The nucleotide sequence and genome organization of Japanese iris necrotic ring virus, a new species in the genus Carmovirus

The genome of Japanese iris necrotic ring virus (JINRV) consists of a posit ive-sense ssRNA of 4014 nucleotides with six major open reading frames (ORF s). A 5'-non-coding region of 31 nucleotides precedes the first initiation codon. Like Carnation mottle virus (CarMV), the 5'-proximal three ORFs enco de a 26 kDa protein (p26) and two readthrough proteins, i.e. an 85 kDa puta tive RNA replicase (p85) and a 99 kDa protein (p99). The central ORF encode s a small 8 kDa protein (p8). The 3'-proximal ORF encodes a 38 kDa capsid p rotein (p38). Another ORF encoding a 12 kDa protein (p12) overlaps the p99 ORE JINRV RNA treated with bacterial alkaline phosphatase and tobacco acid pyrophosphatase could not be ligated to an oligoribonucleotide using T4 RNA ligase, indicating that the 5' end of the viral RNA is uncapped. The 3' en d is not polyadenylated. Comparison of the genomic organization and the pre dicted amino acid sequences with those of other viruses confirmed that JINR V should be classified as a member of the genus Carmovirus, family Tombusvi ridae.