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

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