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Exploration of plant transcriptomes reveals five putative novel poleroviruses and an enamovirus

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Abstract

Transcriptome datasets available in public domain serve as valuable resource for identification and characterization of novel viral genomes. Poleroviruses are economically important plant-infecting RNA viruses belonging to the family Solemoviridae. In the present study, we explored the plant transcriptomes available in public domain and identified five putative novel poleroviruses tentatively named as Foeniculum vulgare polerovirus (FvPV), Kalanchoe marnieriana polerovirus (KmPV), Paspalum notatum polerovirus (PnPV), Piper methysticum polerovirus (PmPV), Trachyspermum ammi polerovirus (TaPV) and a novel enamovirus named as Celmisia lyallii enamovirus (ClEV) in Foeniculum vulgare, Kalanchoe marnieriana, Paspalum notatum, Piper methysticum, Trachyspermum ammi and Celmisia lyallii, respectively. Coding-complete genomes (5.56–5.74 kb) of CIEV, KmPV, PnPV, PmPV and TaPV were recovered while only the partial genome of FvPV could be recovered. The genome organization of identified viruses except ClEV is 5’–ORF0–ORF1–ORF2–ORF3a–ORF3–ORF4–ORF5–3’ while that of ClEV is 5’–ORF0–ORF1–ORF2–ORF3–ORF5–3’. Phylogenetic analysis revealed that poleroviruses of apiaceous plants formed a monophyletic clade within the genus Polerovirus.

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Data availability

The viral genome sequences described in the study are available at NCBI Third Party Annotation database with accession numbers BK059370-BK059376.

References

  1. Sõmera M, Fargette D, Hébrard E, Sarmiento C (2021) ICTV virus taxonomy profile: Solemoviridae. J Gen Virol 102:001707

    Article  Google Scholar 

  2. Delfosse VC, Barrios Barón MP, Distefano AJ (2021) What we know about poleroviruses: advances in understanding the functions of polerovirus proteins. Plant Pathol 70:1047–1061

    Article  Google Scholar 

  3. Bejerman N, Dietzgen RG, Debat H (2021) Illuminating the plant rhabdovirus landscape through metatranscriptomics data. Viruses 13:1304

    Article  CAS  Google Scholar 

  4. Debat HJ, Bejerman N (2019) Novel bird’s-foot trefoil RNA viruses provide insights into a clade of legume-associated enamoviruses and rhabdoviruses. Arch Virol 164:1419–1426

    Article  CAS  Google Scholar 

  5. Sidharthan VK, Baranwal VK (2021) Mining of the water hyssop (Bacopa monnieri) transcriptome reveals genome sequences of two putative novel rhabdoviruses and a solendovirus. Arch Virol 166:1985–1990

    Article  CAS  Google Scholar 

  6. Sidharthan VK, Kalaivanan NS, Baranwal VK (2021) Identification of two putative novel RNA viruses in the transcriptome datasets of small cardamom. Plant Gene 27:100305

    Article  CAS  Google Scholar 

  7. Simmonds P, Adams MJ, Benkő M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R (2017) Consensus statement: virus taxonomy in the age of metagenomics. Nat Rev Microbiol 15:161–168

    Article  CAS  Google Scholar 

  8. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Bushmanova E, Antipov D, Lapidus A, Prjibelski AD (2019) rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. GigaScience 8:giz100

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  11. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188–1190

    Article  CAS  Google Scholar 

  12. Pooggin MM (2018) Small RNA-omics for plant virus identification, virome reconstruction, and antiviral defense characterization. Front Microbiol 9:2779

    Article  Google Scholar 

  13. Silva JM, Al Rwahnih M, Blawid R, Nagata T, Fajardo TV (2017) Discovery and molecular characterization of a novel enamovirus, grapevine enamovirus-1. Virus Genes 53:667–671

    Article  CAS  Google Scholar 

  14. Firth AE, Brierley I (2012) Non-canonical translation in RNA viruses. J Gen Virol 93:1385–1409

    Article  CAS  Google Scholar 

  15. Brown CM, Dinesh-Kumar SP, Miller WA (1996) Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV coat protein gene stop codon. J Virol 70:5884–5892

    Article  CAS  Google Scholar 

  16. Krueger EN, Beckett RJ, Gray SM, Miller WA (2013) The complete nucleotide sequence of the genome of Barley yellow dwarf virus-RMV reveals it to be a new polerovirus distantly related to other yellow dwarf viruses. Front Microbiol 4:205

    Article  CAS  Google Scholar 

  17. Howyzeh MS, Noori SA, Shariati V, Amiripour M (2018) Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L. Sci Rep 8:13405

