Figure 1

Coding potential statistics for okavirus ORF3 and the overlapping ORFX. (A) Okavirus genome map (GAV [GenBank:AF227196]). (B2-B10) Coding potential statistics based on an alignment of seven okavirus full-length ORF3 sequences (see text for accession numbers). (B2-B4) Positions of stop codons in each of the three forward reading frames. Note the conserved absence of stop codons in the +2 frame within ORFX. (B5-B6) Conservation at synonymous sites within ORF3 (see [15]). (B5) depicts the probability that the degree of conservation within a given window could be obtained under a null model of neutral evolution at synonymous sites, while (B6) depicts the ratio of the observed number of substitutions within a given window to the number expected under the null model. (B7-B9) MLOGD sliding-window plots (see [12]). 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 given reading frame. Positive scores favour the alternative model and, as expected, there is a strong coding signature in the +0 frame (B7) throughout ORF3 except where ORF3 is overlapped by ORFX. In the +1 and +2 frames (B8-B9), scores are generally negative. However, the ORFX region has consecutive high positively scoring windows (B9). (B10) MLOGD statistics restricted to ORFX. Here, for increased sensitivity, the null and alternative models were fitted specifically for the ORFX region. The null model is that only the ORF3 frame is coding, while the alternative model is that both the ORF3 frame and ORFX are coding.