Circular representation of RNA-seq data for the Lactobacillus iners pan-transcriptome. RNA-seq reads were mapped to 12 available L. iners genomes (listed in Additional file 1: Table S4) after clustering redundant coding sequences by nucleotide identity (see Methods). Breaks in the circle separate blocks of contiguous coding sequences (CDS) ordered by scaffolding on the genome assemblies (Ring 1). The height of the plot represents in how many of the 12 genomes the CDS occurs. The first contiguous block (dark blue) are the 954 CDS present in all genomes and are considered the core L. iners gene set. Ring 2 shows the clusters of orthologous groups (COG) color-coded function of each CDS. Ring 3 The differential expression of each CDS between non-bacterial vaginosis (BV) and BV samples. The absolute height of the bar shows the fold-change (log2) in expression (positive for up BV, and negative for up non-BV). Bars are colored if significantly differential (red for BV and blue for non-BV). Regions of interest are labeled in the centre of the circle. Rings 4, and 5, show a heatmap representation of the median CDS expression in BV and non-BV samples, respectively. Darker blue represents higher expression. Regions of interest noted in the results are marked by lettered triangles.