Figure 1

Coding potential statistics for an alignment of four plant fijivirus segment 5 sequences. (1)-(3) The positions of stop codons in each of the four sequences in each of the three forward reading frames (frame defined by alignment to the reference sequence [GenBank: NC_003736]). The FDV sequence has been put into the same frame as the other sequences via the arbitrary insertion of an extra 'U' into the run of five 'U's at NC_007160 nucleotides 2714–2718, as discussed in the text. Note the conserved absence of stop codons in the +0 frame within ORF5-1 and in the +1 frame within ORF5-2. (4)-(6) MLOGD sliding-window plots (window size 75 codons; step size 25 codons). Each window is represented by a small circle (showing the likelihood ratio score for that window), and grey bars showing the width (ends) of the window. See [9] for further details of the MLOGD software. In (4) the null model, in each window, is that the sequence is non-coding, while the alternative model is that the sequence is coding in the +0 (i.e. ORF5-1) frame. Positive scores favour the alternative model and, as expected, there is a strong coding signature throughout ORF5-1. In (5)-(6) the null model, in each window, is that only ORF5-1 is coding, while the alternative model is that both ORF5-1 and the window frame are coding. Scores are generally negative with some scatter into low positive scores, except for the ORF5-2 region which has consecutive high-positively scoring windows (5). Note that the generally lower MLOGD signal within the overlap region itself (4)-(5), and also at the 5' end of ORF5-1 (4), is due to there being fewer substitutions with which to discrimate the null model from the alternative model in these regions of above-average nucleotide conservation. (7) Map of the reference sequence [GenBank: NC_003736]. (8) Conservation at synonymous sites within ORF5-1 (see text and [18] for details). Note that the relatively large window size (75 codons) – used here for improved statistical power – explains the broad smoothing of the conservation peak at the edges of the region where ORF5-2 and ORF5-1 overlap.