Figure 2
From: Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene
MLOGD statistics for the alignment of 48 BTV sequences. The input alignment comprised a CLUSTALW [39] alignment of the VP6 amino acid sequences only, back-translated to nucleotide sequences. (1) The positions of alignment gaps in each of the 48 sequences. In fact most of the alignment is ungapped, though a few sequences are incomplete. (2)–(4) The positions of stop codons in each of the 48 sequences in each of the three forward reading frames. Note the conserved absence of stop codons in the +0 frame (i.e. the VP6 CDS) and in the +1 frame in the ORFX region. (5)–(8) MLOGD sliding-window plots. Window size = 20 codons. Step size = 10 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 [16] for further details of the MLOGD software. In (5)–(6) 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 window frame. Positive scores favour the alternative model. There is a strong coding signature in the +0 frame (5) throughout the VP6 CDS, except where the VP6 CDS overlaps ORFX. In this region there is a strong coding signature in the +1 frame (6) indicating that ORFX is subject to stronger functional constraints than the overlapping section of VP6. In (7)–(8) the null model, in each window, is that only the VP6 frame is coding, while the alternative model is that both the VP6 frame and the window frame are coding. Only the +1 (7) and +2 (8) frames are shown because the +0 frame is the VP6 frame which is included in the null model. Scores are generally negative with occasional random scatter into low positive scores, except for the ORFX region which has consecutive high-positively scoring windows (7). Note that there are four non-overlapping – and hence completely independent – positively scoring windows in the ORFX region (7). Formally, and within the MLOGD model, p < 10-40. (9) Genome map for the reference sequence [GenBank: NC_006008]. (10) Phylogenetically summed sequence divergence (mean number of base variations per nucleotide) for the sequences that contribute to the statistics at each position in the alignment. In any particular column, some sequences may be omitted from the statistical calculations due to alignment gaps. Statistics in regions with lower summed divergence (i.e. partially gapped regions) have a lower signal-to-noise ratio.