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.