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Molecular characterization of a new badnavirus infecting green Sichuan pepper (Zanthoxylum schinifolium)

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Abstract

A new virus with a circular double-stranded DNA genome was discovered in green Sichuan pepper with vein clearing symptoms. Its complete genome of 8,014 bp contains three open reading frames (ORF) on the plus strand, which is typical of members of the genus Badnavirus in the family Caulimoviridae. Sequence comparisons revealed that the new virus has the highest nucleotide sequence identity with grapevine vein-clearing virus (GVCV). In particular, the identity of the two viruses in the ORF3 RT-RNase H region is 71.9%, which is below the species demarcation cutoff of 80% for badnaviruses. Phylogenetic analysis also placed the new virus with GVCV in a cluster. The virus was tentatively named “green Sichuan pepper vein clearing-associated virus” (GSPVCaV). The geographical distribution and genetic diversity of GSPVCaV were studied. Another isolate was found to be highly divergent.

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Acknowledgements

This research was supported by the Intergovernmental International Science, Technology and Innovation (STI) Collaboration Key Project of China’s National Key R&D Programme (NKP) (2017YFE0110900), Fundamental Research Funds for the Central Universities (XDJK2018AA002), Chongqing Research Program of Basic Research and Frontier Technology (cstc2017jcyjBX0016), and Overseas Expertise Introduction Project for Discipline Innovation (111 Center) (B18044). We thank the editor and two anonymous reviewers for their constructive comments and suggestions.

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Authors and Affiliations

  1. National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China

    Min Xu, Song Zhang, Zhiyou Xuan, Jiaxing Wu, Yan Zhou & Mengji Cao

  2. Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China

    Min Xu, Song Zhang, Zhiyou Xuan, Jiaxing Wu, Yan Zhou & Mengji Cao

  3. Chongqing Agricultural Technology Extension Station, Chongqing, 401121, China

    Peng Dong

  4. National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD, 20705, USA

    Ruhui Li

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  1. Min Xu
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  2. Song Zhang
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Correspondence to Mengji Cao.

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All authors declare they have no conflict of interest.

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Handling Editor: F. Murilo Zerbini.

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Min Xu and Song Zhang are co-first authors.

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Supplementary Fig. S1

Detection of viral mRNAs by RT-PCR and HTS (transcriptome read mapping). M, DL2000 DNA marker; 1 and 2, ORF1; 3 and 4, ORF2; 4 and 5, ORF3 (JPEG 182 kb)

Supplementary material 2 (DOCX 21 kb)

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Xu, M., Zhang, S., Xuan, Z. et al. Molecular characterization of a new badnavirus infecting green Sichuan pepper (Zanthoxylum schinifolium). Arch Virol 164, 2613–2616 (2019). https://doi.org/10.1007/s00705-019-04357-z

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  • DOI: https://doi.org/10.1007/s00705-019-04357-z

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