Xhv_BS0339
DNA extraction was performed using the Qiagen DNeasy UltraClean Microbial Kit (cat. no. 12224; Valencia, CA) according to the manufacturers instructions, with the following change: 5 replicates were completed for each strain, and after eluting each first replicate, that elute was used to elute the next replicate, and so on. This resulted in >2.0 ug of total DNA per strain, as measured using the ThermoFischer Qubit Fluorometer 3.0 and the Invitrogen dsDNA Broad Range Assay Kit (cat nos. Q33216 and Q32850; Waltham, MA). Library preparation and 250 x 250 paired-end whole genome sequencing was performed at the Pennsylvania State University Genomics Facility using the TruSeq DNA PCR Free Library Construction and the Illumina MiSeq System (cat. nos. FC-121-3001 and SY-410-1003; San Diego, CA).