L, Kearney C M. Recombination between a 3-kilobase tobacco mosaic virus transgene and a homologous viral construct in the restoration of viral and nonviral genes. Arch Virol, 2000. 145(9): 1867–1883
28. Adams M J, Antoniw J F. DPVweb: a comprehensive database of plant and fungal virus genes and genomes. Nucleic Acids Res, 2006. 34: D382–D385
29. Alabi O J, Martin R R, Naidu R A. Sequence diversity, population genetics and potential recombination events in grapevine rupestris stem pitting-associated virus in Pacific North-West vineyards. J Gen Virol, 2010. 91: 265–276
30. Alejska M, Kurzyniska-Kokorniak A, Broda M, Kierzek R, Figlerowicz M. How RNA viruses exchange their genetic material. Acta Biochim Pol, 2001. 48(2): 391–407
31. Aleman Verdaguer M E, Goudou U C, Dubern J, Beachy R N, Fauquet C. Analysis of the sequence diversity of the P1, HC, P3, Nlb and CP genomic regions of several yam mosaic potyvirus isolates: implications for the intraspecies molecular diversity of potyviruses. Gen Virol, 1997. 78(6): 1253–1264
32. Aranda M A, Fraile A, Dopazo J, Malpica J M. Contribution of mutation and RNA recombination to the evolution of a plant pathogenic RNA. J Mol Evol, 1997. 44: 81–88
33. Arboleda M, Azzam O. Inter- and intra-site genetic diversity of natural field populations of rice tungro bacilliform virus in the Philippines. Arch Virol, 2000. 145: 275–289
34. Ayme V, Petit-Pierre J, Souche S, Palloix A, Moury B. Molecular dissection of the potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper. J Gen Virol, 2007. 88: 1594–1601
35. Baratova L A, Efimov A V, Dobrov E N, Fedorova N V, Hunt B, Badun G A, Ksenofontov A L, Torrance L, J?rvekülg L. In situ spatial organization of potato virus A coat protein subunits as assessed by tritium bombardment. J Virol, 2001. 75: 9696–9702
36. Barker H, McGeachy K D, Toplak N, Gruden K, Zel J, Browning I. Comparison of genome sequence of PVY isolates with biological properties. Am J Potato Res, 2009. 86: 227–238
37. Bass B L. RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem, 2002. 71(1): 817–846
38. Blanco-Urgoiti B, Sánchez F, Pérez de San Román C, Dopazo J, Ponz F. Potato virus Y group C isolates are a homogeneous pathotype but two different genetic strains. J Gen Virol, 1998a. 79: 2037–2042
39. Boni M F, Posada D, Feldman M W. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics, 2007. 176: 1035–1047
40. Bonnet J, Fraile A, Sacristan S, Malpica J M, Garcia-Arenal F. Role of recombination in the evolution of natural populations of Cucumber mosaic virus, a tripartite RNA plant virus. Virology, 2005. 332 (1): 359–368
41. Boonham N, Walsh K, Hims M, Preston S, North J, Barker I. Biological and sequence comparisons of Potato virus Y isolates associated with potato tuber necrotic ringspot disease. Plant Pathol, 2002. 51: 117–126
42. Bousalem M, Douzery E J P, Fargette D. High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution. J Gen Virol, 2004. 81: 243–255
43. Browning I, Charlet K, Chrzanowska M, Dedic P, Kerlan C, Kryszczuk A, Schubert J, Varveri C, Werkman A, Wolf I. What is PVYNTN? The reaction of potato cultivars to inoculation with a range of PVY isolates. In: Abstracts 12th EAPR Virology Section Meeting, Rennes, France, 2004. 48–50
44. Brunt A, Crabtree K, Dallwitz M, Gibbs A, Watson L. Viruses of Plants: Descriptions and Lists from the VIDE Database. CAB International, Wallingford, UK, 1996
45. Bujarski J J, Kaesberg P. Genetic recombination between RNA components of a multipartite plant virus. Nature, 1986. 321(6069): 528–531
46. Bujarski J J, Nagy P D, Flasinski S. Molecular studies of genetic RNA-RNA recombination in brome mosaic virus. Adv Virus Res, 1994. 43: 275–302
47. Cerovska N, Moravec T, FiligarováM, Petrzik K. Nucleotide sequences of 5′- temrinal parts of coat protein genes of various isolates of NTN strain of potato virus Y. Acta Viorl, 2001. 45(l): 55–59
48. Chang B Y, Huang C R, Yeh S D, Chiang J K, Hung L M, Hu H Y. Nucleotide-sequence of the coat protein-coding region of the potyvirus Tobacco vein-banding mosaic virus. Arch Virol, 1994. 138: 17–25
49. Chare E R, Holmes E C. A phylogenetic survey of recombination frequency in plant RNA viruses. Arch Virol, 2006. 151: 933–946
