Skip to main content
SpringerLink
Log in

Identification and genomic characterization of a novel tobamovirus from prickly pear cactus

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

Abstract

In this work, we describe the complete sequence and genome organization of a novel tobamovirus detected in a prickly pear plant (Opuntia sp.) by high-throughput sequencing, tentatively named “opuntia virus 2”. The full genome of opuntia virus 2 is 6,453 nucleotides in length and contains four open reading frames (ORFs) coding for the two subunits of the RNA polymerase, the movement protein, and the coat protein, respectively. Phylogenetic analysis using the complete nucleotide sequence revealed that the virus belongs to the genus Tobamovirus (family Virgaviridae), showing the highest nucleotide sequence identity (49.8%) with cactus mild mottle virus (CMMoV), being indicating that it belongs in the Cactaceae subgroup of tobamoviruses.

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. Sánchez LDL, López GC, Ávalos HI (2013) Nomenclatura vernácula, uso y manejo de Opuntia spp. en Santiago Bayacora, Durango, México. Revista Chapingo Serie Horticultura 19:367–380

    Google Scholar 

  2. Alonso BB, Mora AG, Valdovinos PG, Ochoa MDL, Rodríguez LE, De La Torre AR (2015) Asociación de un Potexvirus como agente causal de manchas cloróticas en Opuntia ficus-indica. Rev Mex Fitopatol 33:75–86

    Google Scholar 

  3. De La Torre AR, Salgado OH, Salazar SM, Pallás V, Sánchez NJA, Valverde RA (2016) First report of Schlumbergera virus X in prickly pear (Opuntia ficus-indica) in Mexico. Plant Dis 100(8):1799

    Google Scholar 

  4. De La Torre AR, Salgado OH, Salazar SM, Pallás V, Sánchez NJA, Valverde RA (2016) First report of Rattail cactus necrosis-associated virus in prickly pear fruit (Opuntia albicarpa Scheinvar) in Mexico. Plant Dis 100(11):2339

    Google Scholar 

  5. Min BE, Chung BN, Kim MJ, Ha JH, Lee BY, Ryu KH (2006) Cactus mild mottle virus is a new cactus-infecting tobamovirus. Arch Virol 151(1):13–21

    Article  CAS  Google Scholar 

  6. Kim NR, Hong JS, Song YS, Chung BN, Park JW, Ryu KH (2012) The complete genome sequence of a member of a new species of tobamovirus (rattail cactus necrosis-associated virus) isolated from Aporocactus flagelliformis. Arch Virol 157(1):185–187

    Article  CAS  Google Scholar 

  7. Adams MJ, Antoniw JF, Kreuze J (2009) Virgaviridae: a new family of rod-shaped plant viruses. Arch Virol 154(12):1967–1972. https://doi.org/10.1007/s00705-009-0506-6

    Article  CAS  PubMed  Google Scholar 

  8. Lecoq H, Desbiez C (2012) Viruses of cucurbit crops in the Mediterranean region: an ever-changing picture. Adv Virus Res 84:67–126

    Article  Google Scholar 

  9. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Regev A (2013) De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nat Protoc 8(8):1–43

    Article  Google Scholar 

  10. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    Article  CAS  Google Scholar 

  11. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  Google Scholar 

  12. Song YS, Min BE, Hong JS, Rhie MJ, Kim MJ, Ryu KH (2006) Molecular evidence supporting the confirmation of Maracuja mosaic virus as a species of the genus Tobamovirus and production of an infectious cDNA transcript. Arch Virol 151:2337–2348

    Article  CAS  Google Scholar 

  13. Gibbs AJ, Wood J, Garcia-Arenal F, Ohshima K, Armstrong JS (2015) Tobamoviruses have probably co-diverged with their eudicotyledonous hosts for at least 110 million years. Virus Evol 1(1):vev019

    Article  Google Scholar 

  14. Adams MJ, Adkins S, Blagard C et al (2018) International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Virgaviridae. http://www.ictv.global/report/virgaviridae. Accessed 19 Oct 2018

Download references

Acknowledgements

The first author would like to thank Consejo Nacional de Ciencia y Tecnología for the Grant (number 446131) that supported his Doctoral scholarship, and Posgrado de Ciencias Biológicas of Universidad Nacional Autónoma de México (UNAM). We thank the Instituto de Biotecnologia-UNAM for giving us access to their computer cluster.

Funding

This study was funded by project no. IN216317 of UNAM-Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT) and by Grant BIO2017-88321-R from the Spanish Agencia Estatal de Investigación (AEI) and Fondo Europeo de Desarrollo Regional (FEDER).

Author information

Authors and Affiliations

  1. Unidad de Biotecnología y Prototipos, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, 54074, Tlalnepantla, Estado de México, Mexico

    Héctor Salgado-Ortíz & Rodolfo De La Torre-Almaraz

  2. Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Ciudad Politécnica de la Innovación Ingeniero Fausto Elio, s/n, 46022, Valencia, Spain

    Jesús Ángel Sánchez-Navarro & Vicente Pallás

Authors
  1. Héctor Salgado-Ortíz
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rodolfo De La Torre-Almaraz
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jesús Ángel Sánchez-Navarro
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Vicente Pallás
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Héctor Salgado-Ortíz.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

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

Additional information

Handling Editor: Ralf Georg Dietzgen.

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 (DOCX 19 kb)

Supplementary material 2 (DOCX 13 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Salgado-Ortíz, H., De La Torre-Almaraz, R., Sánchez-Navarro, J.Á. et al. Identification and genomic characterization of a novel tobamovirus from prickly pear cactus. Arch Virol 165, 781–784 (2020). https://doi.org/10.1007/s00705-020-04528-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-020-04528-3

Search

Navigation