2.3 Nanopore sequencing and assembly
We prepared DNA using Oxford Nanopore Technologies’ standard ligation sequencing kit SQK-LSK109DNA. Genomic DNA was size-selected using high-pass mode (> 20 kb) using a BluePippin BLF7510 cassette (Sage Science). After completion of sequencing, the raw nanopore sequencing reads were corrected using the program Canu version 1.5 with the parameters ‘minReadLength 3000–min Overlap Length 500’ and Smartdenovo with the parameters ‘-k 17 -c 1’ (Koren et al., 2017). A preliminary de novo assembly was constructed using the Nanopore sequence, then we aligned the Illumina reads to the draft genome assemblies using BWA-MEM (Li, 2013).