50. Chen J, Chen J P, Adams M J. Variation between Turnip mosaic virus isolates in Zhejiang Province, China and evidence for recombination. J Phytopathol, 2002. 150: 142–145
51. Cheng C P, Nagy P D. Mechanism of RNA recombination in carmo- and tombusviruses: evidence for template switching by the RNA-dependent RNA polymerase in vitro. J Virol, 2003. 77(22): 12033–12047
52. Chetverin A B, Chetverina H V, Demidenko A A, Ugarov V I. Nonhomologous RNA recombination in a cell-free system: evidence for a transesterification mechanism guided by secondary structure. Cell, 1997. 88(4): 503–513
53. Chikh Ali M C, Maoka T, Natsuaki K T. Whole genome sequence and characterization of a novel isolate of PVY inducing tuber necrotic ringspot in potato and leaf mosaic in tobacco. J Phytopathol, 2008. 155: 409–415
54. Chin W T. A survey of tobacco mosaic viruses in central Taiwan. J Agric Ass China, 1966. 55: 85–88
55. Chrzanowska M. Differentiation of Potato virus Y (PVY) isolates. Phytopathol Polon, 1994. 8: 15–20
56. Chrzanowska M. New isolates of the necrotic strain of potato virus Y (PVYN) found recently in Poland. Potato Res, 1991. 34: 179–182
57. Chung B Y W, Miller W A, Atkins J F, Firth A E. An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA, 2008. 105, 5897–5902
58. De Bokx J A. Waardplanten van het aardappel-YN-virus [Host plants of the potato virus YN (Tobacco veinal necrosis virus). Eur J Plant Pathol, 1961. 67: 273–277
59. Dean C E, Clark F. Vein-banding on tobacco in North Florida. Plant Dis Rep, 1968. 52: 887–889
60. Domingo-Calap P, Jose′M C, Sanjua′n R. The fitness effects of random mutations in single-stranded DNA and RNA Bacteriophages. Plos Genetics, 2009. 5(11): 1–7
61. Drake J W, Charlesworth B, Charlesworth D, Crow J F. Rates of spontaneous mutation. Genetics, 1998. 148: 1667–1686
62. Drake J W, Holland J J. Mutation rates among RNA viruses. Proc Natl Acad Sci USA, 1999. 96: 13910–13913
63. Drake J W. Rates of spontaneous mutation among RNA viruses. Proc Natl Acad Sci USA, 1993. 90:4171–4175
64. Esfandiari N, Kohi-Habibi M, Hohn T, Pooggin M M. Complete genome sequence of an Iranian isolate of Potato virus X from the legume plant Pisum sativum. Virus Genes, 2009. 39: 141–145
65. Excoffier L. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol. 2004. 13: 853–864
66. Fajolu O L, Wen R H, Windham A S, Windham M T, Moulton J K, Hajimorad M R. Genetic variability and phylogenetic analysis of hosta virus X. Arch Virol, 2009. 154: 1909–1916
67. Falk B W, Bruening G. Will transgenic crops generate new viruses and new diseases?. Science, 1994. 263(5152):1395–1396
68. Fan Z, Chen H, Cai S, Deng C, Wang W, Liang X, Li H. Molecular characterization of a distinct potyvirus from whitegrass in China. Arch Virol, 2003. 148: 1219–1224
69. Fauquet C M, Mayo M A, Maniloff J, Desselberger U, Ball L A. Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, CA. 2005
70. Fellers J P, Tremblay D, Handest M F, Lommel S A. The Potato virus Y MSNR NIb-replicase is the elicitor of a veinal necrosis-hypersensitive response in root knot nematode resistant tobacco. Mol Plant Pathol, 2002. 3: 145–152
71. Fields B N, Joklik W K. Isolation and preliminary genetic and biochemical characterization of temperature-sensitive mutants of reovirus. Virology, 1969. 37: 335–342
72. Fraile A, Alonso-Prados J L, Aranda M A, Bernal J J, Malpica J M, García-Arenal F. Genetic exchange by recombination or reassortment is infrequent in natural populations of a tripartite RNA plant virus. J Virol, 1997. 71: 934–940
73. Fraile A, Escriu F, Aranda M A, Malpica J M, Gibbs A J, García-Arenal F. A century of tobamovirus evolution in an Australian population of Nicotiana glauca. J Virol, 1997. 71: 8316–8320
74. Frenkel M J, Ward C W, Shukla D D. The use of 3′noncoding nucleotide sequence in the taxonomy of potyviruses: application to water melon mosaic virus and soybean mosaic virus. J Gen Virol, 1989. 70: 2775–2783
75. Froissart R, Roze D, Uzest M, Galibert L, Blanc S, Michalakis Y. Recombination every day: abundant recombination in a virus during a single multi-cellular host infection. PLoS Biol, 2005. 3(3): 389–395
76. Fu Y X, Li W H. Statistical tests of neutrality of mutations. Genetics, 1993. 133: 693–709
