Skip to main content
SpringerLink
Log in

Complete genome sequence of a tentative new member of the genus Badnavirus identified in Codonopsis lanceolata

  • Annotated Sequence Record
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

High-throughput sequencing revealed a tentative new badnavirus infecting Codonopsis lanceolata, provisionally named Codonopsis vein clearing virus (CoVCV). The complete 8,112-nt CoVCV genomic DNA sequence (GenBank accession: MK044821) comprises three open reading frames (ORFs) encoding conserved domains, with typical features of badnaviruses. Additionally, BLASTn searches indicated the CoVCV genome sequence is most similar to the grapevine vein clearing virus (GVCV) genome (72% identity and 46% query coverage). Moreover, the polyprotein encoded in CoVCV ORF3 is most similar to the corresponding protein of GVCV, with 60% amino acid sequence identity (89% query coverage). These results suggest that CoVCV is a new member of the genus Badnavirus in the family Caulimoviridae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Bhat AI, Hohn T, Selvarajan R (2016) Badnaviruses: the current global scenario. Viruses 8(6):E177

    Article  CAS  PubMed  Google Scholar 

  2. Brister JR, Ako-Adjei D, Bao Y, Blinkova O (2015) NCBI viral genomes resource. Nucleic Acids Res 43(Database issue):D571–D577

    Article  CAS  PubMed  Google Scholar 

  3. Geering ADW, Hull R (2012) Family Caulimoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy: ninth Report of the International Committee on Taxonomy of Viruses. Elsevier, London

    Google Scholar 

  4. He X, Kim SS, Park SJ, Seong DH, Yoon WB, Lee HY, Park DS, Ahn J (2010) Combined effects of probiotic fermentation and high-pressure extraction on the antioxidant, antimicrobial, and antimutagenic activities of deodeok (Codonopsis lanceolata). J Agric Food Chem 58(3):1719–1725

    Article  CAS  PubMed  Google Scholar 

  5. Hohn T, Rothnie H (2013) Plant pararetroviruses: replication and expression. Curr Opin Virol 3(6):621–628

    Article  CAS  PubMed  Google Scholar 

  6. Kalischuk ML, Fusaro AF, Waterhouse PM, Pappu HR, Kawchuk LM (2013) Complete genomic sequence of a Rubus yellow net virus isolate and detection of genome-wide pararetrovirus-derived small RNAs. Virus Res 178(2):306–313

    Article  CAS  PubMed  Google Scholar 

  7. Lee YJ, Kwak HR, Lee YK, Kim MK, Choi HS, Seo JK (2015) Complete genome sequence of yacon necrotic mottle virus, a novel putative member of the genus Badnavirus. Arch Virol 160(4):1139–1142

    Article  CAS  PubMed  Google Scholar 

  8. Lim S, Igori D, Zhao F, Yoo RH, An TJ, Lim HS, Lee SH, Moon JS (2015) Complete genome sequence of a tentative new caulimovirus from the medicinal plant Atractylodes macrocephala. Arch Virol 160(12):3127–3131

    Article  CAS  PubMed  Google Scholar 

  9. Lim S, Kim KH, Zhao F, Yoo RH, Igori D, Lee SH, Moon JS (2015) Complete genome sequence of a novel endornavirus isolated from hot pepper. Arch Virol 160(12):3153–3156

    Article  CAS  PubMed  Google Scholar 

  10. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39(Database issue):D225–D229

    Article  CAS  Google Scholar 

  11. Tzafrir I, Ayala-Navarrete L, Lockhart BE, Olszewski NE (1997) The N-terminal portion of the 216-kDa polyprotein of Commelina yellow mottle badnavirus is required for virus movement but not for replication. Virology 232(2):359–368

    Article  CAS  PubMed  Google Scholar 

  12. Xu D, Mock R, Kinard G, Li R (2011) Molecular analysis of the complete genomic sequences of four isolates of Gooseberry vein banding associated virus. Virus Genes 43(1):130–137

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This study was supported by the KRIBB Research Initiative Program, which is funded by the Ministry of Science and ICT, Republic of Korea. We thank Edanz Group (http://www.edanzediting.com/ac) for editing a draft of this manuscript.

Author information

Authors and Affiliations

  1. Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea

    Seungmo Lim, Jeong Mee Park, Suk-Yoon Kwon, Hye Sun Cho, Hyun-Soon Kim & Jae Sun Moon

  2. School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, Republic of Korea

    Su-Heon Lee

Authors
  1. Seungmo Lim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jeong Mee Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Suk-Yoon Kwon
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hye Sun Cho
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hyun-Soon Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Su-Heon Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jae Sun Moon
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Su-Heon Lee or Jae Sun Moon.

Ethics declarations

Funding

This study was funded by KRIBB (Ministry of Science and ICT), Republic of Korea.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Data availability

The dataset generated during the current study is available in the GenBank repository (accession: MK044821).

Additional information

Handling Editor: Sead Sabanadzovic.

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 68 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lim, S., Park, J.M., Kwon, SY. et al. Complete genome sequence of a tentative new member of the genus Badnavirus identified in Codonopsis lanceolata. Arch Virol 164, 1733–1737 (2019). https://doi.org/10.1007/s00705-019-04238-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-019-04238-5

Search

Navigation