Skip to main content
SpringerLink
Log in

Population structure of blackberry chlorotic ringspot virus in the United States

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

Abstract

Blackberry chlorotic ringspot virus is a subgroup 1 ilarvirus, detected in several rosaceous hosts exhibiting disease symptoms in Europe and the United States. The population structure of the virus was studied using isolates collected from wild and cultivated plants from six states in the United States. The results suggest a homogeneous virus population in the United States, similar to what observed within single orchards for other ilarviruses. Given the lack of evidence for host or geography-driven adaptation, it is hypothesized that the virus was recently introduced into the New World.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

References

  1. Bachmair A, Finley D, Varshavskey A (1986) In-vivo halflife of a protein is a function of its amino terminal residue. Science 234:179–186

    Article  PubMed  CAS  Google Scholar 

  2. Brigneti G, Voinnet O, Li WX, Ji LH, Ding SW, Baulcombe DC (1998) Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J 17:6739–6746

    Article  PubMed  CAS  Google Scholar 

  3. Bristow PR, Martin RR (1999) Transmission and the role of honeybees in field spread of blueberry shock ilarvirus, a pollen-borne virus of high bush blueberry. Phytopathology 89:124–130

    Article  PubMed  CAS  Google Scholar 

  4. Cerni S, Ruscić J, Nolasco G, Gatin Z, Krajacić M, Skorić D (2008) Stem pitting and seedling yellows symptoms of Citrus tristeza virus infection may be determined by minor sequence variants. Virus Genes 36:241–249

    Article  PubMed  CAS  Google Scholar 

  5. Fiore N, Fajardo TMV, Prodan S, Herranz MC, Aparicio F, Montealegre J, Elena SF, Pallás V, Sánchez-Navarro J (2008) Genetic diversity of the movement and coat protein of South American isolates of Prunus necrotic ringspot virus. Arch Virol 153:909–919

    Article  PubMed  CAS  Google Scholar 

  6. Greber RS, Teakle DS, Mink GI (1992) Thrips-facilitated transmission of prune dwarf and prunus necrotic ringspot virus from cherry pollen to cucumber. Plant Dis 76:1039–1041

    Article  Google Scholar 

  7. Hall TA (1999) BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  8. Hammond RW (2003) Phylogeny of isolates of Prunus necrotic ringspot virus from the ilarvirus ringtest and identification of group-specific features. Arch Virol 148:1195–1210

    Article  PubMed  CAS  Google Scholar 

  9. Herranz MC, Al Rwahnih M, Sánchez-Navarro JA, Elena SF, Choueiri E, Myrta A, Pallás V (2008) Low genetic variability in the coat and movement proteins of American plum line pattern virus isolates from different geographic origins. Arch Virol 153:367–373

    Article  PubMed  CAS  Google Scholar 

  10. Herranz MC, Pallas V (2004) RNA-binding properties and mapping of the RNA-binding domain from the movement protein of Prunus necrotic ringspot virus. J Gen Virol 85:761–768

    Article  PubMed  CAS  Google Scholar 

  11. Herron CM, Mirkov TE, Solís-Gracia N, Kahlke CJ, Skaria M, da Graça JV (2005) Severity of Citrus tristeza virus isolates from Texas. Plant Dis 89:575–580

    Article  CAS  Google Scholar 

  12. Huang X, Madan A (1999) CAP3, A DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed  CAS  Google Scholar 

  13. Jones AT, McGavin WJ, GePP V, Scott SW, Zimmerman MT (2006) Purification and properties of blackberry chlorotic ringspot, a new virus species in Subgroup 1 of the genus Ilarvirus found naturally infecting blackberry in the UK. Ann Appl Biol 149:125–135

    Article  CAS  Google Scholar 

  14. Kaiser WJ, Wyatt SD, Pesho GR (1982) Natural hosts and vectors of tobacco streak virus in eastern Washington. Phytopathology 72:1508–1512

    Article  Google Scholar 

  15. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  PubMed  CAS  Google Scholar 

  16. Korber B (2000) HIV signature and sequence variation analysis. In: Rodrigo AG, Learn GH (eds) Computational analysis of HIV molecular sequences, Chap. 4. Kluwer, Dordrecht, pp 55–72

  17. Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283–292

    Article  PubMed  CAS  Google Scholar 

  18. Lakshmi V, Hallan V, Ram R, Ahmed N, Zaidi AA, Varma A (2011) Diversity of Apple mosaic virus isolates in India based on coat protein and movement protein genes. Indian J Virol 22:44–49

    Article  Google Scholar 

  19. Laney AG, Keller KE, Martin RR, Tzanetakis IE (2011) A discovery 70 years in the making: characterization of the Rose rosette virus. J Gen Virol 92:1727–1732

