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Archives of Virology

, Volume 163, Issue 3, pp 761–765 | Cite as

Molecular characterization of a novel luteovirus infecting apple by next-generation sequencing

  • Pan Shen
  • Xin Tian
  • Song Zhang
  • Fang Ren
  • Ping Li
  • Yun-qi Yu
  • Ruhui Li
  • Changyong Zhou
  • Mengji Cao
Annotated Sequence Record

Abstract

A new single-stranded positive-sense RNA virus, which shares the highest nucleotide (nt) sequence identity of 53.4% with the genome sequence of cherry-associated luteovirus South Korean isolate (ChALV-SK, genus Luteovirus), was discovered in this work. It is provisionally named apple-associated luteovirus (AaLV). The complete genome sequence of AaLV comprises 5,890 nt and contains eight open reading frames (ORFs), in a very similar arrangement that is typical of members of the genus Luteovirus. When compared with other members of the family Luteoviridae, ORF1 of AaLV was found to encompass another ORF, ORF1a, which encodes a putative 32.9-kDa protein. The ORF1-ORF2 region (RNA-dependent RNA polymerase, RdRP) showed the greatest amino acid (aa) sequence identity (59.7%) to that of cherry-associated luteovirus Czech Republic isolate (ChALV-CZ, genus Luteovirus). The results of genome sequence comparisons and phylogenetic analysis, suggest that AaLV should be a member of a novel species in the genus Luteovirus. To our knowledge, it is the sixth member of the genus Luteovirus reported to naturally infect rosaceous plants.

Notes

Acknowledgements

This research was supported by the National Natural Science Foundation of China (31501611), Chongqing Research Program of Basic Research and Frontier Technology (cstc2017jcyjBX0016), Fundamental Research Funds for the Central Universities (XDJK2016B021, SWU116012), Special Fund for Agro-Scientific Research in the Public Interest (201203076-01), and the Innovation Foundation of Chongqing City for Postgraduate (CYS17071).

Compliance with ethical standards

Ethical standards

I have read and have abided by the statement of ethical standards for manuscripts submitted to Archives of Virology.

Conflict of interest

All authors declare they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animal performed by any of the authors.

Supplementary material

705_2017_3633_MOESM1_ESM.txt (6 kb)
Supplementary material 1 (TXT 5 kb)
705_2017_3633_MOESM2_ESM.doc (410 kb)
Supplementary material 2 (DOC 410 kb)

References

  1. 1.
    Ali M, Hameed S, Tahir M (2014) Luteovirus: insights into pathogenicity. Arch Virol 159:2853–2860CrossRefPubMedGoogle Scholar
  2. 2.
    Domier LL (2012) Luteoviridae. 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, pp 1045–1053Google Scholar
  3. 3.
    Bag S, Al Rwahnih M, Li A, Gonzalez A, Rowhani A, Uyemoto JK, Sudarshana MR (2015) Detection of a new luteovirus in imported nectarine trees: a case study to propose adoption of metagenomics in post-entry quarantine. Phytopathology 105:840–846CrossRefPubMedGoogle Scholar
  4. 4.
    Igori D, Lim S, Baek D, Cho IS, Moon JS (2017) Complete nucleotide sequence of a highly divergent cherry-associated luteovirus (ChALV) isolate from peach in South Korea. Arch Virol.  https://doi.org/10.1007/s00705-017-3418-x Google Scholar
  5. 5.
    Lenz O, Pribylova J, Franova J, Koloniuk I, Spak J (2017) Identification and characterization of a new member of the genus luteovirus from cherry. Arch Virol 162:587–590CrossRefPubMedGoogle Scholar
  6. 6.
    Salem NM, Miller WA, Rowhani A, Golino DA, Moyne A-L, Falk BW (2008) Rose spring dwarf-associated virus has RNA structural and gene-expression features like those of Barley yellow dwarf virus. Virology 375:354–360CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Wu LP, Liu HW, Bateman M, Liu Z, Li R (2017) Molecular characterization of a novel luteovirus from peach identified by high-throughput sequencing. Arch Virol.  https://doi.org/10.1007/s00705-017-3388-z Google Scholar
  8. 8.
    Salem N, Golino DA, Falk BW, Rowhani A (2008) Identification and partial characterization of a new luteovirus associated with rose spring dwarf disease. Plant Dis 92:508–512CrossRefGoogle Scholar
  9. 9.
    Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874CrossRefPubMedGoogle Scholar
  10. 10.
    Li R, Mock R, Huang Q, Abad J, Hartung J, Kinard G (2008) A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens. J Virol Methods 154:48–55CrossRefPubMedGoogle Scholar
  11. 11.
    Domier Leslie L, McCoppin Nancy K, Larsen RC, D’Arcy CJ (2002) Nucleotide sequence shows that Bean leafroll virus has a Luteovirus-like genome organization. J Gen Virol 83:1791–1798CrossRefPubMedGoogle Scholar
  12. 12.
    Kim K-H, Lommel SA (1998) Sequence element required for efficient 21 ribosomal frameshifting in red clover necrotic mosaic dianthovirus. Virology 250:50–59CrossRefPubMedGoogle Scholar
  13. 13.
    Palanga E, Martin DP, Galzi S, Zabre J, Bouda Z, Neya JB, Sawadogo M, Traore O, Peterschmitt M, Roumagnac P, Filloux D (2017) Complete genome sequences of cowpea polerovirus 1 and cowpea polerovirus 2 infecting cowpea plants in Burkina Faso. Arch Virol 162:2149–2152CrossRefPubMedGoogle Scholar
  14. 14.
    Smirnova E, Firth AE, Miller WA, Scheidecker D, Brault V, Reinbold C, Rakotondrafara AM, Chung BY, Ziegler-Graff V (2015) Discovery of a small non-AUG-initiated ORF in poleroviruses and luteoviruses that is required for long-distance movement. PLoS Pathog 11:e1004868CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Miller WA, Dinesh-Kumar SP, Paul CP (1995) Luteovirus gene expression. Crit Rev Plant Sci 14:179–211CrossRefGoogle Scholar
  16. 16.
    Guo L, Allen EM, Miller WA (2001) Base-pairing between untranslated regions facilitates translation of uncapped, nonpolyadenylated viral RNA. Mol Cell 7:1103–1109CrossRefPubMedGoogle Scholar
  17. 17.
    Gilmer R, Mink GI, Shay JR, Stouffer RF, McCrum RC (1971) Latent viruses of apple. I. Detection with woody indicators. Search (Agric) 1 (10): 1–21. NY State Agric Exp St, Geneva, NYGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria 2017

Authors and Affiliations

  1. 1.National Citrus Engineering Research Center, Citrus Research InstituteSouthwest UniversityChongqingChina
  2. 2.Academy of Agricultural Sciences, Southwest UniversityChongqingChina
  3. 3.Research Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
  4. 4.USDA-ARS, National Germplasm Resources LaboratoryBeltsvilleUSA

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