2.6 Chromosome assembly using Hi-C library
To obtain a chromosomal assembly ofC. undulatus , the Hi-C technique was applied to obtain the interaction information among contigs, which are strongly dependent on the one-dimensional distance between a pair of loci (Xiao et al.2019). The Hi-C library was constructed using 1 g of muscle tissue from the same one individual. The steps involved in the process, as previously described (Xiao et al. 2019), include tissue fixation with formaldehyde, lysis, chromatin digestion (DpnII), biotin marking, proximity ligation, DNA purification, physical shearing, and DNA amplification. The Hi-C library was sequenced using the Illumina NovaSeq 6000 platform with PE150 mode. After the low-quality reads were filtered using Fastp (Chen et al. 2018) with default parameters, the clean read pairs were mapped to the polished C. undulatus genome using Bowtie2 (Langmead & Salzberg 2012) in end-to-end mode. Clean read pairs that did not provide interaction information were excluded by alignment to the sequences at the restriction site of DpnII. With valid interaction information, the contigs from nanopore sequencing ofC. undulatus were clustered into 24 groups using Lachesis (Burtonet al. 2013), which were further ordered and oriented into chromosomes.