Next-generation sequencing technologies have
dramatically increased the rate at which new genomes are sequenced.
Accordingly, automated-annotation programs have become adept at identifying and
annotating protein coding regions, as well as common and conserved RNAs.
Additionally, RNAseq techniques have advanced our ability to identify and
annotate regulatory RNAs (sRNAs), which remain significantly understudied.
Recently, our group catalogued and annotated all previously known and newly
identified sRNAs in several Staphylococcus
aureus strains. These complete annotation files now serve as tools to
compare the sRNA content of S. aureus to
other bacterial strains to investigate the conservation of their sRNomes.
Accordingly, in this study we performed RNAseq on two staphylococcal species, S. epidermidis and S. carnosus, identifying 118 and 89 sRNAs in these organisms,
respectively. The sRNA content of all three species were then compared to
elucidate their common and species-specific sRNA content, identifying a core
set between 53 and 36 sRNAs encoded in each organism. In addition, we
determined that S. aureus has the
largest set of unique sRNAs (137) while S.
epidermidis has the fewest (25). Finally, we identify a highly conserved
sequence and structural motif differentially represented within, yet common to,
both S. aureus and S. epidermidis. Collectively, in this
study, we uncover the sRNome common to three staphylococcal species, shedding
light on sRNAs that are likely to be involved in basic physiological processes
common to the genus. More significantly, we have identified species-specific
sRNAs that are likely to influence the individual lifestyle and behavior of
these diverse staphylococcal strains.