We therefore undertook a calibration using the Established Repeats alignments (here including the N-and C-terminal repeats).
COACH analysis is performed with template HMMs derived from the Established Repeats alignments (Supporting Information S2) and the returned "SAM-style reverse scores" are recorded.
To further examine relationships among basal eudicot taxa, the slowly-evolving IR region of the Macadamia cp genome was aligned to a 159-taxa eudicot subset of the inverted repeat alignment of Moore et al. [ 5] in Geneious Pro with the outgroup taxon Ceratophyllum.
This was repeated three times and averaged after acquisition and cross-repeat alignment.
In particular, we focused our attention on the Xin repeat alignment.
After repeated alignment and classification, the final projection map showed two striking features.
These mutations occur at conserved positions in the LRR repeat alignment having a structural role in folding the LRR domain (Figure 3 and Figure 4).
We used Bayesian inference (MrBayes V3.0b4, [47] with the Xin repeat alignment using the JTT+Γ+I model to calculate posterior probabilities for nodes in the RAxML tree.
This idea was tested by applying Tajima's relative rate test for 3 sequences using MEGA4 [12] and the Xin repeat alignment (1,201 aa).
To add the PUR protein from B. burgdorferi to this repeat alignment, we constructed a multiple alignment of homologs of B. burgdorferi PUR by searching with BLAST through the spirochete genomes on the Bioinformatics Toolkit.
Three mutations are classified as structural variants (p.I298T, p.F318C, p.E383A), as they affect conserved positions in the repeat alignment and map into the space between the two β-sheets of repeats 2 and 3 (Figures 4 and 5).
