Insertion site mapping for repeated elements in Mycobacterium tuberculosis

Insertion elements not only act as genetic markers for differentiation of bacteria but their movement in bacterial genomes likely plays an essential role in changing the physical and biochemical traits of the organisms when adapting to new environments. Genomic Insertion Site mapping of transposable elements could shed light on the putative altered function of adjacent genes. In the era of whole genome sequencing where repeat elements are difficult to sequence with short read technologies and in the absence of high throughput technologies especially in poorer resource settings, an alternative approach to their characterisation is needed. A rapid and simple method of insertion site mapping that uses Insertion Sequence 6110 (IS6110) fluorescent amplified fragment length polymorphism (FAFLP) PCR as a foundation and then uses additional selective bases to reduce the number of fragments generated was developed. This was applied to Mycobacterium tuberculosis H37Rv sequenced strain to compare the experimental data with the in silico results. This was successfully achieved for all but two of the sixteen fragments generated by FAFLP and demonstrated that, by using this technique, insertion sites can be mapped onto the genomes of M. tuberculosis.

► A robust and simple FAFLP technique to map the insertion sites in bacterial genomes
► Selective base at the 3′end of the primer greatly improves technique efficiency.
► IS6110 insertion sites map to H37Rv genome and correlate with in silico results