For two post-duplication outgroups, the KNST branch length is e2-e1 (if both outgroups retain the same duplicate; Figure 3b,e) or 2d-e2-e1 (if different duplicates are retained; Figure 3c,d).
The combined alignment of the five RvhB6 proteins was performed using only the VirB6/TrbL domains, which average 413 aa in each duplicate (Figure S4).
The regions flanking the VirB6/TrbL domains are particularly divergent across the five duplicates (Figure 3A) and are similar only in a few instances to the sister taxon of Rickettsia, Orientia tsutsugamushi (Figure S4).
Such an outgroup may diverge from the ABC ancestor before the duplication (Figure 1b) or may diverge after the duplication and subsequently lose one duplicate copy (Figure 1c e; if the outgroup retains both duplicates, the gene will be recognized as not a one-to-one ortholog, and should be discarded).
"It's just stunning," says Lydia Sohn, a Princeton University physicist who was one of the first people to point out duplicate figures.
In addition a 100 Kb region of chromosome XIV between the telomere and the Ty1 element YNLCTy1-1 was duplicated (Figure 2A and B).
The MHC class II region of the giant panda ultimately evolved into its current species-specific genomic structure after losing the entire DYA locus, expanding the DQ subregion, and extinguishing the duplicate DRB gene (Figure 7E).
It contains all the conserved NB domain motifs of NB-LRR proteins defined by [18], [19], including the P-loop, RNBS-A, Kinase 2, RNBS-C, GLPL, RNBS-D and MHD domains, the latter of which is duplicated (Figure 4).
Branch support was assessed with 1000 bootstrap replications, except for the combined analysis of all five RvhB6 duplicates (Figure S4), in which 500 bootstrap replications were performed, and the combined analysis (Figure 10), in which 1 million bootstrap replications were performed.
Now let us focus on an extreme case (as in the examples above) where after a WGD there is deletion of all extra non-coding DNA and only the genes encoding the TF and its targets are left as duplicates (Figure 4).
The database searches identified 10 380 citations, of which 1204 were duplicates (figure 1).
