Alignments with TyrRSs from several species reveals 34% identity with yeast and similarly low identity across the board, with greatest conservation confined to the N-terminus [ 69].
Interestingly, C-subgenome QTL were associated with considerably greater conservation of LD than their corresponding A-subgenome homoeologues.
Among residues with 80% or greater conservation in M2, we identified a γV590I variation in toothed whales, a γV593I variation in all toothed whales except for the beaked whale (Mesoplodon densirostris), and a αM596V variation in cetaceans.
Although the number of putative common genes (∼1,430) is similar, the MGCS10565 proteins average ∼5% greater conservation with strain MGAS2096 than with strain NEM316 (59% identical and 67% similar versus 53% identical and 63% similar, respectively).
Note that, phastCons scores estimate the probability that each nucleotide belongs to a conserved element, and thus are between 0 and 1 with greater values indicating greater conservation.
These data are consistent with the observation of greater conservation in gene synteny between human and elephant shark genomes than between human and zebrafish genomes [ 19].
We compared the overall expression levels of the three gene sets [ 32] and found that greater conservation correlates with higher levels of transcription, with the transcription levels of the most highly conserved genes being twice that of the genes that are not conserved.
The phylogenetic age and expression of miRNA genes correlate inversely with their rate of evolution, with greater sequence conservation for miRNAs of more ancient origin and higher expression level (Ruby et al. 2007; Lu, Shen, et al. 2008; Liang and Li 2009; Fahlgren et al. 2010; Nozawa et al. 2010; Lenz et al. 2011; Shen et al. 2011; Nozawa et al. 2012; Jovelin 2013; Meunier et al. 2013).
However, the pXO1-16-like proteins showed significantly greater conservation (P < 2.2e-16, Mann–Whitest test), with sequence identities>65%.
