In all three-helix members of the LHC protein superfamily investigated so far only helices I and III are conserved while helix II shows much lower sequence conservation; in contrast to this, sequence conservation also occurred in the second helix of RedCAPs from different organisms, see Additional file 3).
We find that across the genus Anopheles, lncRNAs display much lower sequence conservation than protein-coding genes.
We find that the lncRNA gene set exhibits much lower sequence conservation across anophelines, when compared with either previously annotated protein-coding genes or protein-coding genes discovered in our study.
Nonetheless, the conservation rates of hub interactions are still much lower than the conservation of sequence data and they provide only a limited explanation for the even lower conservation rates of all interactions.
For instance, an alignment of orthologous sequences of the phosphatase Glc7p, which was found to be a NatB target, shows that the protein is in general very well conserved; however, the N- and C-terminal regions display a much lower degree of conservation, making Glc7p not a NatB substrate in even closely related species.
Dipteran codon families showed slightly more divergence (avg-%INUC = 60.84 ± 8.59), while coleopteran (avg-%INUC = 38.92 ± 8.84) and hymenopteran (avg-%INUC = 37.19 ± 8.22) codon families exhibited much lower levels of conservation.
When the two classes of IESs are considered, incompletely excised IESs share the canonical consensus, whereas the termini of cryptic IESs display a much lower level of conservation (fig. 2; supplementary tables S2A and S2B, Supplementary Material online).
However, the most striking feature of this analysis is that in all non-mammalian organisms considered, the non-nucleolar group displays a much lower degree of conservation than any of the nucleolar association groups, and the gap between the non-nucleolar and nucleolar groups greatly increases with evolutionary distance.
The study also suggests that even ecologically friendly agricultural matrices may be of much lower value for tropical conservation than indicated by mere biodiversity value.
Comparisons of the human Hoxa cluster to those of marsupials and amphibians reveal a much lower level of sequence conservation over similar periods of time, indicating either a faster rate of molecular evolution in the tetrapod and mammalian lineages or a slower rate of evolution in the cartilaginous fish.
