Whole Genome Sequencing Protocol

Whole genome sequencing was conducted at Omega Bioservices (Norcross, GA, USA). Briefly, DNA was extracted using the E.Z.N.A.^® Bacterial DNA Kit (Omega Bio-tek, Norcross, GA, USA). The concentration was measured using the QuantiFluor dsDNA System on a Quantus Fluorometer (Promega, Madison, WI, USA). A Kapa Biosystems HyperPlus kit (Kapa Biosystems, Wilmington, MA, USA) was used for the whole-genome library construction. DNA was fragmented, and ends were repaired, 3’ adenylated, and ligated to adapters. The resulting adapter-ligated libraries were PCR-amplified. After Illumina indexes were added, they were pooled for multiplexed sequencing on an Illumina X10 platform (Illumina, San Diego, CA, USA) using the pair-end 150 bp run format. de novo assembly was performed on Ridom SeqSphere + v9.0 (Ridom GmbH, Germany) using SKESA 2.4.0 (Souvorov et al., 2018 (link)).