Fig. 5

The rli133 coevolution ties. rli133 shows significant coevolution with six CDS and nine 5′-UTR regions. Figures 5a to 5d show an example of a coevolution pattern and a putative mechanism of interaction between rli133 and the lmo0333 5’UTR region corresponding to the promoter of an Internalin IntI protein. a Coevolution patterns observed between rli133 (left) and the 5’UTR of lmo0333 (right). Yellow circles correspond to observed (or ancestral) sRNA/CDS presence. Blue circles correspond to observed (or ancestral) sRNA/CDS absence. A yellow branch indicates a sRNA/CDS gain event while a blue branch indicates a loss event along the branch. b Predicted interaction regions between rli133 and lmo0333. The figure presents the interaction regions between the 5’UTR (and the beginning of the coding region) and the sRNA. Highlighted and numbered regions correspond to predicted interaction zones according to the RNAplex software. c Predicted structure of the sRNA rli133. Structure was generated using LocaRNA software and a multiple alignment of all conserved rli133 sRNAs in the genomic dataset. Highlighted numbered regions correspond to Lmo0333–5’UTR predicted interaction zones of Fig. 5b. Representation of structure was performed with FoRNA. d Predicted structure of the 5’UTR region of Lmo0333. Structure was generated using LocaRNA and a multiple alignment of all conserved Lmo0333 5’UTRs in the genomic dataset. Highlighted numbered regions correspond to rli133 predicted interaction zones of Fig. 5b. Representation of structure was performed with FoRNA