Whole genome sequencing of C. autoethanogenum after two rounds of Target-AID mutagenesis
DNA concentration was measured using the Qubit Fluorometer and the Qubit dsDNA BR Assay Kit (ThermoFisher; Q32853). 250 ng input DNA was used in the sequencing library preparation. Indexed sequencing libraries were prepared using the Nextera DNA Flex Library Prep Kit (Illumina; 20018705) and IDT for Illumina Nextera DNA CD Indexes (Illumina; 20018708). 5 cycles of PCR were used. Libraries were quantified using the Qubit Fluorometer and the Qubit dsDNA HS Kit (ThermoFisher Scientific; Q32854). Library fragment-length distribution was assessed using the Agilent TapeStation 4200 and the Agilent High Sensitivity D1000 ScreenTape Assay (Agilent; 5067-5584 and 5067-5585). Final library quantification was performed using the KAPA Library Quantification Kit for Illumina (Roche; KK4824) and the library was sequenced on an Illumina MiSeq using the MiSeq Reagent Kit v3 (600 cycle) (Illumina; MS-102-3003) to generate 300-bp paired-end reads.