Extended Data Fig. 5: Assessment of ppsC homopolymeric tract mutations.
From: Propionate prevents loss of the PDIM virulence lipid in Mycobacterium tuberculosis
a, Schematic showing the location of a homopolymeric tract region in the ppsC gene. Sequence inserts show two adjacent 7-cytosine homopolymeric tracts (c.2668 and c.2685) ± 5 bp on either side. Numbers in black indicate the position in the ppsC gene and numbers in red the genomic position in the H37Rv genome. b–d, Analysis of the ppsC homopolymeric tract region in Δtgs1 mutants and identification of frameshift mutations. WGS variant calling failed to identify PDIM mutations in Δtgs1-5, Δtgs1-8 and Δtgs1-9 despite a PDIM(-) result in VAN-P MICs (Fig. 2b) and validation of Δtgs1-9 as PDIM(-) by TLC (Fig. 2c). Close manual inspection of WGS reads showed the ppsC homopolymeric tract region is poorly covered by Illumina MiSeq and identified potentially missed variant calls. PCR and Sanger sequencing confirmed the presence of a 2668(C)7→6 frameshift mutation in both Δtgs1-5 (b) and Δtgs1-9 (d) and identified a 2668(C)7→8 mutation in Δtgs1-8 that was not covered at all by WGS (c). (b–d) were created with Geneious Prime® 2022.2.2 and Illustrator 26.4.1. Coverage has been cropped to a read depth of 60 ×. See also Supplementary Table 5.