    Article  PubMed  CAS  Google Scholar 

  20. Lutcke HA, Chow KC, Mickel FS, Moss KA, Kern HF, Scheelel GA (1987) Selection of AUG initiation codons differs in plants and animals. EMBO J 6:43–48

    PubMed  CAS  Google Scholar 

  21. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P (2010) RDP3, a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462–2463

    Article  PubMed  CAS  Google Scholar 

  22. Martin RR, MacFarlene S, Sabadnazovic S, Quito-Avila DF, Poudel B, Tzanetakis IE (2012) Virus and virus diseases of Rubus. Plant Dis. doi:10.1094/PDIS-04-12-0362-FE

    Google Scholar 

  23. Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and non-synonymous nucleotide substitutions. Mol Biol Evol 3:418–426

    PubMed  CAS  Google Scholar 

  24. Oliver JE, Freer J, Andersen RL, Cox KD, Robinson TL, Fuchs M (2009) Genetic diversity of Prunus necrotic ringspot virus isolates within a cherry orchard in New York. Plant Dis 93:599–606

    Article  CAS  Google Scholar 

  25. Petrzik K (2005) Capsid protein sequence gene analysis of Apple mosaic virus infecting pears. Eur J Plant Path 111:355–360

    Article  CAS  Google Scholar 

  26. Poudel B (2011) Epidemiological studies on Blackberry yellow vein associated virus and Blackberry chlorotic ringspot virus. MS Thesis, University of Arkansas, Fayetteville, AR. p 88

  27. Susaimuthu J, Tzanetakis IE, Gergerich RC, Kim KS, Martin RR (2008) Viral interactions lead to decline of blackberry plants. Plant Dis 92:1288–1292

    Article  CAS  Google Scholar 

  28. Tadu G, Winter S, Gadelseed AMA, Dafalla GA (2006) Association of East African cassava mosaic virus-Uganda (EACMV-UG) with cassava mosaic disease in Sudan. Plant Path 55:287

    Article  Google Scholar 

  29. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  PubMed  CAS  Google Scholar 

  30. Tripathi S, Suzuki JY, Ferreireira SA, Gonsalvis D (2008) Papaya ringspot virus-P, characteristics, pathogenicity, sequence variability and control. Mol Plant Pathol 9:269–280

    Article  PubMed  CAS  Google Scholar 

  31. Tzanetakis IE, Gergerich RC, Martin RR (2006) A new ilarvirus found in rose. Plant Pathol 55:568

    Article  Google Scholar 

  32. Tzanetakis IE, Halgren A, Mosier N, Martin R (2007) Identification and characterization of Raspberry mottle virus, a novel member of the Closteroviridae. Virus Res 127:26–33

    Article  PubMed  CAS  Google Scholar 

  33. Tzanetakis IE, Martin RR, Scott SW (2010) Genomic sequences of blackberry chlorotic ringspot virus and strawberry necrotic shock virus and the phylogeny of viruses in subgroup 1 of the genus Ilarvirus. Arch Virol 155:557–561

    Article  PubMed  CAS  Google Scholar 

  34. Tzanetakis IE, Postman PD, Martin RR (2007) First report of Blackberry chlorotic ringspot virus in Rubus sp. in the United States. Plant Dis 91:463

    Article  Google Scholar 

  35. Zuckerkandl E, Pauling L (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ (eds) Evolving genes and proteins. Academic Press, New york, pp 97–166

    Google Scholar 

Download references

Acknowledgments

The work presented here was made possible with funds from the North American Raspberry and Blackberry Association, USDA-NIFA-SCRI (2009-51181-06022) and USDA-APHIS-NCPN (10-8100-1572-CA), the Southern Region Small Fruit Consortium and the Arkansas Agricultural Experimental Station. The authors acknowledge Dr. S. Sabanadzovic and Mr. A. Laney for providing samples used in the study, and members of the Rubus Virus Disease Consortium for reviewing the manuscript.

Author information

Authors and Affiliations

  1. Division of Agriculture, Department of Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA

    Bindu Poudel & Ioannis E. Tzanetakis

Authors
  1. Bindu Poudel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ioannis E. Tzanetakis
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ioannis E. Tzanetakis.

Additional information

Sequences reported in this communication have been deposited in GenBank and assigned accession numbers JX429864-JX429895.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 98 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Poudel, B., Tzanetakis, I.E. Population structure of blackberry chlorotic ringspot virus in the United States. Arch Virol 158, 667–672 (2013). https://doi.org/10.1007/s00705-012-1523-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-012-1523-4

Keywords

Search

Navigation