Skip to main content
SpringerLink
Log in

Comparative analysis of cherry virus A genome sequences assembled from deep sequencing data

  • Brief Report
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Cherry virus A (CVA) is a ubiquitous graft-transmissible virus that mainly infects Prunus spp. Next-generation sequencing was applied to 39 tree fruit specimens infected with CVA, and 75 full and 16 partial-length CVA genome sequences were assembled. Phylogenetic analysis of these and 11 previously sequenced CVA genomes resulted in six major clusters with no observable relationship between the host and the assembled genome sequences. Recombination analysis detected four recombinants. Consistent single-nucleotide polymorphism (SNP) patterns were observed between the 75 full-length genomes and their sequence clouds, which supports a quasispecies model for CVA evolution.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

References

  1. Jelkmann W (1995) Cherry virus A: cDNA cloning of dsRNA, nucleotide sequence analysis and serology reveal a new plant capillovirus in sweet cherry. J Gen Virol 76(8):2015–2024

    Article  CAS  PubMed  Google Scholar 

  2. James D, Jelkmann W (1998) Detection of Cherry virus A in Canada and Germany. Acta Hortic 472:299–303

    Article  CAS  Google Scholar 

  3. Foissac X, Svanella-Dumas L, Gentit P, Dulucq MJ, Marais A et al (2005) Polyvalent degenerate oligonucleotides reverse transcription-polymerase chain reaction: a polyvalent detection and characterization tool for Trichoviruses, Capilloviruses, and Foveaviruses. Phytopathology 95(6):617–625

    Article  CAS  PubMed  Google Scholar 

  4. Eastwell KC, Bernardy MG (1998) Relationship of Cherry virus A to little cherry disease in British Columbia. Acta Hortic 472:305–313

    Article  CAS  Google Scholar 

  5. Mandic B, Matic S, Al Rwahnih M, Jelkmann W, Myrta A (2007) Viruses of sweet and sour cherry in Serbia. J. Plant Pathol. 89:103–108

    CAS  Google Scholar 

  6. Marais A, Svanella-Dumas L, Candresse T, Barone M, Ragozzino A et al (2008) Genomic diversity of cherry capillovirus a (CVA) and suitability of various assays for its detection, International Society for Horticultural Science (ISHS). Belgium, Leuven

    Google Scholar 

  7. Koinuma H, Nijo T, Iwabuchi N, Yoshida T, Keima T et al (2016) First complete genome sequence of Cherry virus A. Genome Announc 4(3):00498-16. doi:10.1128/genomeA.00498-16

    Article  Google Scholar 

  8. Wang J, Zhai Y, Liu W, Dhingra A, Pappu HR et al (2016) Structure and genome organization of Cherry virus A (Capillovirus, Betaflexiviridae) from China using small RNA sequencing. Genome Announc 4(3):e00364-16. doi:10.1128/genomeA.e00364-16

    Article  PubMed  PubMed Central  Google Scholar 

  9. Kesanakurti P, Belton M, Saeed H, Rast H, Boyes I et al (2016) Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control. J Virol Methods 236:35–40

    Article  CAS  PubMed  Google Scholar 

  10. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33(7):1870–1874

    Article  CAS  PubMed  Google Scholar 

  13. Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1(1):vev003. doi:10.1093/ve/vev003

  14. Fourment M, Gibbs AJ, Gibbs MJ (2008) SWeBLAST: a sliding window web-based BLAST tool for recombination analysis. J Virol Methods 15(1–2):98–101

    Article  Google Scholar 

  15. Aaskov J, Buzacott K, Thu HM, Lowry K, Holmes EC (2006) Long-term transmission of defective RNA viruses in humans and Aedes mosquitoes. Science 311(5758):236–238

    Article  CAS  PubMed  Google Scholar 

  16. Lauring AS, Andino R (2010) Quasispecies theory and the behavior of RNA viruses. PLoS Pathog 6(7):e1001005. doi:10.1371/journal.ppat.1001005

    Article  PubMed  PubMed Central  Google Scholar 

  17. Simon-Loriere E, Holmes EC (2011) Why do RNA viruses recombine? Nature Rev Microbiol 9(8):617–626

    Article  CAS  Google Scholar 

  18. Bujarski JJ (2013) Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives. Front Plant Sci 4

  19. Schneider WL, Roossinck MJ (2001) Genetic diversity in RNA virus quasispecies is controlled by host-virus interactions. J Virol 75(14):6566–6571

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, BC, V8L 1H3, Canada

    Prasad Kesanakurti, Hanaa Saeed, Heidi Rast, Ian Boyes & Michael Rott

  2. Department of Fisheries and Oceans Canada, 4250 Commerce Circle, Victoria, BC, V8Z 4M2, Canada

    Mark Belton

Authors
  1. Prasad Kesanakurti
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mark Belton
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hanaa Saeed
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Heidi Rast
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Ian Boyes
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Michael Rott
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael Rott.

Ethics declarations

Funding information

This work was supported by funding from Genomics Research and Development Initiative, Protection of Canadian Biodiversity and Trade from the Impacts of Global Change through improved ability to monitor Invasive Alien and Quarantine Species.

Conflict of interest

The authors declare no competing interests.

Additional information

Depositories

The GenBank accession numbers for genome sequences: KY510845–KY510919.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kesanakurti, P., Belton, M., Saeed, H. et al. Comparative analysis of cherry virus A genome sequences assembled from deep sequencing data. Arch Virol 162, 2821–2828 (2017). https://doi.org/10.1007/s00705-017-3394-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-017-3394-1

Search

Navigation