ONT library preparation and sequencing

A total sample quantity of 2 μg of high molecular weight genomic DNA was used for ONT library construction. The ONT sequencing library was prepared from the genomic DNA following the standard protocol with a Ligation Sequencing Kit SQK-LSK109 (Oxford Nanopore Technologies, Cambridge, UK). For reference genome assembly, two libraries (for mycelium and conidia) were sequenced in R9.4.1 SpotON flow cells, then sequenced on a MinION device using ONT MinKNOW software version 22.05.5. At least three gigabases (Gb) of data were obtained from each sequencing run to obtain approximately 80–100 coverages for genome assembly. There are total three replications of ONT sequencing were performed and subjected to the analysis of DNA methylome and differentially DNA methylated regions (DMRs).