In addition, we found that three genes annotated as major royal jelly protein-like (mrjpl9: Nasvi2EG014218, mrjpl6: Nandi2EG021396 and mrjpl5: Nandi2EG014323) and one annotated as yellow x-2 (Nasvi2EG010358) were differentially expressed in association with "host treatment".
In each of the two Bacillus strains, we identified two highly similar operons, one annotated as encoding proteins involved in gramicidin biosynthesis and one annotated as encoding proteins involved in biosynthesis of a putative, uncharacterized, antibiotic.
The outer distribution describes all ALPS similarities between pairs of intervals, one annotated as miRNA, the other not annotated as miRNA.
The expression patterns of 17 genes detected by qRT-PCR fit well with those from RNA-Seq results, with one annotated as a basic helix-loop-helix DNA-binding superfamily protein being inconsistent.
Specimens that cannot be accurately named or those belonging to groups other than the ones under consideration should be annotated as far as possible.
The remaining missing ones are annotated as putative transposases or IS elements that have not been deposited in ISfinder (column IPuative and INovel of Additional file 1, Table S2).
Only one sequence, annotated as encoding a putative ortholog of one Arabidopsis calcium-transporting ATPase 9, showed a strong positive Tajima D value (2.63; P < 0.01) which could suggest the possible existence of balancing selection operating in this locus [ 40].
In SL, one gene annotated as "unknown" in the cGRASP annotation file, was identified through the re-BLAST methods as "far upstream binding element protein 3" (Entrez Gene ID 100194998).
In the read retrieval, we used two of these annotated variants of the gene as well as one gene annotated as calcium-binding protein, which collapsed with the two FCBs but was not in the same COG, as queries.
Of these, only one, PF04233, annotated as a homolog of phage Mu protein gp30, was found in only one genome (ΦCP13O).
