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Complete nucleotide sequence of loquat virus A, a member of the family Betaflexiviridae with a novel genome organization

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Abstract

Analysis of a loquat tree with leaf curl symptoms by deep sequencing revealed a novel virus with a single-stranded RNA genome, for which the name “loquat virus A” (LoVA) was proposed. The complete genome sequence comprised 7553 nucleotides (nt) and an additional poly(A) tail at the 3′ terminus. Sequence comparisons of LoVA showed moderate similarity to cherry virus A (CVA), currant virus A (CuVA), and mume virus A (MuVA), which are members of the genus Capillovirus in the family Betaflexiviridae. Phylogenetic analysis of the full-genome nt sequence and replicase-like protein supported the placement of LoVA within the genus Capillovirus. However, it has a distinct genome organization, differing from recognized capilloviruses, as it contains three open reading frames (ORFs), with the coat protein (CP) expressed separately from the replication-associated protein (RP) rather than being encoded in the same ORF. This indicates that LoVA is a novel member of the genus Capillovirus in the family Betaflexiviridae with a distinct genomic organization.

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References

  1. Roossinck MJ, Martin DP, Roumagnac P (2015) Plant virus metagenomics: advances in virus discovery. Phytopathology 105:716–727

    Article  CAS  Google Scholar 

  2. Adams MJ, Candresse T, Hammond J, Kreuze JF, Martelli GP, Namba S, Pearson MN, Ryu KH, Saldarelli P, Yoshikawa N (2012) Family Betaflexiviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier Academic Press, San Diego, pp 920–941

    Google Scholar 

  3. ICTV Master Species List (version MSL34). https://talk.ictvonline.org/taxonomy/vmr/m/vmr-file-repository/8287. Accessed Apr 2019

  4. Tatineni S, Afunian MR, Gowda S, Hilf ME, Bar-Joseph M, Dawson WO (2009) Characterization of the 5′- and 3′-terminal subgenomic RNAs produced by a capillovirus: evidence for a CP subgenomic RNA. Virology 385:521–528

    Article  CAS  Google Scholar 

  5. Sgroi F, Di Trapani AM, Squatrito R, Tudisca S, Testa R (2014) Economic assessment of Sicilian loquat orchards. Acta Hortic 1092:33–36. https://doi.org/10.17660/ActaHortic.2015.1092.3

    Article  Google Scholar 

  6. Liu Q, Xuan Z, Wu J, Qiu Y, Li M, Zhang S, Wu D, Li R, Cao M (2019) Loquat is a new natural host of apple stem grooving virus and apple chlorotic leaf spot virus in China. Plant Dis. https://doi.org/10.1094/PDIS-04-19-0721-PDN

    Article  PubMed  Google Scholar 

  7. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D et al (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839

    Article  CAS  Google Scholar 

  8. Cao M, Li P, Zhang S, Yang F, Zhou Y, Wang X, Li R, Li Z (2018) Molecular characterization of a novel citrivirus from citrus using next-generation sequencing. Arch Virol 163:3479–3482

    Article  CAS  Google Scholar 

  9. Petrzik K, Pribylova J, Koloniuk I, Spak J (2016) Molecular characterization of a novel capillovirus from red currant. Arch Virol 161:1083–1086

    Article  CAS  Google Scholar 

  10. Mushegian AR, Elena SF (2015) Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes. Virology 476:304–315

    Article  CAS  Google Scholar 

  11. Simon-Loriere E, Holmes EC (2011) Why do RNA viruses recombine? Nat Rev Microbiol 9:617–626

    Article  CAS  Google Scholar 

  12. Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003

    Article  Google Scholar 

Download references

Acknowledgements

This research was supported by the Intergovernmental International Science, Technology and Innovation (STI) Collaboration Key Project of China′s National Key R&D Program (NKP) (2017YFE0110900), Fundamental Research Funds for the Central Universities (XDJK2018AA002), Chongqing Research Program of Basic Research and Frontier Technology (cstc2017jcyjBX0016), Overseas Expertise Introduction Project for Discipline Innovation (111 Center) (B18044). We thank LetPub (www.letpub.com) for its linguistic assistance during the preparation of this manuscript. We thank the editor and three anonymous reviewers for their constructive comments and suggestions.

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Authors and Affiliations

  1. National Citrus Engineering Research Center, Citrus Research Institute, Southwest University, Chongqing, 400712, China

    Qiyan Liu, Liu Yang, Zhiyou Xuan, Jiaxing Wu, Yuanjian Qiu, Song Zhang, Changyong Zhou & Mengji Cao

  2. Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China

    Qiyan Liu, Liu Yang, Zhiyou Xuan, Jiaxing Wu, Yuanjian Qiu, Song Zhang, Changyong Zhou & Mengji Cao

  3. College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China

    Di Wu

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  1. Qiyan Liu
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Correspondence to Mengji Cao.

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Fig. S1

Scheme of rapid amplification of cDNA ends (RACE), RT-PCR amplification of overlapped fragments, and Sanger sequencing (JPEG 75 kb)

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Supplementary material 3 (TXT 7 kb)

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Liu, Q., Yang, L., Xuan, Z. et al. Complete nucleotide sequence of loquat virus A, a member of the family Betaflexiviridae with a novel genome organization. Arch Virol 165, 223–226 (2020). https://doi.org/10.1007/s00705-019-04444-1

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  • DOI: https://doi.org/10.1007/s00705-019-04444-1

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