2.6 Chromosome assembly using Hi-C technology
Muscle tissue of C. sonnerati was used for Hi-C library construction in our study. The Hi-C experiment included the following steps (Belaghzal, Dekker, & Gibcus, 2017). First, a white muscle sample of C. sonnerati was cross-linked using formaldehyde and then lysed. Subsequently, chromatin digestion was carried out with MboI and proximity ligated with T4 DNA ligase. After ligation, cross-linking was reversed by 200 μg/mL proteinase K (Thermo) at 65°C overnight. DNA purification was achieved through the QIAamp DNA Mini Kit(Qiagen) according to the manufacturer’s instructions, and the purified DNA was sheared to a length of 300–500 bp. Lastly, the purified DNA was used for Hi-C library construction, and genomic DNA was sequenced on the MGI-SEQ2000 platform in 150PE mode.
The reads from the Hi-C library sequencing were mapped to the polished genome using BWA (bwa 0.7.17) with the default parameters. Paired reads that were mate mapped to different contigs were used to construct the Hi-C associated scaffolding. Lachesis (Burton et al., 2013) was further applied to order and orient the clustered contigs. Then, Jucier (v1.6.2) (Durand et al., 2016) was used to corrected the assembly error in visually.