DNA Extraction, Library Preparation and Genome Sequencing for Baseline Strain PA77

The genome sequencing was performed at the NGS Competence Center Tübingen (NCCT) using both short (Illumina) and long Oxford Nanopore Technology (ONT) reads for the baseline strain PA77. For ONT, genomic DNA was isolated using Qiagen Genomic Tip G/20, the integrity and quality of the preparations were evaluated on a Femto Pulse capillary electrophoresis device (Agilent, Santa Clara, CA, United States). Library preparation was performed with Ligation Sequencing Kit (SQK-LSK109) with Native Barcoding Expansion (NBD104). The pooled libraries were sequenced on a MinION flow cell (FLO-MIN106D) for 48 h. For short read sequencing, the DNA was extracted with the DNeasy UltraClean Microbial Kit (Qiagen). Illumina sequencing libraries were prepared using Nextera DNA Flex library prep kit (Illumina), using combinatorial dual indexing. The Illumina libraries were pooled and sequenced on a NextSeq 500 High-Output flow cell with 2 × 150 bp.