Figure 5

Nucleotide conservation of novel sRNAs in bacteria. The nucleotide sequence conservation of the 80 most abundant candidate sRNAs among 106 closely related bacterial strains is shown. Red indicates high nucleotide conservation and black indicates no conservation. The name of each sRNA is shown on the right. sRNAs expressed from prophage regions (blue letters) and sRNAs identified by northern blot analysis (red circles) are indicated. The phylogenetic tree for 16S rRNA sequences was constructed based on the neighbour-joining method using ClustalW version 1.83 [64]. The names of the organisms and their corresponding NCBI IDs for the complete genome sequence are described in Additional File 10. Evolutionary distance is shown by the branch lengths in the phylogenetic tree. For three strains, the lines have been shortened (the real evolutionary distances are *, 0.49; **, 0.48; ***, 0.07; and ****, 0.42).