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Complete genome sequence of a Capsicum chlorosis virus in China and the structural variation and evolutionary origin of its S RNA intergenic region

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Abstract

The complete genome sequence of a Capsicum chlorosis virus from China (CaCV-Hainan) was determined. The tripartite genome of CaCV-Hainan consists of small (S), medium (M), and large (L) RNAs of 3629, 4859, and 8912 nucleotides (nt), respectively. The S and M RNAs contain intergenic regions (IGRs) of 1348 and 462 nt, respectively. Strikingly, sequence comparisons among CaCV isolates revealed that the S RNA IGR of CaCV-Hainan derived from the CaCV-Qld-3432 Australia isolate through deletion of two stretches of 25- and 325-nt sequences within the S RNA IGR of CaCV-Qld-3432. Moreover, the S RNA IGR of CaCV-Hainan was inserted with two stretches of 10- and 20-nt sequences of an unknown origin. The S RNA IGR of CaCV-Ph from Taiwan and CaCV-NRA from Thailand also derived from the CaCV-Qld-3432 through deletion of 218-nt sequences. Our findings provide valuable new insight into the structural variations and evolutionary origin of CaCV IGRs.

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Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (31630062 and 31471746), the Special Fund for Agro-Scientific Research in the Public Interest (201303028), the Youth Talent Support Program of China and Distinguished Professor of Jiangsu Province to X. T., the Fundamental Research Funds for the Central Universities (KYTZ201403), the Specialized Research Fund for the Doctoral Program of Higher Education (20130097110004).

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Authors and Affiliations

  1. Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China

    Ying Huang, Hao Hong, Xiao-Hui Zhao, Jia Li & Xiao-Rong Tao

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  1. Ying Huang
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  2. Hao Hong
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  3. Xiao-Hui Zhao
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  4. Jia Li
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Correspondence to Xiao-Rong Tao.

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Supplementary material 1 (DOCX 24 kb)

705_2017_3448_MOESM2_ESM.pdf

Supplementary material 2 Supplemental Figure 1: Alignment of nucleotide sequences of S RNA intergenic regions (IGRs) among CaCV-Qld-3432, CaCV-Hainan, CaCV-Ph, CaCV-NRA, CaCV-Ch-Pan, and CaCV-AIT. The nucleotide sites that are identical among the CaCV isolates are highlighted. The accession numbers of the IGR sequences of the CaCV isolates, and of watermelon silver mottle virus (WSMoV) and tomato zonate spot virus (TZSV), are provided in the main text. Supplemental Figure 2: Phylogenetic analysis of the nucleotide sequences of S RNA intergenic regions (IGRs) of CaCV-Qld-3432, CaCV-Hainan, CaCV-Ph, CaCV-NRA, CaCV-Ch-Pan, and CaCV-AIT. The phylogenetic tree was constructed using the maximum likelyhood method. Bootstrap values on the branches are derived from a 1,000-bootstrap replicate analysis. The accession numbers of the IGR sequences of the CaCV isolates are described in the main text. The scale bar represents the genetic distance (PDF 80 kb)

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Huang, Y., Hong, H., Zhao, XH. et al. Complete genome sequence of a Capsicum chlorosis virus in China and the structural variation and evolutionary origin of its S RNA intergenic region. Arch Virol 162, 3229–3232 (2017). https://doi.org/10.1007/s00705-017-3448-4

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  • DOI: https://doi.org/10.1007/s00705-017-3448-4

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