Remarkably, the major patterns that appeared in the filtered map for complete genomes (Figure 6B) were related to UpA-rich hexanucleotides that produce weak codon-anticodon interactions in coding regions and should hence be under differential selective pressure in both types of sequences.
Both types of sequences reside in all three elements we have defined.
The information acquired from these both types of sequences allows a better characterization of the transgenic cassette.
Some authors emphasize high spatial resolution [ 32, 39] while others prefer high temporal resolution [ 26] and yet again others performed both types of sequences in succession [ 30, 38].
Glutamic acid and serine had the largest enrichment in T4S sequences, whereas isoleucine, tyrosine and glycine were enriched in non-T4S sequences (tryptophan and methionine were not considered because of their low occurrence in both types of sequences).
Importantly, this finding is an exact replication of our previous experiments (Kornysheva, Sierk & Diedrichsen, 2013, Figure 3) showing that the relative behavioural difference between trained temporal and untrained sequences emerges with further trial repetitions of both types of sequences.
However, in parallel to the steady accumulation of new mt genome data, new nuclear data (e.g., Expressed Sequence Tags – ESTs) need also to be gathered, and only the combination of both types of sequence data might render better results.
Since the publication by Lukacs et al. [ 29], nomenclature incorporates both types of sequences in the "Z lineage", and newly identified ZE-type loci have been given a "Z" identifier (and not ZE) in their name (eg. [ 34]).
Unlike H3K4me2 or H3K9me3, it was not clearly correlated with coding sequences or transposable elements (Additional file 13: Table S8), indicating that its distribution was broader, covering both types of sequences.
In order to test the effect of the homeobox and the repetitive regions in our estimates of nucleotide substitutions, we repeated the previous analyses excluding one or both types of sequence.
