Table 1 Main characteristics of the S. agalactiae transcriptome (strain NEM316)

Genes and pseudogenes

2207

Coding genes

2084

2082 previously annotated CDS, including 11 for which the initiation codon has been reannotated; 2 new CDS identified in this study

Pseudogenes

36

rRNA operons

7

tRNAs genes

80

14 located outside the rRNA regions

TSS identified in the study

1210

Primary TSS

891

Secondary TSS

36

TSS internal to CDS, same orientation as CDS

191

TSS initiating antisense transcription

39

34 TSS inside CDS, 5 TSS located close to CDS

Intergenic TSS

53

including 8 TSS upstream tRNAs genes and one upstream a rRNA operon

Sigma70 promoters

1179

Transcript ends

655

602 corresponding to predicted rho-independent terminators

Transcription units

891

Operons identified in the study

407

including 56 operons with internal promoters, 26 operons with internal terminators and 15 operons with both internal promoters and internal terminators

Monocistrons

484

sRNAs identified in the study

120

Cis-regulatory sequences

39

23 belonging to rfam families and acting through attenuation of transcription

5 belonging to rfam families and acting through regulation of translation (no sRNA)

11 not belonging to rfam families and acting through attenuation of transcription

Cis-antisense sRNAs

39

Trans acting sRNAs

47

44 with TSS in intergenic regions, 1 with TSS at the end of a transcriptionally inactive gene and 2 likely resulting from the cleavage of longer transcripts