Although the pioneering study was done with eukaryotic organisms, RNA sequencing technology has more recently been applied to prokaryotes, mainly bacteria.
Even today, after many years of studies of bacteria, new discoveries continue to surprise us. Through RNA-seq, it can be seen how the microbial transcriptome is more complex than initially thought and how it approximates that of eukaryotes in various aspects. Perhaps it is because of this transcriptomic versatility that bacteria are able to adapt to diverse environments with such agility.
Pinto AC, Melo-Barbosa HP, Miyoshi A, Silva A, Azevedo V. (2011) Application of RNA-seq to reveal the transcript profile in bacteria. Genet Mol Res 10 (3), 1707 – 18. [article]