Skip to main content
SpringerLink
Log in

DNA virome of Brazilian sugarcane germplasm via high-throughput sequencing reveals divergent badnavirus species

  • Short Communication
  • Published:
Tropical Plant Pathology Aims and scope Submit manuscript

Abstract

To analyze the circular DNA virome from badnavirus-infected sugarcane (Saccharum spp.) accession materials, viral genomes were amplified via rolling circle amplification (RCA) using total DNA from PCR-positive samples as template. The RCA products were individually (n = 3) subjected to high-throughput sequencing. Complete genomes of the badnaviruses, sugarcane bacilliform GA virus (SCBGAV) and sugarcane bacilliform IM virus (SCBIMV), were assembled using Illumina short reads with a coverage depth of 487 to 3,331x. The SCBGAV-BR-RB10 isolate was further validated using MinION sequencing, which shared > 99.0% sequence identity with the Illumina-derived genome. The new SCBGAV isolates are putative recombinant sequences, with recombination breakpoints at the nucleotide positions 6940 and 7014, which are located in the viral intergenic region, and SCBIMV and banana streak MY virus were identified as putative minor and major parents, respectively. To our knowledge, these are the first complete badnavirus genome sequences characterized from sugarcane in Brazil.

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
Fig. 3
Fig. 4

Data availability

The nucleotide sequence datasets generated during the current study are available in the NCBI-GenBank repository, under accession numbers OQ282506 to OQ282508.

References

  • Altschul SF (1990) Basic local alignment search tool. Journal of Molecular Biology 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov AS, Lesin V, Nikolenko S, Pham S, Prjibelski A, Pyshkin A, Sirotkin A, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: A flexible trimmer for illumina sequence data. Bioinformatics 30(15):2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bömer M, Rathnayake AI, Visendi P, Silva G, Seal SE (2018) Complete genome sequence of a new member of the genus Badnavirus, Dioscorea bacilliform RT virus 3, reveals the first evidence of recombination in yam badnaviruses. Archives of Virology 163:533–538

    Article  PubMed  Google Scholar 

  • Cheng CP, Lockhart BE, Olszewski NE (1996) The Orf I and Ii Proteins of commelina yellow mottle virus are virion-associated. Virology 223:263–271

    Article  CAS  PubMed  Google Scholar 

  • CONAB (2022) Cana-de-açúcar, safra 2022–2023. https://www.conab.gov.br/info-agro/safras/cana. Accessed 28 Dec 2022.

  • Edgar RC (2004) Muscle: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5:1–19

    Article  Google Scholar 

  • Ferreira CHLH, Jordão LJ, Ramos-Sobrinho R, Ferro MMM, Silva SJC, Assunção IP, Lima GSA (2019) Diversification into the genus Badnavirus: phylogeny and population genetic variability. Ciência Agrícola 17:59–72

    Article  Google Scholar 

  • Gao Y, Liu B, Wang Y, Xing Y (2019) TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Bioinformatics 35:i200–i207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267

    Article  CAS  PubMed  Google Scholar 

  • Inoue-Nagata AK, Albuquerque LC, Rocha WB, Nagata T (2004) A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase. Journal of Virological Methods 116:209–211

    Article  CAS  PubMed  Google Scholar 

  • Jacquot E, Hagen LS, Jacquemond M, Yot P (1996) The open reading frame 2 product of cacao swollen shoot badnavirus is a nucleic acid-binding protein. Virology 225:191–195

    Article  CAS  PubMed  Google Scholar 

  • Karuppaiah R, Viswanathan R, Kumar VG (2013) Genetic diversity of sugarcane bacilliform virus isolates infecting Saccharum spp. In India. Virus Genes 46:505–516

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lodhi MA, Ye G-N, Weeden NF, Reisch BI (1994) A simple and efficient method for DNA extraction from grapevine cultivars and -Vitis species. Plant Molecular Biology 12:6–13

    Article  CAS  Google Scholar 

  • Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolution 1:1–5

    Article  Google Scholar 

  • Martins TP, Souza TA, da Silva PS et al (2021) Nanopore sequencing of tomato mottle leaf distortion virus, a new bipartite begomovirus infecting tomato in Brazil. Archives of Virology 166:3217–3220

    Article  CAS  PubMed  Google Scholar 

  • Medberry SL, Lockhart BEL, Olszewski NE (1990) Properties of commelina yellow mottle virus complete DNA sequence, genomic discontinuities and transcript suggest that it is a pararetrovirus. Nucleic Acids Res 18:5505–5513

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller MA, Holder MT, Vos R, Midford PE Liebowitz T, Chan L, Hoover P, Warnow T (2010) The cipres portals. Cipres. http://www.phylo.org/sub-sections/portal. Accessed 20 Sep 2022

  • Muhire BM, Varsani A, Martin DP (2014) SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE 9:e108277

    Article  PubMed  PubMed Central  Google Scholar 

  • Muller E, Ravel S, Agret C, Abrokwah F, Dzahini-Obiatey H, Galyuon I, Kouakou K, Jeyaseelan EC, Allainguillaume J, Wetten A (2018) Next generation sequencing elucidates cacao badnavirus diversity and reveals the existence of more than ten viral species. Virus Res 244:235–251

    Article  CAS  PubMed  Google Scholar 

  • Muller E, Dupuy V, Blondin L, Bauffe F, Daugrois J-H, Nathalie L, Iskra-Caruana (2011) High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species. Virus Research 160:414–419

