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Complete genomic sequence of crow-dipper mosaic-associated virus, a novel macluravirus infecting Pinellia ternata

  • Rong Wang
  • Bingwei Chen
  • Yong Li
  • Tianyou Wang
  • Wanlong DingEmail author
Annotated Sequence Record
  • 22 Downloads

Abstract

A new macluravirus infecting Pinellia ternata in China was identified by high-throughput sequencing (HTS) and tentatively named “crow-dipper mosaic-associated virus” (CrdMV). The complete genome sequence of CrdMV was determined by reverse transcription (RT) PCR and rapid amplification of cDNA ends (RACE) PCR. The genomic RNA of CrdMV consists of 8,454 nucleotides (nt), excluding the poly(A) tail at the 3′ end. CrdMV has a genomic structure typical of macluraviruses, with large open reading frame encoding a polyprotein of 2,696 amino acids (aa). CrdMV shares 54.40%–59.37% nt sequence identity at the genome sequence level, 48.00%–58.58% aa sequence identity, at the polyprotein sequence level and 37.27%–49.22% aa sequence identity at the CP sequence level with other members of the genus Macluravirus. These values are well below the species demarcation threshold for the family Potyviridae. Phylogenetic analysis based on the amino acid sequences of polyproteins confirmed that CrdMV clusters closely with broad-leafed dock virus A (BDVA, GenBank accession no. KU053507). These results suggest that CrdMV should be considered a distinct member of the genus Macluravirus.

Notes

Funding

This work was supported by the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (Grant number 2016-I2M-3-017).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Human and animal rights

This study did not include experiments with human participants or animals performed by any of the authors.

Supplementary material

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References

  1. 1.
    Adams MJ, Zerbini FM, French R et al (2012) Potyviridae. In: King AMQ, Adams MJ, Carstens EB et al (eds) Virus taxonomy: ninth report of the international committee on taxonomy of viruses. Elsevier, San Diego, pp 1069–1089Google Scholar
  2. 2.
    Elangovan S, Srikakulam N, Pandi G et al (2019) The first complete genomic sequence of cardamom mosaic virus, a member of the genus Macluravirus (family Potyviridae). Arch Virol 164:1723–1726CrossRefGoogle Scholar
  3. 3.
    Lan P, Meng Y, Shen P et al (2018) Complete genome sequence of yam chlorotic necrosis virus, a novel macluravirus infecting yam. Arch Virol 163:2275–2278CrossRefGoogle Scholar
  4. 4.
    Zhang P, Peng J, Guo H et al (2016) Complete genome sequence of yam chlorotic necrotic mosaic virus from Dioscorea parviflora. Arch Virol 161:1715–1717CrossRefGoogle Scholar
  5. 5.
    Chen J, Li D (1994) Separating and partial characterization of two viruses from natural-infected Pinellia ternata. Biotechnology 4(4):24–28Google Scholar
  6. 6.
    Chen J, Zheng HY, Lin L et al (2004) A virus related to Soybean mosaic virus from Pinellia ternata in China and its comparison with local soybean SMV isolates. Arch Virol 149(2):349–363CrossRefGoogle Scholar
  7. 7.
    Cui LY, Pang XJ, Qi YH et al (2018) Identification of the pathogens of Pinellia ternata virus by small RNA deep sequencing. Chin J Biochem Mol Biol 34(12):1334–1341Google Scholar
  8. 8.
    Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829CrossRefGoogle Scholar
  9. 9.
    Scotto-Lavino E, Du G, Frohman MA (2006) 3’ end cDNA amplification using classic RACE. Nat Protoc 1(6):2742–2745CrossRefGoogle Scholar
  10. 10.
    Scotto-Lavino E, Du G, Frohman MA (2006) 5’ end cDNA amplification using classic RACE. Nat Protoc 1(6):2555–2562CrossRefGoogle Scholar
  11. 11.
    Urcuqui-Inchima S, Haenni AL, Bernardi F (2001) Potyvirus proteins: a wealth of functions. Virus Res 74:157–175CrossRefGoogle Scholar
  12. 12.
    Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739CrossRefGoogle Scholar
  13. 13.
    Martin DP, Murrell B, Golden M et al (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol.  https://doi.org/10.1093/ve/vev003 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina

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