Scientia Agricultura Sinica ›› 2015, Vol. 48 ›› Issue (2): 270-279.doi: 10.3864/j.issn.0578-1752.2015.02.07

• PLANT PROTECTION • Previous Articles     Next Articles

Complete Genome Analysis of a PVYNTN-NW Recombinant Isolate from Yulin of China

GAO Fang-luan1, CHANG Fei1, SHEN Jian-guo 2, XIE Lian-hui 1, ZHAN Jia-sui1   

  1. 1Institute of Plant Virology, Fujian Agriculture and Forestry University/Key Laboratory of Plant Virology of Fujian Province, Fuzhou 350002
    2Inspection & Quarantine Technology Center of Fujian Entry-Exit Inspection and Quarantine Bureau/Fujian Key Laboratory for Technology Research of Inspection and Quarantine, Fuzhou 350001
  • Received:2014-07-07 Online:2015-01-16 Published:2015-01-16

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Abstract: 【Objective】 Potato virus Y (PVY) is a typical member of the genus Potyvirus in the family Potyviridae. It is one of the most destructive pathogens affecting potato and tobacco and causes significant economic losses worldwide. The objective of this study is to determine the genomic structure of an isolate of PVY from Yulin of China and its phylogenetic relationship with reported PVY strains.【Method】The complete genome of the ShX14 was amplified and sequenced from overlapping fragments using 11 pairs of primers designed from the conserved regions of the known PVY isolates. Genomic structure and recombination events of the isolate were evaluated by various bioinformatics approaches. Phylogenetic tree was reconstructed by maximum likelihood (ML) method using nucleotide sequences of coding regions. In addition, phylogeny-trait association analysis was used to evaluate the relationship between PVY isolate and the reported stains. 【Result】The complete sequence of ShX14 had 9 724 nucleotides, excluding the 3′- terminal poly (A) tail. It contains a single open reading frame of 9 186 nucleotides and encodes a polyprotein of   3 061 amino acids. An additional protein, termed ‘PIPO’, is also translated by +2 nucleotide frame shifting within the P3 cistron. The isolate shares 98%-99% nucleotide identity and 98%-100% amino acid identity with HN2 and SYR-NB-16 (PVYNTN-NW strain, SYR-I genotype), respectively. Similar to the PVYNTN-NW (SYR-I) genomic structure, three recombination breakpoints were identified at nucleotide positions 2 318, 5 674 and 8 385 in the P1, HC-Pro/P3 and the 5′-terminus of CP gene respectively with high confidence. Phylogenetic analysis indicated that ShX14 was clustered together with HN2 and SYR-NB-16, suggesting that it shared high sequence homology with PVYNTN-NW (SYR-I) strain. Association index (AI), parsimony score (PS) and maximum monophyletic clade (MC) all indicated that ShX14 was strongly associated with the PVYNTN-NW (SYR-I) group. Three fragments of about 1 000, 600 and 400 bp in size were also amplified from the isolate by a multiplex RT-PCR, consisting with the expected band of the PVYNTN-NW (SYR-I) strain. Overall, these analyses strongly indicate that ShX14 is likely to be a PVYNTN-NW strain(SYR-I). 【Conclusion】 ShX14 is a N×O recombinant isolate, classified to PVYNTN-NW strain (SYR-I). It will provide useful information in the further study of the biology of this pathogen.

Key words: Potato virus Y, complete genome, recombination, phylogeny, phylogeny-trait association analysis