77. Gagarinova A G, Babu M, Str?mvik M V, Wang A. Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes. Virol J, 2008. 5 (143): 1–8
78. Garcia-Arenal F, Fraile A, Malpica J M. Variation and evolution of plant virus populations. Int Microbiol, 2003. 6(4): 225–232
79. García-Arenal F, Fraile A, Malpica J M. Variability and genetic structure of plant virus populations. Annu Rev Phytopathol, 2001b. 39: 157–186
80. Gibbs M J, Armstrong J S, Gibbs A J. Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics, 2000. 16: 573–582
81. Gierer A, Mundry K W. Production of mutants of tobacco mosaic virus by chemical alteration of its ribonucleic acid in vitro. Nature, 1958. 182 (4647): 1457–1458
82. Glais L, Kerlan C, Tribodet M, Tordo V M J, Robaglia C, Astier-Manifacier S. Molecular characterization of Potato virus YN isolates by PCR-RFLP. Eur J Plant Pathol, 1996. 102: 655–662
83. Glais L, Tribdet M, Kerlan C. Genomic variability in Potato potyviurs Y (PVY): evidence that PVYNW and PVYNTN variants are single to multiple recombinants between PVYO and PVYN isolates. Arch Virol, 2002. 147: 363–378
84. Glais L, Tribodet M, Gauthier J P, Manifacier S A, Robaglia C, Kerlan C. RFLP mappingof the whole genome of ten viral isolates representative of different biological groups of potato virus Y. Arch Virol, 1998. 143: 2077–2091
85. Glasa M, Palkovics L, Kominek P, Labonne G, Pittnerova S, Kudela O, Candresse T, Subr Z. Geographically and temporally distant natural recombinant isolates of Plum pox virus (PPV) are genetically very similar and form a unique PPV subgroup. J Gen Virol, 2004. 85: 2671–2681
86. Gooding G V, Tolin S A. Strains of potato virus Y affecting flue-cured tobacco in the southeastern United States. Plant Dis Rep, 1973. 57: 200–204
87. Gooding G V. Relationship between strains of potato virus Y and breeding for resistance, cross protection, and interference. Tobacco Sci, 1985. 29: 99–104
88. Grant W S, Bowen B W. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered, 1998. 89: 415–426
89. Gray S M, Lampert E P. Relationship between inoculum density and vector phenology on the incidence of potato virus Y in tobacco. Ann Appl Biol, 1988. 112:303–312
90. Greene A E, Allison R F. Recombination between viral RNA and transgenic plant transcripts. Science, 1994. 263(5152):1423–1425
91. Guan H, Simon A E. Polymerization of nontemplate bases before transcription initiation at the 3′ends of templates by an RNA-dependent RNA polymerase: an activity involved in 3′end repair of viral RNAs. Proc Natl Acad Sci USA, 2000. 97(23):12451–12456
92. Habera L F, Berger P H, Reddick B B. Molecular evidence from 3′-terminus sequence-analysis that Tobacco vein-banding mosaic virus is a distinct member of the Potyvirus group. Arch Virol, 1994. 138: 27–38
93. Harpending H, Rogers A. Genetic perspectives on human origins and differentiation. Annual Review of Genomics Human. Genetics, 2000. 1: 361–385
94. Hema M, Gopinath K, Kao C. Repair of the tRNA-like CCA sequence in a multipartite positive-strand RNA virus. J Virol, 2005. 79(3):1417–1427
95. Hewitt G M. Some genetic consequences of ice ages, and their role in divergence and speciation. Biol J of Linn Soc, 1996. 58(3): 247–276
96. Hewitt G M. Speciation, hybrid zones and phylogeography or seeing genes in space and time. Mol Ecol, 2001. 10: 537–549
97. Hillman B I, Carrington J C, Morris J. A defective interfering RNA that contains a mosaic of a plant virus genome. Cell, 1987. 51(3): 427–433
98. Hong X Y, Chen J, Shi Y H, Chen J P. The‘6K1’protein of a strain of Soybean mosaicvirus localizes to the cell periphery. Arch Virol, 2007. 152: 1547–1551
99. Hu X J, Meachama T, Ewing L, Gray S M, Karasev A V. A novel recombinant strain of Potato virus Y suggests a new viral genetic determinant of vein necrosis in tobacco. Virus Research, 2009c. 143: 68–76
100.Hu X, He C, Xiao Y, Xiong X, Nie X. Molecular characterization and detection of recombinant isolates of potato virus Y from China. Arch. Virol, 2009a. 154: 1303–1312
101.Hu X, Karasev A V, Brown C J, Lorenzen J H. Sequence characteristics of potato virus Y recombinants. J Gen Virol, 2009b. 90: 3033–3041
102.Hudson R R, Boos D D, Kaplan N L. A statistical test for detecting geographic subdivision. Mol Biol Evol, 1992. 9:138–151
