Mycobacterium tuberculosis complex genome assembly. Mycobacterium tuberculosis complex

Complete de novo genome assembly (based on a hybrid strategy of combining PacBio and Illumina sequencing data) of selected representative Mycobacterium tuberculosis complex of lineage 1 & 2 for proteogenomics studies. We acknowledge that the genomes of the three lineage 2 strains (SUB5661854, SUB5661760 & SUB5661883) contain a tandem repeat of variable length, as has been reported previously (Domenech P et al. J Bacteriol, 2010, 192(18):4562-70.), and that we cannot resolve using PacBio data. Based on PacBio read coverage, the repeat varied in length from roughly 240 kb (N0145) to 380 kb (N0052). We thus report a quasi-final genome sequence with advantages over the more fragmented Illumina short-read based assemblies. Additional approaches like optical mapping are required to resolve this tandem repeat sequence. It is unclear whether the repeats may be of relevance (modern lineage 2 strains are more pathogenic than ancient lineage 1 strains), as the repeats get lost in in vivo mouse models (Domenech P et al. Infect Immun, 2014, 82(7):2902-12).