In the absence of manual refinement, repeats may remain undetected if they are particularly divergent between the different sequences, and poorly aligned by automated methods.
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).
In carp mH2A, the percentage identity between both subtypes is lower (61%), with macro domain being particularly divergent (51%).
Recombination between loci may explain the occurrence of sequence variants that are particularly divergent, which may then provide particular advantage against parasitic attack.
The Tox-URI domains can be divided into two major clades, with the second clade being particularly divergent (Additional File 1).
Unlike these single gene approaches, our characterisation of the phage head-neck-tail module is not hindered when one of the genes is particularly divergent, and this gene can even be detected, provided its genome position is canonical.
We found lower correlations in the abundances of gene transcripts to proteins than previous studies utilizing undifferentiated cell lines, suggesting that the relationship in the expression of these molecules is particularly divergent in brain tissue of humans and chimpanzees.
Therefore, commercial expression arrays could in principle be used for the task, especially because many probes are designed on the 3'-untranslated regions of the transcripts, which are particularly divergent across species [ 10].
This could be partially caused by a failure to report autoregulation in some cases –which can be particularly difficult to resolve for divergent architectures [31].
