Fig. 6
Variation between RMV8 genotypes. (A) RNA-seq analysis of S. pneumoniae RMV8. The outer rings represent the annotation of the complete genome of the S. pneumoniae RMV8rare variant (accession code OX244288). Labels mark the positions of the mobile elements present in this isolate, corresponding to a prophage, two phage-related chromosomal isolates (PRCIs; inserted near tadA and malA [4]) and a Tn5253 scar [88]. The inner rings show the differences in expression between RMV8domi, the most frequently isolated genotype in RMV8 cultures, and derived genotypes. The outermost of these rings shows the comparison with RMV8domitvr::cat, in which the tvr locus was replaced with a cat resistance marker. The next ring shows the comparison with RMV8rare, in which significant differences at the prophage locus were detected. The innermost ring shows the comparison with RMV8raretvr::cat, which highly expressed the comC gene. B Quantification of ϕRMV8 lytA and comC expression by qRT-PCR in RMV8domi and RMV8rare samples collected at early (OD600 = 0.2) and late (OD600 = 0.5) exponential phase growth. Six points are shown, corresponding to three technical replicate measurements of each of two biological replicates. Data are coloured according to the genotype being tested. C Quantification of the relative levels of csRNA3L and csRNA3 in early and late exponential phase growth. Data are shown as in panel (B). D Scatterplot showing the spontaneous transformation efficiency of the RMV8 variants. Each point represents an independent experiment, with the overall medians and interquartile ranges summarised by the box plots. A two-tailed Wilcoxon rank-sum test was used to compare the transformation frequencies of the variants. Significance is coded as: p < 0.05, *; p < 0.01, **; p < 10−3, ***; p < 10−4, ****