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.