    Article  Google Scholar 

  18. Palumbo F, Vannozzi A, Vitulo N, Lucchin M, Barcaccia G (2018) The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants. Sci Rep 8:10459

    Article  Google Scholar 

  19. Pluskal T, Torrens-Spence MP, Fallon TR, De Abreu A, Shi CH, Weng JK (2019) The biosynthetic origin of psychoactive kavalactones in kava. Nat Plants 5:867–878

    Article  Google Scholar 

  20. Podio M, Colono C, Siena L, Ortiz JP, Pessino SC (2021) A study of the heterochronic sense/antisense RNA representation in florets of sexual and apomictic Paspalum notatum. BMC Genomics 22:185

    Article  CAS  Google Scholar 

  21. Kuligowska K, Lütken H, Christensen B, Müller R (2015) Quantitative and qualitative characterization of novel features of Kalanchoë interspecific hybrids. Euphytica 205:927–940

    Article  Google Scholar 

  22. Bejerman N, Debat H (2021) Exploring the tymovirids landscape through metatranscriptomics data. bioRxiv. https://doi.org/10.1101/2021.07.15.452586

    Article  Google Scholar 

  23. Samarth LR, Song J, Macknight RC, Jameson PE (2019) Identification of flowering-time genes in mast flowering plants using de novo transcriptomic analysis. PLoS ONE 14:e0216267

    Article  CAS  Google Scholar 

  24. Samarth LR, Kelly D, Turnbull MH, Macknight RC, Poole AM, Jameson PE (2021) Molecular control of the floral transition in the mast seeding plant Celmisia lyallii (Asteraceae). Mol Ecol 30:1846–1863

    Article  CAS  Google Scholar 

  25. Hu Z, Nie Z, Yan C, Huang H, Ma X, Wang Y, Ye N, Tuskan GA, Yang X, Yin H (2021) Transcriptome and degradome profiling reveals a role of miR530 in the circadian regulation of gene expression in Kalanchoë marnieriana. Cells 10:1526

    Article  CAS  Google Scholar 

  26. Ortiz JP, Leblanc O, Rohr C, Grisolia M, Siena LA, Podio M, Colono C, Azzaro C, Pessino SC (2019) Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum. BMC Genomics 20:487

    Article  Google Scholar 

  27. Ortiz JP, Revale S, Siena LA, Podio M, Delgado L, Stein J, Leblanc O, Pessino SC (2017) A reference floral transcriptome of sexual and apomictic Paspalum notatum. BMC Genomics 18:318

    Article  Google Scholar 

  28. Xiao M, Zhang Y, Chen X, Lee EJ, Barber CJ, Chakrabarty R, Desgagné-Penix I, Haslam TM, Kim YB, Liu E, MacNevin G (2013) Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest. J Biotechnol 166:122–134

    Article  CAS  Google Scholar 

  29. Mayo MA, Ziegler-Graff V (1996) Molecular biology of luteoviruses. Adv Virus Res 46:413–460

    Article  CAS  Google Scholar 

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Acknowledgements

We thank ICAR for the Advanced Supercomputing Hub for Omics Knowledge in Agriculture (ASHOKA) facility available at ICAR-IASRI, New Delhi, India. The authors are grateful to the Head, Division of Genetics and Tree Improvement, the GCR, the Director, IFB (ICFRE), Hyderabad, the Head, Division of Plant Pathology and the Director, ICAR-IARI, New Delhi, for their support. The authors are also thankful to the original submitters of datasets/contigs explored/used in the study.

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Authors and Affiliations

  1. Division of Genetics and Tree Improvement, Institute of Forest Biodiversity (ICFRE), Hyderabad, India

    V. Kavi Sidharthan

  2. ICAR-Indian Institute of Vegetable Research, Varanasi, India

    Krishnan Nagendran

  3. Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India

    V. K. Baranwal

Authors
  1. V. Kavi Sidharthan
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  2. Krishnan Nagendran
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  3. V. K. Baranwal
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Contributions

VKS involved in conceptualization, methodology, formal analysis, investigation and writing—original draft preparation; KN contributed to formal analysis and investigation, writing—review and editing; VKB participated in conceptualization, resources, supervision, writing—review and editing.

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Correspondence to V. K. Baranwal.

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Kavi Sidharthan, V., Nagendran, K. & Baranwal, V.K. Exploration of plant transcriptomes reveals five putative novel poleroviruses and an enamovirus. Virus Genes 58, 244–253 (2022). https://doi.org/10.1007/s11262-022-01896-7

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