[1]    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 with North American and European populations. Virus Research, 2008, 131(2): 199-212.
[2]    Hu X, Nie X, He C, Xiong X. Differential pathogenicity of two different recombinant PVYNTN isolates in Physalis floridana is likely determined by the coat protein gene. Virology Journal, 2011, 8: 207.
[3]    高芳銮, 沈建国, 史凤阳, 方治国, 谢联辉, 詹家绥. 中国马铃薯Y病毒的检测及CP基因的分子变异. 中国农业科学, 2013, 46(15): 3125-3133.
Gao F L, Shen J G, Shi F Y, Fang Z G, Xie L H, Zhan J S. Detection and molecular variation of Potato virus Y CP gene in China. Scientia Agricultura Sinica, 2013, 46(15): 3125-3133. (in Chinese)
[4]    Glais L, Tribodet M, Kerlan C. Genomic variability in Potato potyvirus Y (PVY): evidence that PVYNW and PVYNTN variants are single to multiple recombinants between PVYO and PVYN isolates. Archives of Virology, 2002, 147(2): 363-378.
[5]    Nolte P, Whitworth J L, Thornton M K, McIntosh C S. Effect of seedborne Potato virus Y on performance of Russet Burbank, Russet Norkotah, and Shepody potato. Plant Disease, 2004, 88(3): 248-252.
[6]    Whitworth J L, Nolte P, McIntosh C, Davidson R. Effect of Potato virus Y on yield of three potato cultivars grown under different nitrogen levels. Plant Disease, 2006, 90(1): 73-76.
[7]    Rahman M S, Akanda A K. Performance of seed potato produced from sprout cutting, stem cutting and conventional tuber against PVY and PLRV. Bangladesh Journal of Agricultural Research, 2009, 34(4): 609-622.
[8]    罗红香, 李余湘, 刘会忠, 徐明勇, 王林玉, 赵中汇, 何玉安, 李章海, 江彤. 贵州黔南烟草马铃薯Y病毒(PVY)株系的血清学鉴定. 中国烟草科学, 2012, 33(5): 60-62.
Luo H X, Li Y X, Liu H Z, Xu M Y, Wang L Y, Zhao Z H, He Y A, Li Z H, Jiang T. Serological identification of strains of Potato virus Y infecting tobacco derived from qiannan Guizhou province. Chinese Tobacco Science, 2012, 33(5): 60-62. (in Chinese)
[9]    Chung B Y, Miller W A, Atkins J F, Firth A E. An overlapping essential gene in the Potyviridae. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(15): 5897-5902.
[10]   高芳銮, 沈建国, 史凤阳, 常飞, 谢联辉, 詹家绥. 马铃薯Y病毒pipo基因的分子变异及结构特征分析. 遗传, 2013, 35(9): 1125-1134.
Gao F L, Shen J G, Shi F Y, Chang F, Xie L H, Zhan J S. Sequence variation and protein structure of pipo gene in Potato virus Y. HEREDITAS,2013, 35(9): 1125-1134. (in Chinese)
[11]   Singh R P, Valkonen J P, Gray S M, Boonham N, Jones R A, Kerlan C, Schubert J. Discussion paper: The naming of Potato virus Y strains infecting potato. Archives of Virology, 2008, 153(1): 1-13.
[12]   Quenouille J, Vassilakos N, Moury B. Potato virus Y: a major crop pathogen that has provided major insights into the evolution of viral pathogenicity. Molecular Plant Pathology, 2013, 14(5): 439-452.
[13]   Hu X, Karasev A V, Brown C J, Lorenzen J H. Sequence characteristics of Potato virus Y recombinants. Journal of General Virology, 2009, 90(Pt 12): 3033-3041.
[14]   Nie X, Singh R P, Singh M. Molecular and pathological characterization of N:O isolates of the Potato virus Y from Manitoba, Canada. Canadian Journal of Plant Pathology, 2004, 26(4): 573-583.
[15]   Chikh Ali M, Maoka T, Natsuaki T, Natsuaki K T. PVYNTN-NW, a novel recombinant strain of Potato virus Y predominating in potato fields in Syria. Plant Pathology, 2010, 59(1): 31-41.
[16]   Tian Y P, Liu J L, Zhang C L, Liu Y Y, Wang B, Li X D, Guo Z K, Valkonen J P. Genetic diversity of Potato virus Y infecting tobacco crops in China. Phytopathology, 2011, 101(3): 377-387.
[17]   Yang J, Roy A, Zhang Y. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. Nucleic Acids Research, 2013, 41: D1096-D1103.
[18]   Wang B, Jia J L, Wang X Q, Wang Z Y, Yang B H, Li X D, Zhu X P. Molecular characterization of two recombinant Potato virus Y isolates from China. Archives of Virology, 2012, 157(2): 401-403.
[19]   Hu X, He C, Xiao Y, Xiong X, Nie X. Molecular characterization and detection of recombinant isolates of Potato virus Y from China. Archives of Virology, 2009, 154(8): 1303-1312.
[20]   Lole K S, Bollinger R C, Paranjape R S, Gadkari D, Kulkarni S S, Novak N G, Ingersoll R, Sheppard H W, Ray S C. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. Journal of Virology, 1999, 73(1): 152-160.
[21]   Kosakovsky Pond S L, Posada D, Gravenor M B, Woelk C H, Frost S D. GARD: a genetic algorithm for recombination detection. Bioinformatics, 2006, 22(24): 3096-3098.
[22]   Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 2011, 28(10): 2731-2739.
[23]   Nylander J A A. MrModeltest v2.3. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, 2008, https://www. abc.se/~nylander/mrmodeltest2/mrmodeltest2.html.
[24]   Drummond A J, Suchard M A, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 2012, 29(8): 1969-1973.
[25]   Parker J, Rambaut A, Pybus O G. Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infection, Genetics and Evolution, 2008, 8(3): 239-246.
[26]   Chikh Ali M, Maoka T, Natsuaki K T, Natsuaki T. The simultaneous differentiation of Potato virus Y strains including the newly described strain PVYNTN-NW by multiplex PCR assay. Journal of Virological Methods, 2010, 165(1): 15-20.
[27]   Adams M J, Antoniw J F, Fauquet C M. Molecular criteria for genus and species discrimination within the family Potyviridae. Archives of Virology, 2005, 150(3): 459-479.
[28]   黄原. 分子系统发生学. 北京: 科学出版社, 2012: 323-324.
Huang Y. Molecular Phylogenetics. Beijing: Science Press, 2012: 323-324. (in Chinese)
[29] Karasev A V, Hu X, Brown C J, Kerlan C, Nikolaeva O V, Crosslin J M, Gray S M. Genetic diversity of the ordinary strain of Potato virus Y (PVY) and origin of recombinant PVY strains. Phytopathology, 2011, 101(7): 778-785.
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