Improvement of the ayu (Plecoglossus altivelis) draft genome using Hi-C sequencing.

ABSTRACT:

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 o

SUBMITTER: Nakamoto M 

PROVIDER: S-EPMC10230677 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature