The complexity of bacterial transcriptomes

•We summarize the recent progress in the field of bacterial transcriptomics.•The contribution of RNA processing is reviewed.•We discuss the evolutionary conservation of transcriptomic features.•We draw conclusions about the biological meaning of the complex architecture of bacterial trancriptomes and their variability. For eukaryotes there seems to be no doubt that differences on the trancriptomic level substantially contribute to the process of species diversification, whereas for bacteria this is thought to be less important. Recent years saw a significant increase in full transcriptome studies for bacteria, which provided deep insight into the architecture of bacterial transcriptomes. Most notably, it became evident that, in contrast to previous scientific consensus, bacterial transcriptomes are quite complex. There exist a large number of cis-antisense RNAs, non-coding RNAs, overlapping transcripts and RNA elements that regulate transcription, such as riboswitches. Furthermore, processing and degradation of RNA has gained interest, because it has a significant impact on the composition of the transcriptome. In this review, we summarize recent findings and put them into a broader context with respect to the complexity of bacterial transcriptomes and its putative biological meanings.