Figure 2

Coding potential statistics for bee paralysis dicistrovirus CDS2 and the overlapping ORFX. (A) Genome map for KBV [GenBank:NC_004807]. (B2-B11) Coding potential statistics based on an alignment of 16 bee paralysis virus CDS2 sequences (see Figure 3 caption 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 +1 frame within ORFX. (B5-B7) Conservation at synonymous sites within CDS2 (see [17]). (B6-B7) depict 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 (B5) depicts the ratio of the observed number of substitutions within a given window to the number expected under the null model. (B8-B10) MLOGD sliding-window plots (see [14]). In (B8) 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/CDS2 frame. Positive scores favour the alternative model and, as expected, there is a strong coding signature throughout CDS2 except where CDS2 is overlapped by ORFX. In (B9-B10) the null model is that only the CDS2 frame is coding, while the alternative model is that both the CDS2 frame and the window frame are coding. The ORFX region has consecutive positively scoring windows, albeit only just (see text; B9). (B11) MLOGD statistics restricted to ORFX. Here, for increased sensitivity, the null and alternative models were fitted specifically for the ORFX region.