Whole Genome Sequencing and Variant Calling

Genomic DNA (gDNA) was extracted from strains of interest using Wizard genomic purification kit (Promega, Madison, WI). Genomic DNA was then quantified using the Qubit system (Thermo Fisher, Waltham, MA). Libraries were then produced using a Nextera XT Kit (Illumina, San Diego, CA). Quality of the libraries was controlled by Fragment Analyzer AATI (Agilent, Santa Clara, CA) and sequencing was performed using MiSeq Reagent Kits v2 on a MiSeq system (Illumina). Obtained reads were assembled with spades v. 3.11.1 (46 (link)) and mapped on reference genomes with bwa v. 0.7.17 (47 (link)). Variant calling was done with gatk 4.0.2.0 (48 (link)). Only variants supported by a minimum of 75% of the reads were considered, and the minimum sequencing depth to call a variant was set to 10. Identified SNPs were manually checked by visualizing the mapping with JBrowse (49 (link)).