Skip to main content
SpringerLink
Log in

Molecular characterization of a putative new cavemovirus isolated from wild chicory (Cichorium intybus)

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

Abstract

A putative new virus with sequence similarity to members of the genus Cavemovirus in the family Caulimoviridae was identified in wild chicory (Cichorium intybus) by next-generation sequencing (NGS). The putative new virus was tentatively named “chicory mosaic cavemovirus” (ChiMV), and its genome was determined to be 7,775 nucleotides (nt) long with the typical genome organization of cavemoviruses. ORF1 encodes a putative coat protein/movement polyprotein (1,278 aa), ORF2 encodes a putative replicase (650 aa), and ORF3 encodes a putative transactivator factor (384 aa). The first two putative proteins have 46.2% and 68.7% amino acid sequence identity to the CP/MP protein (YP_004347414) and replicase (YP_004347415), respectively, of sweet potato collusive virus (SPCV). ORF3 encodes a protein with 38.5% amino acid sequence identity to the putative transactivator factor (NP_056849) of cassava vein mosaic virus (CsVMV). The new putative viral genome and those of three cavemoviruses (epiphyllum virus 4 [EpV-4], SPCV, and CsVMV) differ by 24-27% in the nt sequence of the replicase gene, which exceeds the species demarcation cutoff (>20%) for the family.

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. Van Der Maesen LJG (1996) Asteraceae, cladistics and classification. Sci Hortic (Amsterdam) 66:135–137. https://doi.org/10.1016/0304-4238(96)81078-8

    Article  Google Scholar 

  2. Barcaccia G, Ghedina A, Lucchin M (2016) Current advances in genomics and breeding of leaf chicory (Cichorium intybus L.). Agriculture 6:50

    Article  Google Scholar 

  3. Kearse M, Moir R, Wilson A et al (2012) Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. https://doi.org/10.1093/bioinformatics/bts199

    Article  PubMed  PubMed Central  Google Scholar 

  4. Teycheney PY, Geering ADW, Dasgupta I et al (2020) ICTV Virus taxonomy profile: Caulimoviridae. J Gen Virol 101:1025–1026

    Article  CAS  Google Scholar 

  5. Verdaguer B, De Kochko A, Fux CI et al (1998) Functional organization of the cassava vein mosaic virus (CsVMV) promoter. Plant Mol Biol 37:1055–1067. https://doi.org/10.1023/A:1006004819398

    Article  CAS  PubMed  Google Scholar 

  6. Cuellar WJ, de Souza JD, Barrantes I et al (2011) Distinct cavemoviruses interact synergistically with sweet potato chlorotic stunt virus (genus crinivirus) in cultivated sweet potato. J Gen Virol 92:1233–1243. https://doi.org/10.1099/vir.0.029975-0

    Article  CAS  PubMed  Google Scholar 

  7. Pooggin MM, Fütterer J, Skryabin KG, Hohn T (1999) A short open reading frame terminating in front of a stable hairpin is the conserved feature in pregenomic RNA leaders of plant pararetroviruses. J Gen Virol 80:2217–2228. https://doi.org/10.1099/0022-1317-80-8-2217

    Article  CAS  PubMed  Google Scholar 

  8. Zheng L, Cao M, Wu L et al (2020) First identification and molecular characterization of a novel cavemovirus infecting Epiphyllum spp. Arch Virol 165:2083–2086. https://doi.org/10.1007/s00705-020-04688-2

    Article  CAS  PubMed  Google Scholar 

  9. Guindon S, Dufayard JF, Lefort V et al (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–321. https://doi.org/10.1093/sysbio/syq010

    Article  CAS  PubMed  Google Scholar 

  10. Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 57:758–771. https://doi.org/10.1080/10635150802429642

    Article  PubMed  Google Scholar 

Download references

Funding

This research was funded by Fundação de Apoio à Pesquisa do Distrito Federal, Grant no [193.001532/2016] and Conselho Nacional de Desenvolvimento Científico e Tecnológico, Grant no [305756/2017-6].

Author information

Authors and Affiliations

  1. Laboratory of Baculovirus, Cell Biology Department, UnB-University of Brasília, Brasília, DF, 70910-900, Brazil

    Leonardo A. Silva, Brenda R. de Camargo & Bergmann M. Ribeiro

  2. Lab. Fitovirologia e Fisiopatologia, Centro de Pesquisa de Sanidade Vegetal, Instituto Biológico, São Paulo, SP, 04014-002, Brazil

    Marcelo Eiras & Alexandre L. R. Chaves

Authors
  1. Leonardo A. Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Brenda R. de Camargo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marcelo Eiras
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alexandre L. R. Chaves
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Bergmann M. Ribeiro
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Leonardo A. Silva or Bergmann M. Ribeiro.

Ethics declarations

Conflict of interest

All authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any research involving humans or animals.

Additional information

Handling Editor: Elvira Fiallo-Olivé.

Publisher's Note

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

Supplementary Information

Below is the link to the electronic supplementary material.

705_2021_5172_MOESM1_ESM.pdf

Supplementary file1 Supplementary Fig. S1 The results of alignment and percentage of nucelotide and amino acid sequence identity of chicory mosaic cavemovirus (ChiMV) to sweet potato collusive virus (SPCV), cassava vein mosaic virus (CsVMV), and epiphyllum virus 4 (EpV-4) (PDF 59 KB)

Supplementary file2 (DOCX 14 KB)

Supplementary file3 (DOCX 15 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Silva, L.A., de Camargo, B.R., Eiras, M. et al. Molecular characterization of a putative new cavemovirus isolated from wild chicory (Cichorium intybus). Arch Virol 166, 2865–2868 (2021). https://doi.org/10.1007/s00705-021-05172-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-021-05172-1

Search

Navigation