Lineage-associated small inversions disrupt dosT, dnaE2, and a promoter-adjacent region in Mycobacterium tuberculosis

Background: Large molecular inversions in the genome of Mycobacterium tuberculosis (Mtb) due to factors like the presence of insertion sequences and transposases are widely known. However, smaller inversions within CDS and noncoding control elements are rarely reported. The present study aims to identify inversions and their potential impact on Mtb biology in a lineage-specific manner. Methodology: Structural variations (SVs) could only be detected by long reads. For this, we simulated long reads by de novo assembling the short read sequencing datasets and subsequently aligned representative strains from each lineage to the Progressive Mauve algorithm. Independently, long-read sequencing from the PacBio platform was acquired and analysed using SVIM. Variants were merged, and Fisher’s exact test was carried out to identify the inversion association with lineages. To visualize DNA features, the DNA-features-viewer tool was used. Results: Simulated reads from short read sequencing gave indications of lineage-specific inversions. Long read sequencing approach led to identification of 7 unique inversions (2 associated with L1; 1 associated with L3, 2 associated with L4, and 2 associated with both L3 and L4, P<0.05). The inversions encompassed primarily non-essential genes like sdaA , dosT , Rv2026c, dnaE2 , Rv1341, Rv1342, and lprD . An interesting inversion was observed in the upstream control element of purB and Rv0776c. Conclusion: The study sheds light on small inversions that may be causing alterations in expression, formation of fusion genes, and nonsense mutations that may have a role in lineage-specific phenotypic changes.