Abstract
The plant-infecting members of the genus Fijivirus (family Reoviridae) have linear dsRNA genomes divided into 10 segments, two of which contain two substantial and non-overlapping ORFs, while the remaining eight are apparently monocistronic. However, one of these – namely segment 5 – contains a second long ORF (~200+ codons) that overlaps the 3' end of the major ORF (~920–940 codons) in the +1 reading frame. In this report, we use bioinformatic techniques to analyze the pattern of base variations across an alignment of fijivirus segment 5 sequences, and show that this 3' ORF has a strong coding signature. Possible translation mechanisms for this unusually positioned ORF are discussed.
Highlights
The genus Fijivirus is one of ≥12 genera within the Reoviridae, a family of segmented dsRNA viruses
Two of the plant fijivirus segments (S7 and S9 in Rice black streaked dwarf virus (RBSDV), homologous segments in other sequenced plant fijiviruses) contain two non-overlapping coding sequences (CDSs), each pair separated by a short non-coding sequence [1,2]
One other plant fijivirus segment (S5 in RBSDV) contains a second substantial open reading frame or ORF, that overlaps the 3' end of the 'major' CDS in the +1 reading frame. The presence of this open reading frame has been noted previously in RBSDV [3,4]. It has often been ignored in the fijivirus literature; it is not currently annotated in any of the three GenBank plant fijivirus RefSeqs; and its unusual genomic location means that its coding status remains uncertain without further analysis
Summary
The genus Fijivirus is one of ≥12 genera within the Reoviridae, a family of segmented dsRNA viruses. One other plant fijivirus segment (S5 in RBSDV) contains a second substantial open reading frame or ORF (hereafter ORF5-2; ~200+ codons), that overlaps the 3' end of the 'major' CDS (hereafter ORF5-1; ~920–940 codons) in the +1 reading frame.
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