DNA extraction, genome sequencing and variant analysis

DNA was extracted and purified with the DNeasy Blood and Tissue kit (Qiagen, Les Ulis, France) according to the manufacturer's instructions. For each clone, paired-end libraries (2 × 100) were prepared from 5 μg of total genomic DNA using the TruSeq SBS Kit v3—HS 200-cycles (FC-401-3001, Illumina, Paris, France). Hiseq sequencing was performed at the Imagif platform (Gif-sur-Yvette, France) and the data were analyzed through the CASAVA-1.8.2 (Illumina; demultiplexing), Fastqc 0.10.1 (Babraham, UK; read quality) and Cutadapt-1.3 (Wilmington, DE, USA; adapter trimming) pipeline. Sequence reads were mapped on the annotated reference genome of A. tumefaciens strain C58 (Wood et al., 2001). Mappings were carried out using the CLC Genomics Workbench v7.5 (CLC bio, Aarhus, Denmark) with a read length #0.9 and similarity #0.95. Genomic variant detection was processed using CLC Genomics Workbench with a minimum coverage of 10 and a variant probability of 90%.