103.Hudson R R. A new statistic for detecting genetic differentiation. Genetics, 2000. 155: 2011–2014
104.Huisman M J, Linthorst H J M, Bol J F, Cornelissen B J C. The complete nucleotide sequence of potato virus X and its homologies at the amino acid level with various plus-stranded RNA viruses. J Gen Virol, 1988. 69: 1789–1798
105.James H S, Strauss E G. Evolution of RNA viruses. Ann Rev Microbiol, 1988. 42(6): 57–83
106.Jenner C E, Tomimura K, Ohshima K, Hughes S L, Walsh J A. Mutations in Turnip mosaic virus P3 and cylindrical inclusion proteins are separately required to overcome two Brassica napus resistance genes. Virology, 2002. 300(1): 50–59
107.Jenner C E, Wang X, Ponz F, Walsh J A. A fitness cost for Turnip mosaic_virus to overcome host resistance. Virus research, 2002. 86: 1–6
108.Jenner C E, Walsh J A. Pathotypic variation in turnip mosaic virus with special reference to European isolates. Plant pathology, 1996. 45:848–856
109.Johansen E, Edwards M C, Hampton R O. Seed transmission of viruses: Current perspectives. Annu Rev Phytopathol, 1994. 32: 363–386
110.Jones R A C. Strain group specific and virus specific hypersensitive reactions to infection with potyvirus in potato cultivars. Ann Appl Biol, 1990. 117: 93–105
111.Jones R, Kumar S, Mackie A. Potato virus Y. Department of agriculture Factsheet, 2003. 2: 1443–7783
112.Kagiwada S, Yamaji Y, Nakabayashi H, Ugaki M, Namba S. The complete nucleotide sequence of Potato virus X strain OS: the first complete sequence of a Japanese isolate. J Gen Plant Pathol, 2002. 68, 94–98
113.Kavanagh T, Goulden M, Cruz S S, Chapman S, Barker I, Baulcombe D. Molecularanalysis of a resistance-breaking strain of potato virus X. Virology, 1992. 189: 609–617
114.Kerlan C, Tribodet M, Glais L, Guillet M. Variability of potato virus Y in potato crops in France. J. Phytopathol, 1999. 147: 643–651
115.Kim M J, Kao C. Factors regulating template switch in vitro by viral RNA dependent RNA polymerases: implications for RNA-RNA recombination. Proc Natl Acad Sci USA, 2001. 98(9): 4972–4977
116.Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol, 1980. 16, 111–120
117.Kimura M. Evolution rate at the molecular level. Nature, 1968. 217:624–626
118.Kimura M. The neutral theory of molecular evolution. Cambridge: Cambridge university press.1983
119.Komatsu K, Kagiwada S, Takahashi S, Mori T, Yamaji Y, Hirata H, Ozeki J, Yoshida A, Suzuki M, Ugaki M, Nambe S. Phylogenetic characteristics, genomic heterogeneity and symptomatic variation of five closely related Japanese strains of Potato virus X. Virus Genes, 2005. 31, 99–105
120.Kumar S, Tamura K, Jakobsen I B. MEGA2: molecular evolutionary genetics analysis sofeware. Bioinformatics Applications note, 2001. 17: 1244–1245
121.Kumar S, Tamura K, Nei M. MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform, 2004. 5: 150–163
122.Lai M M. RNA recombination in animal and plant viruses. Microbiol Rev, 1992. 56 (1): 61–79
123.Lapp N A, Gooding G V. Occurrence and sources of inoculums of potato virus Y in tobacco in North Carolina. Plant Dis Rep, 1976. 60:1014–1016
124.Latorre B A, Pe?aloza E, Escaffi O. A severe outbreak of potato virus Y in Chilean tobacco. Plant Dis, 1982. 66: 893–895
125.Le Romancer M, Kerlan C, Nedellec M. Biological characterization of various geographical isolates of potato virus Y inducing superficial necrosis on potato tubers. Plant Pathol, 1994. 43: 138–144
126.Li N, Wang X, Zhou G, Dong J. Molecular variability of the coat protein gene of Potato virus Y from tobacco in China. Acta Virol, 2006. 50:107–113
127.Li W H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol, 1993. 36: 96–99.
128.Li W H. Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics, 1977: 85:331–337
129.Li W H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J Mol Evol, 1993. 36: 96–99
130.Lin H X, Rubio L, Smythe A B, Falk B W. Molecular population genetics of Cucumber Mosaic Virus in California: evidence for founder effects and reassortment. J Virol, 2004. 78: 6666–6675
131.Ling K S, Zhu H Y, Petrovic N, Gonsalves D. Serological detection of Grapevine leafroll virus 2 using an antiserum developed against the recombinant coat protein. J. Phytopathol, 2007. 155: 65–69.
