Molecular characterization and detection of Vicia cryptic virus in different Vicia faba cultivars

Arch Virol. 2007;152(8):1477-88. doi: 10.1007/s00705-007-0966-5. Epub 2007 May 29.

Abstract

After extraction of double-stranded (ds) RNAs from Vicia faba, dsRNA1 and dsRNA2 of Vicia cryptic virus (VCV), a member of the genus Alphacryptovirus (family Partitiviridae), were detected in six out of seven different cultivars by agarose gel electrophoresis. In attempts to sequence the complete VCV genome, the dsRNA1 and dsRNA2 sequences from a total of five different V. faba cultivars were determined. Analysis of these sequences indicated that V. faba cultivars contain almost indistinguishable VCV sequences. The larger dsRNA1 was 2012 bp in length and contained a major open reading frame (ORF) encoding a putative RNA-dependent RNA polymerase (RdRp). The smaller dsRNA2 was 1779 bp in length and comprised a single ORF on its plus-strand encoding the coat protein (CP). The sequences of the dsRNA1 and dsRNA2 ORFs shared highest amino acid sequence identities (84 and 56%, respectively) with the corresponding gene products of the alphacryptovirus white clover cryptic virus 1 (WCCV-1). The 5'-terminal untranslated regions of dsRNA1 and dsRNA2 of VCV were highly conserved and were strikingly similar to the corresponding regions of WCCV-1. RdRp amino acid sequence alignments revealed conserved motifs, which correlate with the phylogenetic clustering of the family Partitiviridae.

MeSH terms

  • Amino Acid Motifs
  • Base Sequence
  • Capsid Proteins / chemistry
  • Capsid Proteins / genetics
  • Molecular Sequence Data
  • Phylogeny
  • Plant Diseases / virology*
  • RNA Viruses / classification*
  • RNA Viruses / genetics*
  • RNA Viruses / isolation & purification
  • RNA, Viral / analysis
  • RNA, Viral / isolation & purification
  • RNA-Dependent RNA Polymerase / chemistry
  • RNA-Dependent RNA Polymerase / genetics
  • Sequence Analysis, DNA
  • Vicia faba / classification
  • Vicia faba / growth & development
  • Vicia faba / virology*
  • Viral Proteins / genetics

Substances

  • Capsid Proteins
  • RNA, Viral
  • Viral Proteins
  • RNA-Dependent RNA Polymerase

Associated data

  • GENBANK/EF173389
  • GENBANK/EF173390
  • GENBANK/EF173391
  • GENBANK/EF173392
  • GENBANK/EF173393
  • GENBANK/EF173394
  • GENBANK/EF173395
  • GENBANK/EF173396
  • RefSeq/NC_007241
  • RefSeq/NC_007242