Figure 2.

Extensive expression and conservation of small RNA elements in Buchnera. Small RNA expression profiles of Buchnera from five aphid strains were compared revealing numerous instances of conserved small RNAs. For example, (a) CspC encodes a particularly long, sequence and structurally conserved 5′ UTR that overlaps a predicted thermoregulatory element (RFAM model RF01766; dashed box). Also discreet small RNAs were identified in 25 intergenic spacers including one between rpoB and rplL (b), which is expressed in the opposite orientation to the flanking genes and ends at the transcriptional terminator predicted for rplL. We also identified over 115 sequence and structurally conserved asRNAs such as those in (c) rmpG and (d) minD. In panels (a–d), RNAseq raw read coverage traces (for example, not normalized) are shown for each Buchnera strain according to the colors indicated in a. Coordinates for the x axes correspond to a global Buchnera genome alignment (see Materials and methods section). Below the read coverage traces, colored horizontal lines indicate the (a) UTR and (b–d) small RNA regions predicted by Rockhopper. Gray and white arrows indicate coding sequence boundaries. Structural conservation diagrams are based on RNAalifold and predicted thermostabilty is indicated when available.