Genomic DNA libraries were prepared for all Australian isolates using an Illumina Nextera™ DNA Flex Library Prep kit with CD indexes according to the manufacturer’s instructions (Illumina, San Diego, CA, USA). The size distribution of libraries was determined using the HSD1000 ScreenTape device on the 2200 TapeStation system (Agilent technologies). Concentration was determined using the Qubit Fluorometer2.0 (Invitrogen) and KAPPA Library Quantification kit (KapaBiosystem) according to the manufacturer’s instructions. Pooled libraries were sequenced (2 × 250 bp paired end reads) using a Miseq v3 reagent kit on an Illumina Miseq® platform (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Illumina reads were quality trimmed using Trimmomatic [70 ] with the following parameters: > 15 quality score, sliding window of 4 and minimum length of 200 bp.
ANI between all possible pairs of 50 representative assembled genomes was calculated using pyani [71 ] and visualised using Pheatmap v1.2.12 in R. Quast version 5 was used to evaluate the assemblies and provide genome metrics including contig number, GC content and N50 values [72 (link)].
ANI between all possible pairs of 50 representative assembled genomes was calculated using pyani [71 ] and visualised using Pheatmap v1.2.12 in R. Quast version 5 was used to evaluate the assemblies and provide genome metrics including contig number, GC content and N50 values [72 (link)].
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