Analysis of the coding potential of the partially overlapping 3' ORF in segment 5 of the plant fijiviruses | Virology Journal BioMed Central Open Access Short report Analysis of the coding potential of the partially overlapping 3 ORF in segment 5 of the plant fijiviruses Andrew E Firth 1 and John F Atkins 1 2 Address 1BioSciences Institute University College Cork Cork Ireland and 2Department of Human Genetics University of Utah Salt Lake City UT 84112-5330 USA Email Andrew E Firth - John F Atkins - Corresponding authors Published 17 March 2009 Received 26 February 2009 Accepted 17 March 2009 Virologyjournal 2009 6 32 doi l743-422X-6-32 This article is available from http content 6 1 32 2009 Firth and Atkins licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http licenses by which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. 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. Findings The genus Fijivirus is one of 12 genera within the Reoviri-dae a family of segmented dsRNA viruses. Fijiviruses have 10 segments and infect plants and insects. Species such as Fiji disease virus FDV Mal de Rio Cuarto virus MRCV and Rice black streaked dwarf virus RBSDV are transmitted by planthoppers and replicate in both the insect and plant .
