Distribution and phylogenetic analysis of the 3′UTR and coat protein gene of Iranian Beet black scorch virus

  • Asghar Samiei
  • Mohsen MehrvarEmail author
  • Claudio Ratti
  • Mohammad Zakiaghl
Original Article


Beet black scorch virus (BBSV) was surveyed in major sugar beet cultivation areas in Iran in 2008–2013 growing seasons. A total of 148 out of 308 samples (48%) collected in seven Iranian provinces were BBSV-infected, as shown by RT-PCR. To investigate the genetic diversity of Iranian BBSV isolates, sequences of the coat protein (CP) gene and of the 3′ untranslated region (3′UTR) were compared to corresponding sequences in GenBank. The CP nucleotide sequence identity among Iranian isolates was 87.9–99.9%. They shared nucleotide sequence identities of 88–89.8% with those of other BBSV isolates available at GenBank. Phylogenetic analyses of CP sequences demonstrated that Iranian isolates were distant from Chinese and US isolates at both nucleotide and amino acid levels. Three isolates from western provinces of the country showed independent divergent lineage compared with other Iranian isolates. Comparison of 3′UTR region of BBSV indicated that all Iranian isolates, except four isolates from the west of the country, were distinct from European, Chinese, and US isolates. Population genetic analyses revealed that BBSV populations from west of Iran had distinct evolutionary divergence and differentiated from eastern BBSV isolates. Our results indicated that purifying selection might have contributed to evolution of the isolates belonging to the four identified BBSV subgroups with infrequent genetic exchanges occurring between them. Phylogenetic analyses and estimation of genetic distance indicated that Iranian isolates in both CP and 3′UTR genomic regions had wider genetic diversity than isolates from other parts of the world. Based on the result of phylogenetic and population analyses, we suggest discriminating two different groups, namely BBSV western and BBSV eastern strains.


Phylogenetic analysis Iran Genetic diversity Beet black scorch virus Beet 


Compliance with ethical standards

Conflict of interest

Asghar Samiei, Mohsen Mehrvar, Claudio Ratti, and Mohammad Zakiaghl declare that they have no conflict of interest.

Supplementary material

41348_2019_261_MOESM1_ESM.docx (181 kb)
Supplementary material 1 (DOCX 180 kb)


  1. Biswas S, Akey JM (2006) Genomic insights into positive selection. Trends Genet 22(8):437–446Google Scholar
  2. Callaway A, Giesman-Cookmeyer D, Gillock E, Sit T, Lommel S (2001) The multifunctional capsid proteins of plant RNA viruses. Annu Rev Phytopathol 39(1):419–460Google Scholar
  3. Coutts RH, Rigden JE, Slabas AR, Lomonossoff GP, Wise PJ (1991) The complete nucleotide sequence of tobacco necrosis virus strain D. J Gen Virol 72(7):1521–1529Google Scholar
  4. Drouzas A, Offei S, Coutis R (1996) Subcellular location and expression of tobacco necrosis Necrovirus p7a protein. J Phytopathol 144(6):297–299Google Scholar
  5. Farzadfar S, Pourrahim R, Golnaraghi A, Ahoonmanesh A (2007) Surveys of beet necrotic yellow vein virus, beet soil borne virus, beet virus Q and polymyxa betae in sugar beet fields in Iran. J Plant Pathol 92:277–281Google Scholar
  6. Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy: VIIIth report of the International Committee on taxonomy of viruses. Academic Press, LondonGoogle Scholar
  7. Fu Y-X, Li W-H (1993) Statistical tests of neutrality of mutations. Genetics 133(3):693–709Google Scholar
  8. González-Vázquez M, Ayala J, García-Arenal F, Fraile A (2009) Occurrence of Beet black scorch virus infecting sugar beet in Europe. Plant Dis 93(1):21–24Google Scholar
  9. Hudson RR (2000) A new statistic for detecting genetic differentiation. Genetics 155(4):2011–2014Google Scholar
  10. Hudson RR, Slatkin M, Maddison W (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132(2):583–589Google Scholar
  11. Jiang J, Zhang J, Che S, Yang D, Yu J, Cai Z, Liu Y (1999) Transmission of Beet black scorch virus by Olpidium brassicae. Acta Agric Univ Jiangxiensis 21(4):525–528Google Scholar
  12. Koenig R, Valizadeh J (2008) Molecular and serological characterization of an Iranian isolate of Beet black scorch virus. Arch Virol 153(7):1397–1400Google Scholar
  13. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452Google Scholar
  14. Liu J, Xian H (1995) Preliminary report on Beet black scorch virus. China Sugar Beet 3:30–31Google Scholar
  15. McDonald JH, Kreitman M (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature 351(6328):652Google Scholar
  16. Mehrvar M (2009) Diversity of soil-borne sugar beet viruses in Iran. Ph.D. thesis, UCL, Louvain-la-Neuve, Belgium, 149 pGoogle Scholar
  17. Moln A, Havelda Z, Dalmay T, Szutorisz H, Burgy J (1997) Complete nucleotide sequence of tobacco necrosis virus strain DH and genes required for RNA replication and virus movement. J Gen Virol 78(6):1235–1239Google Scholar
  18. Moradi Z, Nazifi E, Mehrvar M (2017) Occurrence and evolutionary analysis of coat protein gene sequences of Iranian isolates of Sugarcane mosaic virus. Plant Pathol J 33(3):296Google Scholar
  19. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19(18):2496–2497Google Scholar
  20. Shen R, Miller WA (2007) Structures required for poly (A) tail-independent translation overlap with, but are distinct from, cap-independent translation and RNA replication signals at the 3′ end of Tobacco necrosis virus RNA. Virology 358(2):448–458Google Scholar
  21. Sohi H, Maleki M (2004) Evidence for presence of types A and B of Beet necrotic yellow vein virus (BNYVV) in Iran. Virus Gene 29(3):353–358Google Scholar
  22. Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3):585–595Google Scholar
  23. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680Google Scholar
  24. Tsompana M, Abad J, Purugganan M, Moyer J (2005) The molecular population genetics of the Tomato spotted wilt virus (TSWV) genome. Mol Ecol 14(1):53–66Google Scholar
  25. Weiland JJ, Van Winkle D, Edwards MC, Larson RL, Shelver WL, Freeman TP, Liu H-Y (2007) Characterization of a US isolate of Beet black scorch virus. Phytopathology 97(10):1245–1254Google Scholar
  26. Yuan X, Cao Y, Xi D, Guo L, Han C, Li D, Zhai Y, Yu J (2006) Analysis of the subgenomic RNAs and the small open reading frames of Beet black scorch virus. J Gen Virol 87(10):3077–3086Google Scholar
  27. Zhang X, Zhao X, Zhang Y, Niu S, Qu F, Zhang Y, Han C, Yu J, Li D (2013) N-terminal basic amino acid residues of Beet black scorch virus capsid protein play a critical role in virion assembly and systemic movement. Virol J 10(1):200Google Scholar
  28. Zhao X, Wang X, Dong K, Zhang Y, Hu Y, Zhang X, Chen Y, Wang X, Han C, Yu J (2015) Phosphorylation of Beet black scorch virus coat protein by PKA is required for assembly and stability of virus particles. Sci Rep 5:11585Google Scholar

Copyright information

© Deutsche Phytomedizinische Gesellschaft 2019

Authors and Affiliations

  1. 1.Department of Plant Protection, Faculty of AgricultureFerdowsi University of MashhadMashhadIran
  2. 2.DISTAL - Patologia VegetaleUniversità di BolognaBolognaItaly

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