WGS of Mycobacterium avium subsp. paratuberculosis: IS1311 type S IS900 RFLP type S1 strain
Genomic DNA was prepared by isopropanol precipitation and a 70% ethanol wash of CTAB/phenol/chloroform extracted cellular material after stepwise enzymatic digestion with lysozyme, RNase A, and proteinase K. MiSeq indexed libraries for these DNA extracts were created using Nextera XT DNA sample preparation and index kits (Illumina, San Diego, CA) with a modified version of the standard Nextera XT library preparation as suggested in Votintseva, A.A., et al., (Mycobacterial DNA extraction for whole-genome sequencing from early positive liquid (MGIT) cultures. J Clin Microbiol, 2015. 53(4): p. 1137-43) for WGS of high GC content M. tuberculosis genomes. The libraries were sequenced with a MiSeq v2 500-cycle reagent kit, generating 2  250-bp paired-end reads on the Illumina MiSeq platform.