FIG 4.

Differences in sRNA contents between S. pneumoniae strains D39 and TIGR4. (A) Venn diagram illustrating the overlap between the total numbers of sRNAs identified by RNA-seq in D39W and D39V. (B) Numbers of sRNAs in each category (5′/intergenic, 3′/intergenic, intergenic, or antisense) that were detected in D39W in this study and in D39V by Slager et al. (28). (C) Distribution of sRNAs that were identified in TIGR4 (3, 30), D39V (28), and D39W in this study and their genetic contexts. (D) Overlap of sRNAs identified in TIGR4 and D39W in this study. TIGR4-1 refers to sRNAs identified by Mann et al. (3), and TIGR4-2 refers to sRNAs identified by Acebo et al. (30). Only TIGR4 sRNAs that are also encoded in the genome of D39W are included in this analysis. The number of sRNAs in D39W represents the total number of sRNAs that were identified by sRNA-seq and dRNA-seq in this study. (E and F) Read coverage maps for the TIGR4 sRNAs F14 and F23, which are present in D39W genomes but were not detected as sRNAs by sRNA-seq or dRNA-seq analysis. Northern blots probed for F14 and F23 in D39W (lane 1) and TIGR4 (lane 2) are shown alongside the read coverage maps. (G to J) Read coverage maps for D39W sRNAs Spd-sr71, Spd-sr84, Spd-sr96, and Spd-sr106, which were validated for expression in D39W but were not detected as sRNAs by RNA-seq analysis of TIGR4. Northern blots probed for Spd-sr71, Spd-sr84, Spd-sr96, and Spd-sr106 in D39W (lane 1) and TIGR4 (lane 2) are shown alongside the read coverage maps. Track labels corresponding to coverage graphs are described in the legend of Fig. 2. Probes used are listed in Table S5 in the supplemental material.