Abstract
Potato plants that exhibited mosaic symptoms were collected in Xiangxi, Hunan province, China. Multiplex RT-PCR screening for common viruses revealed the presence of potato virus A (PVA) in these samples. ELISA with virus-specific antibodies confirmed infection by PVA in the plants. Rod-shaped virions of ~750 nm in length and ~13 nm in width were observed by transmission electron microscopy. One virus isolate (designated PVA-Hunan) was subjected to molecular characterization. The viral genome consisted of 9,567 nucleotides, excluding the poly(A) tail, and encoded a polyprotein of 3,059 amino acids. A second characteristic potyvirus open reading frame (ORF), pretty interesting Potyviridae ORF (pipo), was located at nucleotides 2,834-3,139. The isolate shared 84 % to 98 % and 93 % to 99 % sequence identity with other PVA isolates at the nucleotide and amino acid level, respectively. Phylogenetic analysis demonstrated that, within the PVA group, PVA-Hunan clustered most closely with the Finnish isolate Her, then with isolates 143, U, Ali, M and B11. The isolate TamMV stood alone at a separate branch. However, scanning of complete genome sequences using SimPlot revealed 99 %-sequence identity between PVA-Hunan and TamMV in the 3′-proximal end of the genome (~nt 9,160 to the 3′end) and a 50 %-94 % (average ~83 %) identity upstream of nt 9,160. In contrast, 98 % identity between PVA-Hunan and isolates M and B11 was detected for nucleotides 1 to ~9,160, but only ~94 % for the 3′-proximal region, suggesting a genome recombination event (RE) at nt 9,133. The recombination breakpoint also was identified by the Recombination Detection Program (RDP). The RE was further confirmed by analysis of the CP gene, where the apparent RE was located.
References
Bai Y, Nie X, Li X, Gao Y, Fan G, Zhang W, Geng H, Liu W (2010) The seed potato inspection and virus research in China. In: 93rd annual meeting of the potato association of America, The American Journal of Potato Research, vol 87. pp 112–123, Fredericton, 9–13 August 2009
Bartels R (1971) Potato virus A. Descriptions of plant viruses no. 54. CMI/AAB, UK
Chung BY, Miller WA, Atkins JF, Firth AE (2008) An overlapping essential gene in the Potyviridae. Proc Natl Acad Sci USA 105:5897–5902
Dougherty WG, Carrington JC (1988) Expression and function of potyviral gene products. Annu Rev Phytopathol 26:123–143
German TL (2001) Potato virus A. In: Stevenson WR, Loria R, Franc GD, Weingartner DP (eds) Compendium of potato diseases, 2nd edn. APS Press, St. Paul, pp 66–67
Guo D, Rajamaki ML, Saarma M, Valkonen JP (2001) Towards a protein interaction map of potyviruses: protein interaction matrixes of two potyviruses based on the yeast two-hybrid system. J Gen Virol 82:935–939
He C, Nie X (2012) Potato viruses and viral disease control. In: Tai GCC, Xiong X (eds) Research topics in world potato science. ISBN 978-0-9879812-0-2, OmniScience Press, Toronto, pp 189–214
Jansky SH, Jin LP, Xie KY, Xie CH, Spooner DM (2009) Potato production and breeding in China. Potato Res 52:57–65
Kekarainen T, Merits A, Oruetxebarria I, Rajamäki ML, Valkonen JPT (1999) Comparison of the complete sequences of five different isolates of Potato virus A (PVA), genus Potyvirus. Arch Virol 144:2355–2366
Kekarainen T, Savilahti H, Valkonen J (2002) Functional genomics on potato virus A: virus genome-wide map of sites essential for virus propagation. Genome Res 12:584–594
Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160
MacLachlan D, Larson R, Walker J (1954) Potato virus A. Am Potato J 31:67–72
Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462–2463
Merits A, Rajamaki ML, Lindholm P, Runeberg-Roos P, Kekarainen T, Puustinen P, Makelainen K, Valkonen JP, Saarma M (2002) Proteolytic processing of potyviral proteins and polyprotein processing intermediates in insect and plant cells. J Gen Virol 83:1211–1221
Nie X, Singh RP (2001) Differential accumulation of potato virus A and expression of pathogenesis-related genes in resistant potato cv. Shepody upon graft inoculation. Phytopathology 91:197–203
Nie X, Singh RP (2001) A novel usage of random primers for multiplex RT-PCR detection of virus and viroid in aphids, leaves, and tubers. J Virol Methods 91:37–49
Puurand Ü, Mäkinen K, Baumann M, Saarma M (1992) Nucleotide sequence of the 3′-terminal region of potato virus A RNA. Virus Res 23:99–105
Puurand U, Mäkinen K, Paulin L, Saarma M (1994) The nucleotide sequence of potato virus A genomic RNA and its sequence similarities with other potyviruses. J Gen Virol 75:457–461
Puurand Ü, Valkonen J, Mäkinen K, Rabensteind F, Saarmaa M (1996) Infectious in vitro transcripts from cloned cDNA of the potato A potyvirus. Virus Res 40:135–140
Rajamäki M, Merits A, Rabenstein F, Andrejeva J, Paulin L, Kekarainen T, Kreuze JF, Forster RLS, Valkonen JPT (1998) Biological, serological, and molecular differences among isolates of potato A potyvirus. Phytopathology 88:311–321
Singh R, Nie X, Tai GCC (2000) A novel hypersensitive resistance response against potato virus A in cultivar ‘Shepody’. Theor Appl Genet 100:401–408
Slack SA (2001) Potato virus X. In: Stevenson WR, Loria R, Franc GD, Weingartner DP (eds) Compendium of potato diseases, 2nd edn. APS Press, St. Paul, p 69
Slack SA, Singh RP (1998) Control of viruses affecting potatoes through seed potato certification programs. In: Hadidi A, Khetarpal RK, Koganezawa H (eds) Plant virus disease control. American Phytopathological Society Press, St. Paul, pp 249–260
Tamura K, Peterson D, Peterson N, Stecher G. Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882
Visser RG, Bachem CW, de Boer JM, Bryan GJ, Chakrabati SK, Feingold SR, Gromadka R, van Ham CHJ, Huang S, Jacobs JME, Kuznetsov B, de Melo PE, Milbourne D, Orjeda G, Sagredo B, Tang X (2009) Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world’s third most important food crop. Am J Potato Res 86:417–429
Wang B, Ma YL, Zhang ZB, Wu ZM, Wu YF, Li MF, Wang QC (2011) Potato viruses in China. Crop Prot 30:1117–1123
Acknowledgments
This research was supported by the National High Technology Research and Development Program (Project no. 2013AA102603), Hunan Provincial Natural Science Foundation (Project no. 13JJ2029), and the Ministry of Science and Technology of China through the ISTP Canada-China Science and Technology program (Project no. CCRD07-077). The authors thank Virginia Dickson for careful proofreading of the manuscript prior to submission.
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C. He, W. Zhang are co-first authors.
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He, C., Zhang, W., Hu, X. et al. Molecular characterization of a Chinese isolate of potato virus A (PVA) and evidence of a genome recombination event between PVA variants at the 3′-proximal end of the genome. Arch Virol 159, 2457–2462 (2014). https://doi.org/10.1007/s00705-014-2053-z
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DOI: https://doi.org/10.1007/s00705-014-2053-z