132.Liu Y Y, Yu S L, Lan Y F, Zhang C L, Hou S S, Li X D, Chen X Z, Zhu X P. Molecular variability of five Cucumber mosaic virus isolates from China. Acta Virol, 2009. 53: 89–97
133.Lockhart B E L, Fischer H U. A disease of tobacco in morocco caused by a veinal necrosis isolate of Potato virus Y. Plant Dis Rep, 1976. 60: 114–116
134.Lorenzen J H, Meacham T, Berger P H, Shiel P J, Crosslin J M, Hamm P B, Kopp H. Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada. Arch. Virol, 2006. 151: 1055–1074
135.Lutcke H A, Chow K C, Mickel F S, Moss K A, Kern H F, Scheele G A. Selection of AUG initiation codon differs in plants and animals. EMBO J, 1987. 6: 43–48
136.Makino S, Keck J G, Stohlman S A, Lai M M. High-Frequency RNA Recombination of Murine Coronaviruses. J Virol, 1986. 57(3): 729–737
137.Malcuit I, Jong D W, Baulcombe D C, Shields D C, Kavanagh T A. Acquisition of multiple virulence/avirulence determinants by potato virus X (PVX) has occurred through convergent evolution rather than through recombination. Virus Genes, 2000. 20: 165–172
138.Martin D P, Williamson C, Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics, 2005. 21: 260–262
139.Martín S, Sambade A, Rubio L, Vives M C, Moya P, Guerri J, Elena S F, Moreno P. Contribution of recombination and selection to molecular evolution of Citrus tristeza virus. J Gen Virol, 2009. 90: 1527–1538
140.Mayo M A, Robinson D J, Jolly C A, Hyman L. Nucleotide Sequence of Potato Leafroll Luteovirus RNA. J Gen Virol, 1989. 70: 1037–1051
141.McDonald J G, Kristjansson G T. New diseases and epidemics properties of strains of potato virus YN in North America. Plant Dis, 1993. 77: 87–89
142.Mih A M, Atiri G I, Rossel H W. Strain-typing of potato virus Y isolates from potato inNigeria by infectivity tests and ELISA. Afr Crop Sci J, 1995. 3: 99–104
143.Moonan F, Molina J, Mirkov T E. Sugarcane Yellow Leaf Virus: An Emerging Virus That Has Evolved by Recombination between Luteoviral and Poleroviral Ancestors. Virology, 2000. 269(1): 156–171
144.Moreno I M, Malpica J M, Díaz-Pendón J A, Moriones E, FraileA, García-Arenal F. Variability and genetic structure of the population of watermelon mosaic virus infecting melon in Spain. Virology, 2004. 318: 451–460
145.Moret B M, Roshan U, Warnow T. Sequence length requirements for phylogenetic methods. In: Proc 2nd Int'l Workshop Algs in Bioinformatics, 2002. 2452: 343–356
146.Morozov S Y, Solovyev A G. Triple gene block: modular design of a multifunctional machine for plant virus movement. J Gen Virol. 2003: 84: 1351–1366
147.Moury B, Morel C, Johansen E, Jacquemond M. Evidence for diversifying selection in Potato virus Y and in the coat protein of other potyviruses. J Gen Virol, 2002. 83: 2563–2573
148.Nagy P D, Simon A E. New insights into the mechanisms of RNA recombination. Virology, 1997. 235 (1): 1–9
149.Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol, 1986. 3: 18–426
150.Nei M, Kumar S. Molecular Evolution and Phylogenetics. Oxford University Press, New York, USA, 2000
151.Nie X, Singh R P. Specific differentiation of recombinant PVYN:O and PVYNTN strains by multiplex RT-PCR. J Virol Methods, 2003a. 113: 69–77
152.Nie X, Singh R P, Singh M. Molecular and pathological characterization of N:O isolates of the Potato virus Y from Manitoba, Canada. Can J Plant Pathol, 2004. 26: 573–583
153.Nie X, Singh R P. Evolution of North American PVYNTN strain Tu 660 from local PVYN by mutation rather than recombination. Virus Genes, 2003b. 26 (1): 39–47
154.Nie X, Singh R P. Probable geographical grouping of PVYN and PVYNTN based on sequence variation in P1 and 5′-UTR of PVY genome and methods for differentiating North American PVYNTN. J Virol Methods, 2002. 103(2): 145–156
155.Noguchi S, Tajima T, Yamamoto Y, Ohno T, Kubo T. Deletion of a large genomic segment in tobacco varieties that are resistant to potato virus Y (PVY). Mol Gen Genet, 1999. 262: 822–829
156.Ogawa T, Tomitaka Y, Nakagawa A, Ohshima K. Genetic structure of a population of Potato virus Y inducing potato tuber necrotic ringspot disease in Japan; comparison withNorth American and European populations. Virus Res, 2008. 131: 199–212
157.Ohshima K, Tomimura Y, Wood J T, Minematsu Y, Kajiyama H, Tomimura K, Gibbs A J. Patterns of recombination in Turnip mosaic virus genomic sequences indicate hotspots of recombination. J Gen Virol, 2007, 88: 298–315
158.Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh J A, Fletcher J, Chen J, Gera A, Gibbs A. Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol, 2002. 83:1511–1521
