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Background   Streptococcus agalactiae,  also known  as  Group B  Streptococcus  (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as  Streptococcus pneumonia e and  Streptococcus pyogenes.  However, little is known about the genomic distribution of ncRNAs and RNA families in  S. agalactiae .    Results  Comparative genome analysis of 27  S. agalactiae  strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types.    Conclusions  The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4951-z) contains supplementary material, which is available to authorized users.

Functional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes