T541
Total genomic DNA was extracted from overnight grown T541 Bt culture using a DNeasy blood and tissue kit (Qiagen). DNA concentration and purity was estimated using Nanodrop Spectrophotometer and Qubit Flurometer (Thermo Fisher Scientific, MA, USA). Whole genome sequencing (WGS) libraries were prepared with Illumina-compatible SureSelectQXT whole genome library prep kit (Agilent, Santa Clara, CA, U.S.A.). In brief, 30ng of Qubit quantified genomic DNA was fragmented and adapter-tagged using SureSelectQXT Enzyme. Fragmented and adapter-tagged DNA was purified with HighPrep PCR beads and then amplified and indexed in a 6 cycle PCR reaction (68C for 2 min, denaturation at 98C for 30 sec, cycling (98C for 30sec, 56C for 30sec and 72C for 60s). The final PCR product (sequencing library) was purified with HighPrep beads, followed by library quality control check. The Illumina-compatible sequencing library was quantified by Qubit fluorometer and its fragment size distribution was analyzed on Agilent TapeStation. Sequencing was done on the MiSeq instrument, [Illumina MiSeq (300*2)]. Samples were loaded on the reagent cartridge and loaded on the instrument along with the flow cell. All the subsequent steps were performed on the instrument, including cluster generation and paired-end sequencing.