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Diversity of small RNAs expressed in P seudomonas species
Author(s) -
GómezLozano María,
Marvig Rasmus L.,
MolinaSantiago Carlos,
Tribelli Paula M.,
Ramos JuanLuis,
Molin Søren
Publication year - 2015
Publication title -
environmental microbiology reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.229
H-Index - 69
ISSN - 1758-2229
DOI - 10.1111/1758-2229.12233
Subject(s) - biology , strain (injury) , rna , transcriptome , pseudomonas putida , small rna , genetics , transfer rna , rna silencing , gene , computational biology , gene expression , rna interference , anatomy
Summary RNA sequencing ( RNA ‐seq) has revealed several hundreds of previously undetected small RNAs ( sRNAs ) in all bacterial species investigated, including strains of P seudomonas aeruginosa , P seudomonas putida and P seudomonas 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 P . putida DOT ‐ T1E and P seudomonas extremaustralis 14‐3b. This is the first strain of P . extremaustralis and the second strain of P . putida to have their transcriptomes analysed 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 P seudomonas 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 interspecies and intraspecies conservation.