Gene sequences of perA, along with several of the more conserved genes, have previously been used to study relationships between endophytes of perennial ryegrass and members of the closely related grass genus, Festuca (fescues) [ 30, 31], including elucidation of the ancestral lineages that have contributed to contemporary hybrid endophytes [ 32].
In these plots, more conserved genes can be found in the neighboring region of DBC1 as compared to CCAR1, also indicating that DBC1 is more conserved than CCAR1.
Therefore it could be hypothesised that motifs (AAG n and (AGG n are more abundant in more conserved genes.
More conserved genes most likely represent "housekeeping" genes that can be expected to be generally expressed at higher levels.
The more conserved genes might have undergone high selective constraint against changes in the REST sites, and are functionally essential.
There is a trend for higher GC-skew in usually less conserved sequences like nad3, nad4, nad5, compared to more conserved genes like cox1-3, cob.
This subset of contigs likely contains the more conserved genes that are well characterized and thus found in all of these databases.
Thus sequences placed at the deeper nodes of the phylogeny represent more conserved genes relative to the genes on the leaves the tree that are more specific to that species.
That is to say that the B. algerae and E. aedis genomes would not have more conserved genes than the pool remaining in the ancestral microsporidian after this gene loss event.
