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Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions

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Abstract

The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92 % sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.

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Acknowledgments

This research was supported by the Special Fund for Agro-Scientific Research in the Public Interest (Project no. 201303028), the National Natural Science Foundation of China (31101413), the Shen-Nong Visiting Scholar Funding Program of Hunan Agricultural University, and the Science and Technology Funding for Key Projects of Hunan Tobacco Company (13-14ZDAa04 and 14-16ZDAa02).

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Authors and Affiliations

  1. College of Plant Protection, Hunan Agricultural University, Hunan, 410128, China

    Maoyan Liu, Xiangning Liu, Xun Li, Liangyin Dai & Qianjun Tang

  2. Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Hunan, 410128, China

    Maoyan Liu, Xiangning Liu, Liangyin Dai & Qianjun Tang

  3. Virus Research Institute, Hunan Agricultural University, Hunan, 410128, China

    Qianjun Tang

  4. Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50010, USA

    Xun Li

  5. Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Hunan, 410125, China

    Deyong Zhang

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  1. Maoyan Liu
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Correspondence to Liangyin Dai or Qianjun Tang.

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Liu, M., Liu, X., Li, X. et al. Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions. Arch Virol 161, 677–683 (2016). https://doi.org/10.1007/s00705-015-2691-9

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  • DOI: https://doi.org/10.1007/s00705-015-2691-9

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