Analysis of the coding potential of the partially overlapping 3′ ORF in segment 5 of the plant fijiviruses

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 (similar to 200+ codons) that overlaps the 3' end of the major ORF (similar to 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.