title: Grapevine deformation virus: completion of the sequence and evidence on its origin from recombination events between Grapevine fanleaf virus and Arabis mosaic virus.
abstract: The complete nucleotide (nt) sequence of Grapevine deformation virus (GDefV) RNA-1 has been determined. It consists of 7386 nt, excluding the poly(A) tail, and contains a single open reading frame (ORF) encoding a polyprotein (p1) of 252 kDa. P1 comprises the 1A(Pro-cof) proteinase cofactor, the 1B(Hel) NTP-binding protein, the 1C(VPg) viral protein genome-linked, the 1D(Prot) proteinase and the 1E(Pol) RNA-dependent RNA polymerase, all of which are conserved domains in polyproteins of different members of the order Picornavirales. The amino acid (aa) sequence of GDefV RNA1 p1 has the highest identity with the homologous products of Grapevine fanleaf virus (GFLV, 86-88%) and Arabis mosaic virus (ArMV, 73-74%), two nepoviruses of subgroup A. Four cleavage sites for proteins processing were predicted (C/A, C/S, G/E and R/G) and found similar to those of GFLV RNA1. Phylogenetic trees constructed with the complete aa sequences of protein p1 and the RNA2-encoded protein p2 of GDeFV, GFLV and ArMV, showed an incongruent allocation of GDefV in these trees. Pairwise alignment and prediction of recombination sites of both RNA segments showed that GDefV RNA2 has a mosaic structure resulting from recombination events between GFLV and ArMV at the level of the 2A(HP) (homing protein), 2B(MP) (movement protein), 2C(CP) (capsid protein) and the 3'NCR (non coding region). This strongly suggests that GDefV originated from the interspecific recombination between isolates of GFLV and ArMV.
authors.affiliation: Istituto Agronomico Mediterraneo di Bari, Via Ceglie 9, 70010 Valenzano, Bari, Italy. elbeaino@iamb.it
authors.forename: Toufic
authors.initials: T
authors.lastname: Elbeaino
authors.forename: Michele
authors.initials: M
authors.lastname: Digiaro
authors.forename: Saba
authors.initials: S
authors.lastname: Ghebremeskel
authors.forename: Giovanni P
authors.initials: GP
authors.lastname: Martelli
mesh_terms: D016000:Cluster Analysis; D016679:Genome, Viral; D008969:Molecular Sequence Data; D017860:Nepovirus / Q000235:genetics* / Q000302:isolation & purification; D016366:Open Reading Frames; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000235:genetics; D027843:Vitis / Q000821:virology*
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins