2.2 Sequencing methods
R. rhizogenes strain LBA9402 was cultured in TY medium (Beringer, 1974), followed by genomic DNA isolation using QIAGEN gravity-flow columns. The genome of LBA9402 was sequenced using a combination of Illumina and Oxford Nanopore Technologies platforms. Nanopore sequencing was done in house, but Illumina sequencing was performed at the Leiden Genome Technology Center (LGTC) of the Leiden University Medical Center (Leiden, The Netherlands), where TruSeq DNA Libraries were sequenced on an Illumina HiSeq 2000 machine. The Oxford Nanopore sequencing library was generated with 200 ng DNA using the SQK-RBK004 Rapid Barcoding Kit. The library was pooled with another library, followed by in-house sequencing on a MinION flow cell (version R9.4.1).