159.Ohta T, Kimura M. Behavior of neutral mutants influenced by associated overdominant loci in finite populations. Genetics, 1971. 69: 247–260
160.Orman B E, Celnik R M, Mandel A M, Torres H N, Mentaberry A N. Complete cDNA sequence of a South American isolate of potato virus X. Virus Res, 1990. 16(3): 293–305
161.Page R D M, Holmes E C. Molecular evolution: a phylogenetic approach. Blackwell Science Ltd, a Blackwell publishing company, 1998. 1–7
162.Pamilo P, Bianchi N O. Evolution of the Zfx and Zfy genes: rates and interdependence between the genes. Mol Biol Evol, 1993. 10: 271–281
163.Pennington R E, Melcher U. In planta deletion of DNA inserts from the large intergenic region of Califlower mosaic virus DNA. Virology, 1993. 192: 188–196
164.Piche L M, Singh R P, Nie X, Gudmestad N C. Diversity among Potato virus Y isolates obtained from potatoes grown in the United States. Phytopathology, 2004. 94: 1368–1375
165.Pilar D C, Jose′M C, Sanjua′n R. The Fitness Effects of Random Mutations in Single-Stranded DNA and RNA Bacteriophages. Plos genet, 2009: 5 (11): 1–7
166.Plisson C, Drucker M, Blanc S, German-Retana S, Le Gall O, Thomas D, Bron P. Structural characterization of HC-Pro, a plant virus multifunctional protein. J Biol Chem, 2003. 278: 23753–23761
167.Posada D, Crandall K A. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA, 2001. 98: 13757–13762
168.Pringle C R. Genetic characteristics of conditional lethal mutants of vesicular stomatitis virus induced by 5-fluorouracil, 5-azacytidine, and ethyl methane sulfonate. J Virol, 1970. 5(5): 559–567
169.Rao A L, Hall T C. Recombination and polymerase error facilitate restoration of infectivity in brome mosaic virus. J Virol, 1993. 67(2): 969–979
170.Ramos J D A, Teo S M A, Ou K L, Tsai L C, Lee B W, Cheong N, Chua K Y. Comparative allergenicity studies of native and recombinant Blomia ttropicalisparamyosin (Blot 11). Allergy, 2003. 58(5): 412–419
171.Reddick B B, Collins-Shepard M H, Christie R G, Gooding G V. A new virus-disease in North-America caused by Tobacco vein-banding mosaic virus. Plant Dis, 1992. 76: 856–859
172.Revers F, Gall O L, Candresse T, Romancer M L, Dunez J. Frequent occurrence of recombinant potyvirus isolates. J Gen Virol, 1996. 77: 1953–1965
173.Riechmann J L, Lain S, García J A. Highlights and prospects of potyvirus molecular biology. J Gen Virol, 1992. 73: 1–16
174.Rochon D M. Rapid de novo generation of defective interfering RNA by cucumber necrosis virus mutants that do not express the 20-kDa nonstructural protein. Proc Natl Acad Sci USA, 1991. 88(24): 11153–11157
175.Rogers A R, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biological Evology, 1992. 9: 552–569
176.Romero A, Blanco-Urgoiti B, Soto M J, Fereres A, Ponz F. Characterization of typical pepper-isolates of PVY reveals multiple pathotypes within a single genetic strain. Virus Res, 2001. 79: 71–80
177.Roossinck M J. Evolutionary History of Cucumber Mosaic Virus deduced by phylogenetic analyses. J Virol, 2002. 76(7): 3382–3387
178.Roossinck M J. Mechanisms of plant virus evolution. Annual Review of Phytopathology 1997. 35: 191–209
179.Roossinck M J. Plant RNA virus evolution. Curr Opin Microbiol, 2003. 6(4): 406–409
180.Rozas J, Sanchez-DelBarrio J C, Messeguer X, Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 2003. 19: 2496–2497
181.Rubio L, Ayllon M A, Kong P, Fernandez A, Polek M, Guerri J, Moreno P, Falk B W. Genetic variation of Citrus tristeza virus isolates from California and Spain: evidence for mixed infections and recombination. J Virol, 2001. 75(17): 8054–8062
182.Saitou N, Nei M. The Neighbor-joining Method: A New Method for reconstructing phylogenetic trees. Mol Biol Evol, 1987. 4(4): 406–425
183.Sako N, Ogata K. Different helper factors associated with aphid transmission of some potyviurses. Viorlogy, 1981. 112: 762–765
184.Salminen M O, Carr J K, Burke D S, McCutchan F E. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by Bootscanning. AIDS Res Hum Retrov, 1995. 11: 1423–1425
185.Sawyer S A. Geneconv: a computer package for the statistical detection of geneconversion. Distributed by the Author. Department of Mathematics. Washington University in St. Louis, available at http://www.math.wustl.edu/~sawyer, 1999
186.Schalk H J, Matzeit V, Schiller B, Schell J, Gronenborn B. Wheat dwarf virus, a geminivirus of graminaceous plants needs splicing for replication. EMBO J, 1989. 8 (2): 359–364
187.Schneider S, Excoffier L. Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites.: Application to human mitochondrial DNA. Genetics, 1999. 152: 1079–1089
