Improvement of the ayu (Plecoglossus altivelis) draft genome using Hi-C sequencing.
BMC Res Notes
; 16(1): 92, 2023 May 30.
Article
in En
| MEDLINE
| ID: mdl-37254197
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 on bony fishes and for breeding programs in ayu aquaculture.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Osmeriformes
Limits:
Animals
Language:
En
Journal:
BMC Res Notes
Year:
2023
Document type:
Article
Affiliation country:
Japón