Based on the high similarities of the encoded proteins to animal or fungal enzymes, and the divergent codon usage of the contigs, the corresponding transcripts may have originated from other organisms present in the non-axenic culture.
Thus, the question arose whether the divergent codon usage of prokaryotes and eukaryotes was responsible for the aggregates as approximately 60% of the bacterial ntr codons are underrepresented in mammalian genomes (e.g. Mus musculus; Figure 2A and Additional file 1) [ 22].
This could explain the divergent usages seen for Gly and Phe, as well as the unusual pattern of usage for Ser.
We undertook this study as a first step towards understanding the factors underlying the divergent pattern between high ANC utilization rates and low usage of SBA in Ngorongoro, Tanzania.
Further curated contigs in our assembly for presumed AtoB and HMGS, and for a third predicted MVA pathway enzyme, hydroxymethylglutaryl-CoA reductase (HMGR, E.C. 1.1.1.34) display very high identities to fungal sequences and show a highly divergent codon usage compared to that of B. braunii.
Identification of a miRNA target by usage of gene and miRNA datasets taken from two relatively divergent tissues (such as the embryonic and the adult liver) is relatively complex since, as mentioned above, the mRNAs are most likely regulated by additional machineries.
Although both fields recognize this dual role, differing model structures and usage of similar terms for subtly different concepts appear to have led to divergent conclusions regarding optimal selection strength.
Among them, the "sex peptide" Acp70A has been shown to be one of the most divergent genes in the Drosophila genome [ 4, 6] and to be partly responsible for species-specific usage of gametes [ 13].
Usage of the extensive genomic resources available for the house mouse, a moderately 20-400 mln years) divergent relative of the voles, enabled a comprehensive assessment of the transcript completeness.
The divergent expression levels of kapD and the long 5'UTR in B. licheniformis might therefore result from different usage of promoter sites dependent on the respective cell type.