188.Scholthof H, Wu F C, Richins R D, Shepherd R J. A naturally occurring deletion mutant of Figwort mosaic virus (caulimovirus) is generated by RNA splicing. Virology, 1991. 184: 290–298
189.Schubert J, Fomitcheva V, Sztangret–Wisniewska J. Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers. J Virol Methods, 2007. 140: 66–74
190.Seo J K, Ohshima K, Lee H G, Son M, Choi H S, Lee S H, Sohn S H, Kim K H. Molecular variability and genetic structure of the population of Soybean mosaic virus based on the analysis of complete genome sequences. Virology, 2009. 393: 91–103
191.Shukla D D, Strike P M, Tracy S L, Gough K H, Ward C W. The N and C termini of the coat protein of potyviruses are surface-located and N terminus contains the major virus-specific epitopes. J Gen Virol, 1988. 69: 1497–1508
192.Shukla D D, Ward C W. Identifiecation and classification of potyviurses on the basis of coat protein sequence data and serology. Arch of Virol, 1989a. 106: 171–200
193.Shukla D D, Ward C W. Structure of potyvirus coat proteins and its action in the taxonomy of the potyvirus group. Advances in Virus Reserch, 1989b. 36: 273–314
194.Shukla D D, Ward C W, Brunt A A. The Potyviridae. Cambridge University Press, Cambridge. 1994
195.Sievert R C. Effect of potato virus Y on cultivars and hybrids of burley tobacco. Phytopathology, 1978. 68: 974–978
196.Sievert R C. Effect of time of inoculation with potato virus Y on yield and quality of burley tobacco. Phytopathology, 1971. 61: 588–589
197.Singh R P. 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. Can Plant Dis Survey, 1992. 72: 113–119
198.Singh R P, Valkonen J P T, Gray S M, Boonham N, Jones R A C, Kerlan C, Schubert J. The naming of Potato virus Y strains infecting potato. Arch Virol, 2008. 153: 1–13
199.Skryabin K G, Kraev A S, Morozov S Y, Rozanov M N, Chernov B K, Lukasheva L I, Atabekov J G. Nucleic Acids Res, 1988. 16: 10929–10930
200.Slatkin M, Hudson R R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populayions. Genetics, 1991. 129: 555–562
201.Smith J M. Analyzing the mosaic structure of genes. J Mol Evol, 1992. 34: 126–129
202.Smith K M. On the composite nature of certain potato virus diseases of the mosaic group as revealed by the use of plant indicators and selective methods of transmission. Proc Royal Soc B, 1931. 109: 251–267
203.Soto M J, Luis Artega M, Fereres A, Ponz F. Limited degree of serological variability in pepper strains of potato virus Y as revealed by analysis with monoclonal antibodies. Ann Appl Biol, 1994. 124: 37–43
204.Stenseth N C, Mysterud A, Ottersen G. Ecological effects of climate fluctuations. Science, 2002. 297: 1292–1296
205.Sudarsono, Woloshuk S L, Xiong Z, Hellmann G M, Wernsman E A, Weissinger A K, Lommel S A. Nucleotide sequence of the capsid protein cistrons from six potato virus Y (PVY) isolates infecting tobacco. Arch Virol, 1993. 132: 161–170
206.Sudhir K, Sudhindra R, Gadagkar. Efficiency of the Neighbor-Joining Method in Reconstructing Deep and Shallow Evolutionary Relationships in Large Phylogenies. J Mol Evol, 2000. 51: 544–553
207.Swanson W J, Yang Z, Wolfner M F, Aquadro C F. Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals. PNAS, 2001. 98: 2509–2514
208.Swofford D L. PAUP*: Phylogenetic analysis using parsimony(*and other methods)4.0 beta. http://paup.csit.fsu.edu/
209.Taberlet P, Fumagalli L, Wust-Saucy A G, Cosson J F. Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol, 1998. 7: 453–464
210.Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 1989. 123: 585–595
211.Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol, 2007. 24(8): 1596–1599
212.Tan Z Y, Wada Y, Chen J, Ohshima K. Inter- and intralineage recombinants are commonin natural populations of Turnip mosaic virus. J Gen Virol, 2004. 85: 2683–2696
213.Tan Z, Gibbs A J, Tomitaka Y, Sánchez F, Ponz F, Ohshima K. Mutation in Turnip mosaic virus genomes that have adapted to Raphanus sativus. J Gen Virol, 2005. 86:501–510
214.Thompson J D, Higgins D G, Gibson T J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res, 1994. 22: 4673–4680
215.Thomson A D, Wright D S C. Incidence and some effects of potato virus Y on New Zealand flue-cured tobacco. New Zealand J Agric Res, 1966. 9: 886–893
216.Tian Y P, Liu J L, Yu X Q, Lei L P, Zhu X P, Valkonen J P T, Li X D. Molecular diversity of tobacco vein banding mosaic virus. Arch Virol, 2007. 152: 1911–1915
217.Tomimura K, Gibbs A J, Jenner C E, Walsh J A, Ohshima K. The phylogeny of Turnip mosaic virus; comparisons of 38 genomic sequences reveal a Eurasian origin and a recent 'emergence' in East Asia. Mol Ecol. 2003. 12: 2099–2111
