Complete genome sequence of lima bean endornavirus 1: a putative new member of the genus Alphaendornavirus (family Endornaviridae)

Arch Virol. 2024 Sep 21;169(10):206. doi: 10.1007/s00705-024-06135-y.

Abstract

In this study, we completely sequenced the genome of a new member of the genus Alphaendornavirus, family Endornaviridae, from lima bean (Phaseolus lunatus), for which we propose the name "lima bean endornavirus 1" (LbEV1). The complete genome of LbEV1 consists of 15,265 nucleotides, including a stretch of 12 cytosine residues at its 3' end, and contains a long single open reading frame (ORF) coding for a 4980-aa-long polyprotein. Analysis of the polyprotein sequence revealed the presence of four conserved functional domains (in order from the N- to C-terminus): viral helicase 1, peptidase _C97, glycosyltransferase_GTB-type, and viral RNA-dependent RNA polymerase (RdRP). The LbEV1 polyprotein showed the highest amino acid sequence similarity (63% identity and 98% coverage) to Phaseolus vulgaris endornavirus 3 (PvEV3) and also showed 42% identity (95% coverage) to Geranium carolinianum endornavirus. Phylogenetic analysis based on the viral RdRp domain showed that LbEV1 belongs to a subclade within the genus Alphaendornavirus that includes three other viruses infecting plants of the genus Phaseolus.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Genome, Viral* / genetics
  • Open Reading Frames*
  • Phaseolus* / virology
  • Phylogeny*
  • Plant Diseases / virology
  • Polyproteins / genetics
  • RNA Viruses* / classification
  • RNA Viruses* / genetics
  • RNA Viruses* / isolation & purification
  • RNA, Viral* / genetics
  • RNA-Dependent RNA Polymerase / genetics
  • Viral Proteins / genetics
  • Whole Genome Sequencing / methods

Substances

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