Isolation of the MTBC (Mycobacterium tuberculosis complex)  from captive wild animals from India
The whole genome libraries were prepared as per the manufacturers (Thermofisher)instructions. Briefly, the Ion Plus Fragment DNA Library Prep Kit (Thermofisher, Cat. No.4471269) was used. Genomic DNA was first sheared to ~250 bp fragments using the IonShear Plus Kit , followed by adapter ligation and barcode tagging with the Ion XpressBarcode and Adapters Kit (Thermofisher, Cat. No. 4471250). After each step, purification was performed using AMPure beads (Beckman Coulter, Cat. No. A63881). Library size is determined by using 2% agarose gel size select (Thermofisher, Cat. No. G661012).Library quantification was performed using the Qubit High-Sensitivity kit. The libraries werethen diluted to a final concentration of 100pM and subjected to cluster amplification. Thelibraries were loaded onto 540 chip using the Ion Chef System (Thermofisher, Cat. No.2664777) and sequenced on the Ion GeneStudio S5 Plus Series System for comprehensive genome sequencing. The raw sequencing data obtained from the Ion GeneStudio S5 Plus Series System were further processed andanalyzed.