218.Tomimura K, ?pak J, Katis N, Jenner C E, Walsh J A, Gibbs A J, Ohshima K. Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Euroasia. Virology, 2004, 330: 408–423
219.Tomitaka Y, Ohshima K. A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an‘emergent’lineage in Japan. Mol Ecol, 2006. 15: 4437–4457
220.Tomitaka Y, Yamashita T, Ohshima K. The genetic structure of populations of Turnip mosaic virus in Kyushu and central Honshu, Japan. J Gen Plant Pathol, 2007. 73: 197–208
221.Tordo V M, Chaehulska A M, Fakhfakh H, Romancer M L, Robaglia C, Astier-Manifacier S. Sequence Polymorphism in the 5’NTR and in the P1 coding region of potato virus Y genomic RNA . Gen Virol, 1995. 76(4): 939–949
222.Tribodet M, Glais L, Kerlan C, Jacquot E. Characterization of Potato virus Y (PVY) molecular determinants involved in the vein necrosis symptom induced by PVYN isolates in infected Nicotiana tabacum cv. Xanthi. J Gen Virol, 2005. 86: 2101–2105
223.Valkonen J P T, Slack S A, Plaisted R L. Use of the virus strain group concept to characterize the resistance to PVX and to PVYO in the potato cv. Allegany. Amer Potato J, 1994. 60: 507–516
224.Valli A, López-Myoya J J, García J A. Recombination and gene duplication in the evolutionary diversification of P1 proteins in the family Potyviridae. J Gen Virol, 2007. 88: 1016–1028
225.Van der Vlugt R A, Leunissen J, Goldbach R. Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteinsand 3′nontranslated regions. Arch Virol, 1993. 131: 361–375
226.Van der Vlugt R, Allefs S, DeHaan P T, Goldback R W. Nucleotide sequence of the 3'- terminal region of potato virus Y N RNA. J Gen Virol, 1989. 70: 229–233
227.Verbeek M, Piron P G M, Dullemans A M, Cuperus C, van der Vlugt R A A. Determination of aphid transmission efficiencies for N, NTN and Wilga strains of Potato virus Y. Ann Appl Biol, 2010. 156: 39–49
228.Verchot-Lubicz J. A new cell-to-cell transport model for potexviruses. Mol Plabt Microbe Interact, 2005. 8: 283–290
229.Wang H Y, Liu J L, Gao R, Chen J, Shao Y H, Li X D. Complete genomic sequence analyses of Turnip mosaic virus basal-BR isolates from China. Virus Genes, 2009. 38: 421–428
230.Wang H Y, Zhu T S, Cui T T, Hou S S, Yin X, Li X D, Lei L P, Zhu X P. Complete genome sequence of a tobacco isolate of the tobacco vein banding mosaic virus strain prevailing in China. Arch Virol, 2010. 155: 293–295
231.Wei T Y, Yang J G, Liao F L, Gao F L, Lu L M, Zhang X T, Li F, Wu Z J, Lin Q Y, Xie L H, Lin H X. Genetic diversity and population structure of rice stripe virus in China. J Gen Virol, 2009. 90: 1025–1034
232.Weiller G F. Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol, 1998. 15: 326–335
233.White K A, Morris T J. Defective and defective interfering RNAs of monopartite plus-strand RNA plant viruses. Curr Top Microbiol Immunol, 1999. 239: 1–17
234.White K A, Morris T J. RNA determinants of junction site selection in RNA virus recom binants and defective interfering RNAs. RNA, 1995. 1(10): 1029–1040
235.White K A, Nagy P D. Advances in the molecular biology of tombusviruses: gene expression, genome replication, and recombination. Prog Nucleic Acid Res Mol Biol, 2004. 78: 187–226
236.William R, Pearson, Robins G, Zhang T. Generalized Neighbor-Joining: More Reliable Phylogenetic Tree Reconstruction. Mol Biol Evol, 1999. 16(6): 806–816
237.Worobey M, Holmes E C. Evolutionary aspects of recombination in RNA viruses. J Gen Virol, 1999. 80(10): 2535–2543
238.Yang Z, Bielawski J P. Statistical methods for detecting molecular adaptation. Trends Ecol Evol, 2000. 15: 496–503
239.Yang Z, Nielsen R. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol, 2002. 19: 908–917
240.Yang Z, Wong W S W, Nielsen R. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol, 2005. 22: 1107–1118
241.Yang Z. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007. 24: 1586–1591
242.Yu X Q, Lan Y F, Wang H Y, Liu J L, Zhu X P, Valkonen J P T, Li X D.The complete genomic sequence of Tobacco vein banding mosaic virus and its similarities with other potyviruses. Virus Genes, 2007. 35: 801–806
243.Yu X Q, Lan Y, Wang H, Liu J, Zhu X, Valkonen J, Li X D. The complete genomic sequence of Tobacco vein banding mosaic virus and its similarities with other potyviruses. Virus Genes, 2007. 35: 801–806
244.Yu X Q, Wang H Y, Lan Y F, Zhu X P, Li X D, Fan Z F, Li H F, Wang Y Y. J Phytopathol. 2008, 156: 346–351
245.Zimmern. Evolution of RNA viruses. In: Domingo JJHE, Ahlquist P (eds) RNA genetics, vol II CRC, Boca Raton, 1988. pp 211–240