Genome sequencing of Mycobacterium canettii recombinants

We investigated chromosomal DNA transfer between Mycobacterium canettii strains and various strains of the Mycobacterium tuberculosis complex. Library preparation and whole-genome sequencing of donor, recipient and recombinant strains were performed at the Biomics Platform of the Institut Pasteur (Paris, France). Genomic DNA was prepared using either the NEXTFLEX PCR-Free DNA-Seq Kit for Illumina (Bioo Scientific) or the TruSeq DNA PCR-Free Kit (Illumina). Sequencing was performed using either a HiSeq 2500 or a NextSeq 500 device (Illumina) to generate 100/150-bp paired-end reads.