De novo genome assembly and Hi-C scaffolding
All of the filtered Nanopore reads were used for the draft genome assembly in Nextdenovo software (v2.3.1; https://github.com/Nextomics/NextDenovo) with default parameters. The assembled genome was corrected using the filtered Illumina genome reads. BWA software (BWA-MEM module) (Li & Durbin 2009) was used to map short reads to the genome, and Pilon software (Walker et al. 2014) was used for error correction of the sequenced bases. To obtain the chromosome-level genome, the Hi-C reads were aligned to the assembled genome using Juicer software. The software 3D-DNA (Dudchenko et al. 2017) was used to cluster scaffolds into different clusters; in each group, the order of scaffolds was determined by the strength of interactions. Finally, all the possibilities of scaffold orientation and generated finely orientated scaffolds using a weighted directed acyclic graph.