Skip to main content
SpringerLink
Log in

Complete genome analysis of a novel narnavirus in sweet viburnum (Viburnum odoratissimum)

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

Abstract

Trees and shrubs provide important ecological services. However, few studies have surveyed the virome in trees and shrubs. In this study, we discovered a new positive-sense RNA virus originating from Viburnum odoratissimum, which we named "Vo narna-like virus". The complete genome of Vo narna-like virus is 3,451 nt in length with an open reading frame (ORF) encoding the RNA-dependent RNA polymerase (RdRP) protein. Phylogenetic analysis placed this virus within the betanarnavirus clade, sharing 53.63% amino acid sequence identity with its closest relative, Qingdao RNA virus 2. The complete sequence of the virus was confirmed by rapid amplification of cDNA ends (RACE) and Sanger sequencing. Small interfering RNA (siRNA) analysis indicated that this virus interacts with the RNA interference (RNAi) pathway of V. odoratissimum. This is the first report of a narnavirus in V. odoratissimum.

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

Data availability

The genome sequence and RdRP protein sequence of Vo narna-like virus are available in the NCBI database under the accession numbers OR965524.1 and WQM87268.1. The transcriptome sequencing data and siRNA sequencing data are available at NCBI under the BioProject ID PRJNA1053647. The scripts used in this study are available on GitHub (https://github.com/Gyoungwe/novel_virus_analysis). Sequencing data, Trinity assembly, and BLASTx results are available on Zenodo (https://zenodo.org/doi/https://doi.org/10.5281/zenodo.10208202).

References

  1. Rumbou A, Vainio EJ, Büttner C (2021) Towards the forest virome: High-throughput sequencing drastically expands our understanding on virosphere in temperate forest ecosystems. Microorganisms 9:1730. https://doi.org/10.3390/microorganisms9081730

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Roossinck MJ (2012) Plant virus metagenomics: Biodiversity and ecology. Annu Rev Genet 46:359–369. https://doi.org/10.1146/annurev-genet-110711-155600

    Article  CAS  PubMed  Google Scholar 

  3. Mifsud JCO, Gallagher RV, Holmes EC, Geoghegan JL (2022) Transcriptome mining expands knowledge of RNA viruses across the plant kingdom. J Virol 96:e00260-e322. https://doi.org/10.1128/jvi.00260-22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Yang S, Mao Q, Wang Y et al (2022) Expanding known viral diversity in plants: Virome of 161 species alongside an ancient canal. Environ Microbiome 17:58. https://doi.org/10.1186/s40793-022-00453-x

    Article  PubMed  PubMed Central  Google Scholar 

  5. Donoghue MJ, Baldwin BG, Li J, Winkworth RC (2004) viburnum phylogeny based on chloroplast trnK intron and nuclear ribosomal ITS DNA sequences. Syst Bot 29:188–198. https://doi.org/10.1600/036364404772974095

    Article  Google Scholar 

  6. Xie Z, Johansen LK, Gustafson AM et al (2004) Genetic and functional diversification of small RNA pathways in plants. PLOS Biol 2:e104. https://doi.org/10.1371/journal.pbio.0020104

    Article  PubMed  PubMed Central  Google Scholar 

  7. Akbergenov R (2006) Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res 34:462–471. https://doi.org/10.1093/nar/gkj447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. 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 

  9. Jin J-J, Yu W-B, Yang J-B et al (2020) GetOrganelle: A fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21:241. https://doi.org/10.1186/s13059-020-02154-5

    Article  PubMed  PubMed Central  Google Scholar 

  10. Tillich M, Lehwark P, Pellizzer T et al (2017) GeSeq – versatile and accurate annotation of organelle genomes. Nucleic Acids Res 45:W6–W11. https://doi.org/10.1093/nar/gkx391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Yen LT, Park J (2022) The complete nucleotide sequence of viburnum odoratissimum chloroplast genome. Mitochondrial DNA Part B 7:635–636. https://doi.org/10.1080/23802359.2020.1749151

    Article  PubMed  PubMed Central  Google Scholar 

  12. Haas BJ, Papanicolaou A, Yassour M et al (2013) De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis. Nat Protoc 8:1494–1512. https://doi.org/10.1038/nprot.2013.084

    Article  CAS  PubMed  Google Scholar 

  13. Kurtzer GM, Sochat V, Bauer MW (2017) Singularity: Scientific containers for mobility of compute. PLoS ONE 12:e0177459. https://doi.org/10.1371/journal.pone.0177459

