Annex S1: Sequencing metric of the 10 new genomes and obtained with fastqc. A: Metric provide to Illumina metric. B: metric provide to MinION metric. Annex S2 : Alignments of the 12 M. bovis complete genomes (including new genomes, Af2122/97 and Mb3601) was performed using progressiveMauve (annex S4). Annex S3: Pan-genomic study performed on 12 M. bovis complete genomes. “1” shows the presence of CDS and “0” his absence. Annex S4: Annex S4: Indels between the ten new complete genomes and Mb3601 using progressiveMauve. Annotation of these indels was performed with reference genome comparison for gap or with the annotation (with Prokka) of the new complete genome studied for insertion. IS6110 is marked in green. "Indel distribution" sheet shows the indel distribution on the M. bovis genome for the ten new complete genomes. Black arrows show the genomic region with the most of indel found. Annex S5: WgSNP analysis performed on 98 M. bovis. SNPs were annotated and selected according to their specificity to an M.bovis group described in Fig 5. The last common give information on the genetic impact of the SNP. The last sheet presents a graph of SNP number in genomic position.