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

BMC Research Notes

Research Note

Masatoshi Nakamoto¹  Takashi Sakamoto¹ 

[1] Department of Marine Biosciences, Tokyo University of Marine Science and Technology, 108-8477, Tokyo, Japan;

关键词: Ayu;    Sweetfish;    Plecoglossus altivelis;    Genome quality;    Hi-C;   

DOI  :  10.1186/s13104-023-06362-7

 received in 2022-08-02, accepted in 2023-05-19,  发布年份 2023

来源: Springer

【 摘 要 】

ObjectiveThe 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.ResultsThe 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.

【 授权许可】

CC BY   
© The Author(s) 2023

【 图 表 】

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