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Updated: Jul 28, 2025

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.
Published on: May 6, 2010
Improvement of the ayu (Plecoglossus altivelis) draft genome using Hi-C sequencing
Masatoshi Nakamoto1, Takashi Sakamoto2
1Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan.
Objective:
The ayu or sweetfish Plecoglossus altivelis is ray-finned fish that is widely distributed in East Asia. The genome size of ayu was estimated at approximately 420 Mb. Previously, we reported on ayu draft genome assembly by whole-genome shotgun using Illumina short reads and PacBio long reads; however, the assembly was not to chromosome level. Therefore, to improve the draft genome sequence of ayu to chromosome level, we performed in situ Hi-C sequencing as a source of linkage information.
Results:
The ayu genome assembly yielded 28 large scaffolds that corresponded to the karyotype of ayu (n = 28). The resulting ayu genome assembly has a N50 scaffold length of 17.0 Mb, improved from 4.3 Mb. The high-quality reference genome will be helpful for phylogenetic research on bony fishes and for breeding programs in ayu aquaculture.
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