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Eighty-nine of the 126 miRNAs, grouped into 21 families were conserved (Table 3), and 25 were less conserved miRNAs that were only be found in legumes, namely legume-specific (Table 4).
Our phylogenetic and sequence conservation analyses suggest that wild-type residues at mutation sites are highly conserved (Table 2 and Figure 3A).
Conservation analysis using PhyloP and GERP++ shows that all of them are highly conserved (Table 2).
Between Arabidopsis and rice, there are ~20 miRNA families that are evolutionarily conserved (Table 1).
Namely, residues Leu189, Pro193 and Leu266, involved in hydrophobic interactions across the potential dimer interface are strictly conserved (Table 2).
In the 73 HA sequences from the 2009 pandemic A(H1N1), D190 was strictly conserved, while D225 was 94.5% conserved (Table 6).
Notably, most miRNAs predicted and verified here are very poorly conserved (Table S1), which is expected taken the rapid evolution of miRNAs in higher eukaryotes into account [28].
These transcripts appear to be either species-specific or markers of mobile genetic elements found in other staphylococcal species and are highly conserved (Table S1).
Homologs of DinG (BPUM_1971) are present in B. pumilus, B. subtilis and B. licheniformis, although their sequences are not well conserved (Table 2).
The E. coli core genome was further compared with the non-coli Escherichia albertii and Escherichia fergusonii, with 2173 genes found to be conserved (Table S2).
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Ogt (BPUM_1248) is found in B. pumilus, B. subtilis and B. licheniformis, although the protein sequence is not well-conserved (Table 2).
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