Sequence conservation of small RNAs detected by RNA-seq in different Pseudomonas species.

GOMEZ LOZANO MARIA; MARVIN RASMUS*; MOLINA CARLOS*; TRIBELLI PAULA M.*; RAMOS JUAN LUIS; MOLIN SOREN

Environmental Microbiology Reports

Society for Applied Microbiology and John Wiley & Sons Ltd

Año: 2015

1758-2229

RNA sequencing (RNA-seq) has revealed several hundreds of previously undetected small RNAs (sRNAs) in all bacterial species investigated, including strains of Pseudomonas aeruginosa, Pseudomonas putida, and Pseudomonas syringae. Nonetheless, only little is known about the extent of conservation of expressed sRNAs across strains and species. In this study, we have used RNA-seq to identify sRNAs in Pseudomonas putida DOT-T1E and Pseudomonas extremaustralis 14-3b. This is the first strain of P. extremaustralis and the second strain of P. putida to have their transcriptomes analyzed for sRNAs, and we identify the presence of around 150 novel sRNAs in each strain. Furthermore, we provide a comparison based on sequence conservation of all the sRNAs detected by RNA-seq in the Pseudomonas species investigated so far. Our results show that the extent of sRNA conservation across different species is very limited. In addition, when comparing the sRNAs expressed in different strains of the same species we observe that numerous sRNAs exhibit a strain-specific expression pattern. These results support the idea that the evolution of most bacterial sRNAs is rapid, which limits the extent of both inter- and intra-species conservation.