Grapevine leafroll associated virus 4 strain 9: complete genome and quantitative analysis of virus-derived small interfering RNA populations.

Abstract

The complete genome sequence of one isolate of Grapevine leafroll-associated virus 4 strain 9 (GLRaV-4 strain 9) was determined using a library constructed from the sequencing of the small RNA population. The RNA genome consists of 13,858 nucleotides and contains seven open reading frames. A 5’ non coding end (218 nt) is followed by ORF1 encoding the 261.5 kDa methyltransferase/helicase domains then, through a +1 ribosomal frameshift, by ORF1b encoding a 58.28 kDa product corresponding to the replicase RdRp. The ORFs that follow encode the 5.32 kDa P5 protein, the 58.12 kDa HSP70h protein, the 60.18 kDa protein, the 29.9 kDa coat protein and finally the 23.2 kDa p23 protein followed by a 127 nt non coding 3’ end. The analysis of virus-derived siRNA populations aligning to the GLRaV-4 strain 9 genome showed a major representation of 21-nt reads, suggesting the involvement of DCL4 in virus silencing. The profile of the vsiRNAs density along the viral genome differed clearly from that of GLRaV-3, the representative member of subgroup I of the genus Ampelovirus, that was present in the same plant.