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Genetic variation in potato virus M isolates infecting pepino (Solanum muricatum) in China

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Abstract

Potato virus M (PVM, genus Carlavirus, family Betaflexviridae) is considered to be one of most economically important pathogens of pepino in China. However, the details and the mechanisms underlying PVM evolution are unknown. In this study, we determined and analyzed 40 TGB 1 gene sequences, 67 TGB 2 and TGB 3 gene sequences, and 88 CP and NABP gene sequences from viruses isolated from 19 samples of pepino (Solanum muricatum) and one sample of tomato (S. lycopersicum) collected from different areas of China. Recombination analysis identified only one clear recombinant in the TGB2-TGB3-CP region, but no recombinants were detected for each of the five individual genes. Phylogenetic analysis showed that all PVM isolates could be divided into at least two lineages in trees derived from the TGB 2, CP, and NABP gene sequences, and the lineages seemed to reflect geographical origin. The five PVM genes in this study were found to be under strong negative selection pressure. The PVM isolates examined showed frequent gene flow between the Chinese and European populations, and also within the Chinese population. Clear star phylogenies and the neutral equilibrium model test showed that pepino isolates of PVM appear to be experiencing a new expansion after a recent introduction into China, and these isolates display low levels of genetic diversity. To our knowledge, this study is the first report describing genetic structure, recombination, and gene flow in PVM populations, and it provides strong evolutionary evidence for the virus populations from different geographic regions of China.

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Acknowledgments

This work was supported by grants from the Earmarked Fund for China Agriculture Research System (CARS-31), the State Scholarship Fund (No. 201203250024), the Special Fund for Agro-Scientific Research in the Public Interest (Nos. 201203076 and 200903004), the National Basic Research and Development Program of China (973 Program) (No. 2009CB119200) and the National Natural Science Foundation of China (Nos. 31401796, 31171819 and 31000842).

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Authors and Affiliations

  1. State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People’s Republic of China

    Beibei Ge, Zhen He, Zhixiang Zhang & Shifang Li

  2. College of Agronomy and Biotechnology, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing, 100193, People’s Republic of China

    Hongqing Wang

  3. School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No 48, Yangzhou, 225009, Jiangsu Province, People’s Republic of China

    Zhen He

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  1. Beibei Ge
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  2. Zhen He
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  3. Zhixiang Zhang
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  4. Hongqing Wang
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Correspondence to Hongqing Wang or Shifang Li.

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B. Ge and Z. He contributed equally to this work.

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705_2014_2180_MOESM1_ESM.doc

Figure S1. Maximum-likelihood trees calculated from the TGB1 (A) and TGB3 (B) gene sequences of potato virus M obtained in this study. Numbers at each node indicate the percentage of supporting puzzling steps (or bootstrap samples) in the maximum-likelihood and neighbor-joining trees. The horizontal branch length is drawn to scale, with the bar indicating 0.1 nt replacements per site. Isolate names shown in red indicate the PVM isolate sequences determined in this study. (DOC 8388 kb)

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Ge, B., He, Z., Zhang, Z. et al. Genetic variation in potato virus M isolates infecting pepino (Solanum muricatum) in China. Arch Virol 159, 3197–3210 (2014). https://doi.org/10.1007/s00705-014-2180-6

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  • DOI: https://doi.org/10.1007/s00705-014-2180-6

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