Chromosome assembly
Adapter sequences of Hi-C raw reads were trimmed, and low-quality paired-end reads were removed for clean data by using fastp v0.12.6 with default parameters (Chen, et al. 2018). Then clean reads were aligned to contig sequences using Bowtie2 (2.3.2, -end-to-end –very-sensitive -L 30) (Langmead and Salzberg 2012). Valid interaction paired reads were identified and retained by HiC-Pro v2.8.1 from unique mapped paired-end reads for further analysis (Burton, et al. 2013). Invalid read pairs, including dangling-end, self-cycle, re-ligation, and dumped products were filtered by HiC-Pro v2.8.1 (https://github.com/nservant/HiC-Pro). And then, the congtis were clustered, ordered, and oriented onto chromosomes by LACHESIS (https://github.com/shendurelab/LACHESIS), with parameters CLUSTER_MIN_RE_SITES=100, CLUSTER_MAX_LINK_DENSITY=2.5, CLUSTER NONINFORMATIVE RATIO = 1.4, ORDER MIN N RES IN TRUNK=60, ORDER MIN N RES IN SHREDS=60. Finally, placement and orientation errors exhibiting obvious discrete chromatin interaction patterns were manually adjusted.