2.4 Hi-C library construction and chromosome assembly
The raw reads produced by the illumina High-throughput sequencing platform based on the technology of sequencing by synthesis were filtered by SOAPnuke software (Chen et al., 2018). Juicer was employed to compare the obtained clean reads to genome draft (Durand et al., 2016). After filtering the results and removing the misaligned reads, 3d-DNA software was applied to preliminarily cluster, order, and orient the unique, valid interaction pairs onto the pseudochromosomes (Dudchenko et al., 2017). Juicer-box was used to correct pseudochromosomes to improve chromosome assembly level. For the evaluation of the Hi-C assembly results, the final pseudochromosome assemblies were divided into 100 kb bins of equal lengths and a heat map was obtained to visualize the interaction signals generated by the valid mapped read pairs between each bin.