Skip to main content
SpringerLink
Log in

Complete genome sequence of a recombinant isolate of yambean mosaic virus from Canavalia ensiformis

  • Short Report
  • Published:
Virus Genes Aims and scope Submit manuscript

A Correction to this article was published on 03 September 2021

This article has been updated

Abstract

The complete genome sequence of a Brazilian isolate of yambean mosaic virus (YBMV) is presented. High-throughput sequencing (Illumina HiSeq) and Sanger sequencing revealed the complete genome sequence of the YBMV-BRA-6 isolate, found in Canavalia ensiformis. The de novo contigs were assembled into a 9612 nucleotides (nt) long scaffold, excluding the 3’-terminal poly(A) tail, covering the complete genome. The genomic RNA contains an open reading frame (ORF) typical of members of the genus Potyvirus, family Potyviridae, encoding a large putative polyprotein of 3078 amino acids (aa) and a small overlapping PIPO ORF. Pairwise comparisons showed that the YBMV-BRA-6 isolate sequence shares 88.1% nt identity for the complete genome and 90.6% aa identity for the polyprotein with the YBMV-SR isolate. Phylogenetic analysis grouped both isolates together and close to bean common mosaic virus (BCMV). The polyprotein cleavage sites were predicted and a recombination event is described.

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

Change history

References

  1. Fuentes S, Heider B, Tasso RC, Romero E, Felde TZ, Kreuze JF (2012) Complete genome sequence of a potyvirus infecting yam beans (Pachyrhizus spp.) in Peru. Arch Virol 157:773–776. https://doi.org/10.1007/s00705-011-1214-6

    Article  CAS  PubMed  Google Scholar 

  2. Andrade LS, Oliveira IA, Pires LL, Kitajima EW, Silva GS, Beserra JEA Jr (2019) First report of yambean mosaic virus in Brazil. Australas Plant Dis Notes 14:1–4. https://doi.org/10.1007/s13314-019-0349-2

    Article  Google Scholar 

  3. Damayanti TA, Susilo D, Nurlaelah S, Sartiami D, Okuno T, Mise K (2008) First report of bean common mosaic virus in yam bean [Pachyrhizus erosus (L.) Urban] in Indonesia. J Gen Plant Pathol 74:438–442. https://doi.org/10.1007/s10327-008-0122-4

    Article  CAS  Google Scholar 

  4. Ha C, Coombs S, Revill PA, Harding RM, Vu M, Dale JL (2008) Design and application of two novel degenerate primer pairs for the detection and complete genomic characterization of potyviruses. Arch Virol 153:25–36. https://doi.org/10.1007/s00705-007-1053-7

    Article  CAS  PubMed  Google Scholar 

  5. Wingett SW, Andrews S (2018) FastQ Screen: a tool for multi-genome mapping and quality control. F1000Research 7:1338. https://doi.org/10.12688/f1000research.15931.2

    Article  PubMed  PubMed Central  Google Scholar 

  6. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning—a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor

    Google Scholar 

  9. Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Martin DP, Varsani A, Roumagnac P, Botha G, Maslamoney S, Schwab T, Kelz Z, Kumar V, Murrell B (2020) RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets. Virus Evol 7:vev087. https://doi.org/10.1093/ve/veaa087

    Article  Google Scholar 

  11. Revers F, Garcia JA (2015) Molecular biology of potyviruses. Adv Virus Res 92:101–199. https://doi.org/10.1016/bs.aivir.2014.11.006

    Article  CAS  PubMed  Google Scholar 

  12. Wylie SJ, Adams M, Chalam C, Kreuze J, Lopez-Moya JJ et al (2017) ICTV virus taxonomy profile: Potyviridae. J Gen Virol 98:352–354. https://doi.org/10.1099/jgv.0.000740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Pasin F, Simón-Mateo C, García JA (2014) The hypervariable amino-terminus of P1 protease modulates potyviral replication and host defense responses. PLoS Pathog 10:e1003985. https://doi.org/10.1371/journal.ppat.1003985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

This work was funded by CNPq [JEABJ PQ fellowship]. LLP was the recipient of a CAPES scholarship.

Author information

Author notes

  1. Renan de Souza Cascardo and Lorenna L. Pires have contributed equally to this work.

Authors and Affiliations

  1. Dep. de Microbiologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil

    Renan de Souza Cascardo, Lorhan L. Leal & Poliane Alfenas-Zerbini

  2. Dep. de Fitotecnia, Universidade Federal do Piauí, Teresina, PI, 64049-550, Brazil

    Lorenna L. Pires & José Evando A. Beserra Jr.

  3. Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil

    F. Murilo Zerbini

Authors
  1. Renan de Souza Cascardo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lorenna L. Pires
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lorhan L. Leal
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. F. Murilo Zerbini
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Poliane Alfenas-Zerbini
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. José Evando A. Beserra Jr.
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization, JEABJ, PAZ, and FMZ; Investigation, RSC, LLP, and LLL; Writing—Original Draft, JEABJ; Writing—Review and Editing, JEABJ, PAZ, and FMZ.

Corresponding author

Correspondence to José Evando A. Beserra Jr..

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical approval

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

Additional information

Edited by Karel Petrzik.

Publisher's Note

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

The original online version of this article was revised: the correct supplementary files are included.

The sequence reported in this paper has been deposited in GenBank under accession number MZ018226.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 48 kb)

Supplementary file2 (DOC 181 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

de Souza Cascardo, R., Pires, L.L., Leal, L.L. et al. Complete genome sequence of a recombinant isolate of yambean mosaic virus from Canavalia ensiformis. Virus Genes 57, 561–564 (2021). https://doi.org/10.1007/s11262-021-01864-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11262-021-01864-7

Keywords

Search

Navigation