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Buchfink B, Reuter K, Drost H-G (2021) Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat Methods 18:366–368. https://doi.org/10.1038/s41592-021-01101-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Cao X, Liu J, Pang J et al (2022) Common but nonpersistent acquisitions of plant viruses by plant-associated fungi. Viruses 14:2279. https://doi.org/10.3390/v14102279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Shi M, Lin X-D, Tian J-H et al (2016) Redefining the invertebrate RNA virosphere. Nature 540:539–543. https://doi.org/10.1038/nature20167

    Article  CAS  PubMed  Google Scholar 

  17. Langmead B, Wilks C, Antonescu V, Charles R (2019) Scaling read aligners to hundreds of threads on general-purpose processors. Bioinformatics 35:421–432. https://doi.org/10.1093/bioinformatics/bty648

    Article  CAS  PubMed  Google Scholar 

  18. Danecek P, Bonfield JK, Liddle J, et al (2021) Twelve years of SAMtools and BCFtools. GigaScience 10:giab008. https://doi.org/10.1093/gigascience/giab008

  19. Sadiq S, Chen Y-M, Zhang Y-Z, Holmes EC (2022) Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota. Virus Evol 8:veac055. https://doi.org/10.1093/ve/veac055

  20. Rozewicki J, Li S, Amada KM, et al (2019) MAFFT-DASH: Integrated protein sequence and structural alignment. Nucleic Acids Res gkz342. https://doi.org/10.1093/nar/gkz342

  21. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T (2009) TrimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25:1972–1973. https://doi.org/10.1093/bioinformatics/btp348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Minh BQ, Schmidt HA, Chernomor O et al (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 37:1530–1534. https://doi.org/10.1093/molbev/msaa015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Kondo H, Botella L, Suzuki N (2022) Mycovirus diversity and evolution revealed/inferred from recent studies. Annu Rev Phytopathol 60:307–336. https://doi.org/10.1146/annurev-phyto-021621-122122

    Article  CAS  PubMed  Google Scholar 

  24. Shackelton LA, Holmes EC (2008) The role of alternative genetic codes in viral evolution and emergence. J Theor Biol 254:128–134. https://doi.org/10.1016/j.jtbi.2008.05.024

    Article  CAS  PubMed  Google Scholar 

  25. Ruiz-Padilla A, Rodríguez-Romero J, Gómez-Cid I, et al (2021) Novel mycoviruses discovered in the mycovirome of a necrotrophic fungus. mBio 12:e03705-20. https://doi.org/10.1128/mBio.03705-20

  26. Dinan AM, Lukhovitskaya NI, Olendraite I, Firth AE (2020) A case for a negative-strand coding sequence in a group of positive-sense RNA viruses. Virus Evol 6:veaa007

  27. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17:10. https://doi.org/10.14806/ej.17.1.200

  28. Blevins T, Rajeswaran R, Shivaprasad PV et al (2006) Four plant dicers mediate viral small RNA biogenesis and DNA virus induced silencing. Nucleic Acids Res 34:6233–6246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. https://doi.org/10.1186/gb-2009-10-3-r25

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank Jihyun Won for helpful comments. This work was supported by the High-performance Computing Center, Institute of Plant Virology, Ningbo University, Ningbo, China.

Funding

This work was funded by the Ningbo Yongjiang grant (2022A-220-G).

Author information

Authors and Affiliations

  1. State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China

    Yangwei Gao, Zhongtian Xu, Ping Li, Xiaodi Hu, Jian-Ping Chen, Chuan-Xi Zhang & Yiyuan Li

Authors
  1. Yangwei Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhongtian Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ping Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Xiaodi Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jian-Ping Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chuan-Xi Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yiyuan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Yangwei Gao, Zhongtian Xu, and Yiyuan Li designed the research. Yangwei Gao, Zhongtian Xu, Ping Li, Xiaodi Hu, and Yiyuan Li performed the research. The first draft of the manuscript was written by Yangwei Gao and Yiyuan Li. All authors commented on and helped to revise previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Yiyuan Li.

Ethics declarations

Conflict of interest

The authors have no relevant financial or non-financial interests to disclose.

Additional information

Handling Editor: Ioly Kotta-Loizou.

Publisher's Note

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

Supplementary Information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Gao, Y., Xu, Z., Li, P. et al. Complete genome analysis of a novel narnavirus in sweet viburnum (Viburnum odoratissimum). Arch Virol 169, 90 (2024). https://doi.org/10.1007/s00705-024-06000-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00705-024-06000-y

Search

Navigation