  • Nylander JAA (2004) MrModeltest Version 2. Program Distributed by the Author. Evolutionary Biology Centre, Uppsala University, Uppsala

  • Ramos-Sobrinho R, Chingandu N, Gutierrez OA, Marelli J-P, Brown JK (2020) A complex of badnavirus species infecting cacao reveals mixed infections, extensive genomic variability, and interspecific recombination. Viruses 12:443

  • Rannala B, Yang ZH (1996) Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. Journal of Molecular Evolution 43:304–311

    Article  CAS  PubMed  Google Scholar 

  • Rao GP, Susheel KS, Deepti S, Meenakshi A, Priyanka S, Virendra KB (2014) Genetically diverse variants of sugarcane bacilliform virus infecting sugarcane in India and evidence of a novel recombinant badnavirus variant. J Phytopathol 162:779–787

    Article  CAS  Google Scholar 

  • RIDESA (2022) Melhoramento genético de Cana-de-açúcar. https://www.ridesa.com.br/. Accessed 15 Dec 2022

  • Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP (2017) Variant review with the Integrative Genomics Viewer (IGV). Cancer Res 77:31–34

    Article  Google Scholar 

  • Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hohna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61:539–542

    Article  PubMed  PubMed Central  Google Scholar 

  • Sharma SK, Vignesh-Kumar P, Geetanjali AS, Pun KB, Baranwal VK (2015) Subpopulation level variation of banana streak viruses in India and common evolution of banana and sugarcane badnaviruses. Virus Genes 50:450–465

    Article  CAS  PubMed  Google Scholar 

  • Silva JM, Jobim LJ, Ramos-Sobrinho R, Lima JS, Assunção IP, Cruz MM, Lima GSA (2015) Incidence and species diversity of badnaviruses infecting sugarcane from a germplasm collection in Brazil. Tropical Plant Pathology 40:212–217

    Article  Google Scholar 

  • Teycheney PY, Geering AD, Dasgupta I, Hull R, Kreuze JF, Lockhart B, Muller E, Olszewski N, Pappu H, Pooggin MM, Richert-Pöggeler KR, Schoelz JE, Seal S, Stavolone L, Umber M, ICTV Report Consortium (2020) ICTV Virus taxonomy profile: Caulimoviridae. Journal of General Virology 101:1025

  • Yang IC, Hafner GJ, Dale JL, Harding RM (2003) Genomic characterization of taro bacilliform virus. Archives of Virology 148:937–949

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

M.O.L. was the recipients of a CAPES fellowship. I.P.A., G.S.A.L. and T.N. wish to thank CNPq for the research fellowship.

Author information

Authors and Affiliations

  1. Campus de Engenharias e Ciências Agrárias, Universidade Federal de Alagoas, Rio Largo, Alagoas, 57100-000, Brazil

    Mayara O. de Lima, Mayra M. M. Ferro, Roberto Ramos-Sobrinho, Iraildes P. Assunção, Gaus S. A. Lima & Sarah J. C. Silva

  2. Laboratório de Entomologia e Fitopatologia, Universidade Estadual Do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, 28013-602, Brazil

    Roberto Ramos-Sobrinho

  3. Pesquisa e Desenvolvimento, OnSite Genomics, Distrito Federal, Brasília, 70610-433, Brazil

    Fernando L. Melo

  4. Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Distrito Federal, Brasília, 70910-900, Brazil

    Tatsuya Nagata

Authors
  1. Mayara O. de Lima
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mayra M. M. Ferro
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Roberto Ramos-Sobrinho
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Fernando L. Melo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tatsuya Nagata
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Iraildes P. Assunção
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Gaus S. A. Lima
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Sarah J. C. Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization: Mayara O. de Lima; Roberto Ramos-Sobrinho; Fernando L. Melo; Sarah J.C. Silva; Methodology: Mayara O. de Lima; Mayra M.M. Ferro; Roberto Ramos-Sobrinho; Fernando L. Melo; Tatsuya Nagata; Formal analysis and investigation: Mayara O. de Lima; Mayra M.M. Ferro; Roberto Ramos-Sobrinho; Fernando L. Melo; Writing—original draft preparation: Mayara O. de Lima; Mayra M.M. Ferro; Roberto Ramos-Sobrinho; Writing—review and editing: Roberto Ramos-Sobrinho; Fernando L. Melo; Tatsuya Nagata; Iraildes P. Assunção; Gaus S.A. Lima; Sarah J.C. Silva; Funding acquisition: Fernando L. Melo; Tatsuya Nagata; Iraildes P. Assunção; Gaus S.A. Lima; Sarah J.C. Silva; Resources: Fernando L. Melo; Tatsuya Nagata; Iraildes P. Assunção; Gaus S.A. Lima; Sarah J.C. Silva; Supervision: Mayra M.M. Ferro; Roberto Ramos-Sobrinho; Sarah J.C. Silva.

Corresponding authors

Correspondence to Roberto Ramos-Sobrinho or Sarah J. C. Silva.

Ethics declarations

Conflict of interest

The authors declare no conflict of interest.

Additional information

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.

Supplementary file1 (DOCX 118 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

de Lima, M.O., Ferro, M.M.M., Ramos-Sobrinho, R. et al. DNA virome of Brazilian sugarcane germplasm via high-throughput sequencing reveals divergent badnavirus species. Trop. plant pathol. 48, 713–719 (2023). https://doi.org/10.1007/s40858-023-00606-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s40858-023-00606-4

Keywords

Search

Navigation