An evolutionary approach to predict the orientation of CRISPR arrays
Fig 2
Example of a group of arrays with high confidence orientation prediction.
A and B show reconstructions of the same alignment of spacer arrays. B has the orientation provided by CRISPRCasdb, while A is simply the reconstruction of the same arrays, but arranged in reverse order. Note, that in B all spacers are reconstructed to be inserted (green) at the root and thus the exceptional amount of deletion events (red) along the tree (also shown in red in the spacer alignment). The insertions are produced through the first spacer 1 (light yellow) which is present at the root, as it is present in all arrays, and “pulls up” all other spacer insertions through the spacer insertion order. In contrast, in A the insertions are distributed more evenly along the tree and thus the reconstruction avoids a lot of deletions. Comparing both reconstructions clearly indicates that the orientation of A is more likely under the assumption of polarized insertions. To make the figures more concise, acquisition and deletion events in the tree are consolidated, e.g. 9 - 1 in green/red indicates that spacers 9 through 1 were acquired/deleted at this branch. At the leafs “+ (x) +” indicates that x spacers were acquired. They are the leftmost spacers in the alignment for the respective leafs (which are not found in any other array). The shown example is a group of Klebsiella pneumoniae (Cas type I-E) from CRISPRCasdb with small adjustments for readability.