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Virus Genes

, Volume 54, Issue 6, pp 828–832 | Cite as

Molecular characterization and detection of a new closterovirus identified from blackcurrant by high-throughput sequencing

  • Luping Zheng
  • Liping Wu
  • Joseph Postman
  • Huawei Liu
  • Ruhui LiEmail author
Article

Abstract

Two large contigs with high sequence similarities to several closteroviruses were identified by high-throughput sequencing from a blackcurrant plant. The complete genome of this new virus was determined to be 17,320 nucleotides. Its genome contains ten open reading frames (ORF) that include, in the 5′–3′ direction, a large ORF encoding a putative viral polyprotein (ORF 1a) and nine ORFs that encode RNA-dependent RNA polymerase (RdRp, ORF 1b), p6 (ORF 2), heat shock protein 70-like protein (Hsp70h, ORF 3), Hsp-90-like protein (p61, ORF 4), CP minor (ORF 5), CP (ORF 6), p17 (ORF 7), p11 (ORF 8), and p26 (ORF 9), respectively. BCCV-1 shares nucleotide sequence identities of 43–45% with other 9 closteroviruses at genome sequences. The amino acid sequence identities between BCCV-1 and the closteroviruses were 49–55% (RdRp), 37–41% (Hsp70h), 19–33% (p61), 26–38% (CPm), and 19–28% (CP), respectively. Phylogenetic analysis of Hsp70h sequences placed the new virus with members of genus Closterovirus in the same group. The results indicate that this new virus, which is provisionally named as Blackcurrant closterovirus 1, should represent a new species of the genus Closterovirus. A RT-PCR was developed and used to detect BCCV-1 in more germplasm accessions of Ribes spp.

Keywords

Blackcurrant closterovirus 1 Molecular characterization Ribes spp. RT-PCR detection 

Notes

Acknowledgements

This work was supported by U.S. Department of Agriculture, Agriculture Research Service under research project 1215-22000-302-00D “Characterizing and Detecting Pathogens to Ensure Safe Exchange of Plant Germplasm” and the Fujian province scholarship for overseas studies (Grant No. 2016-29).

Author contributions

Study conception and design: RL Acquisition of data: LZ, LW, JP, HL Analysis and interpretation of data: L. Zheng, RL Drafting of manuscript: LZ Critical revision: RL.

Compliance with ethical standards

Conflict of interest

All authors declare that they have no conflict of interest.

Research involving human or animal participants

This article does not contain any research involving human or animal participants.

Supplementary material

11262_2018_1598_MOESM1_ESM.docx (16 kb)
Supplementary Fig. 1 (DOCX 15 KB)
11262_2018_1598_MOESM2_ESM.pptx (51 kb)
Supplementary Fig. 2 (PPTX 50 KB)
11262_2018_1598_MOESM3_ESM.docx (16 kb)
Supplementary Table 1 (DOCX 15 KB)

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Copyright information

© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2018

Authors and Affiliations

  • Luping Zheng
    • 1
    • 2
  • Liping Wu
    • 1
    • 3
  • Joseph Postman
    • 4
  • Huawei Liu
    • 1
  • Ruhui Li
    • 1
    Email author
  1. 1.USDA-ARS, National Germplasm Resources LaboratoryBeltsvilleUSA
  2. 2.College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouChina
  3. 3.Key Laboratory of Poyang Lake Environment and Resource, School of Life SciencesNanchang UniversityNanchangChina
  4. 4.USDA-ARS, National Clonal Germplasm RepositoryCorvallisUSA

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