Scaffolding of the genome using Hi-C technology
The Hi-C technique has been widely applied to construct chromosome-level
genome assemblies. By capturing all DNA interaction patterns in
chromatin, high-throughput sequencing technology, combined with
bioinformatic analyses, allows whole chromosome DNA relationships, in
spatial position within the entire genome, to be studied
(Lieberman-Aiden et al., 2009). Muscle tissue, from the aforementionedT. dalaica, was used for Hi-C library construction, with the
library sequenced on the Illumina HiSeq X Ten platform, using the 150 bp
PE mode. Raw reads were cleaned using fastp (Chen et al., 2018), and
then mapped to the polished genome using Bowtie 2 (version 2.2.5)
(Langmead & Salzberg, 2012). After removing low-quality alignments and
duplicate reads, an inter/intra chromosomal contact map was constructed
and used to anchor and orientate contigs to the chromosomes, using an
agglomerative hierarchical clustering method implemented in Lachesis
(Burton et al., 2013). Gaps between adjacent contigs were filled using
100 Ns.