Paired-end sequencing of Ensifer meliloti strain 1022: derived isolate Q08-313-EPS-
For each of the 40 derived isolates, in addition to nine replicates of each of the ancestral strains (N = 40 + [9  2] = 58 isolates total), we completed DNA extractions using the Sigma-Aldrich GenEluteTM Bacterial Genomic DNA isolation kit (Sigma-Aldrich Corp., St. Louis, Missouri, US). We submitted these 58 sample extractions to the Centre for Analysis of Genome Evolution and Function (CAGEF) at the University of Toronto, Canada, for library preparation and sequencing. Illumina libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA, US) according to the manufacturers guidelines. Libraries were dual barcoded using the Nextera XT Index Kit, pooled in equal amounts, and then denatured and diluted to a sequencing concentration of 1.8 pM. Sequencing was performed on an Illumina NextSeq 500 using the Mid Output V2 sequencing kit with 150  2 PE reads.