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.