Genome assembly
Hifiasm (v0.19.5) was used for whole-genome assembly, utilizing HiFi,
ultralong, and Hi-C reads as input with default parameters. During
chromosome construction, the Hi-C technique was applied. Using HiC-Pro
(Servant et al., 2015), read pairs were mapped the to the genome, with
both ends uniquely aligned retained to ensure data quality. Juicer
(v1.5) (Durand et al., 2016) and 3D-DNA (Dudchenko et al., 2017) were
then employed to construct the chromosome-level genome.
To evaluate the completeness and accuracy of the assembled genome, BUSCO
was used with the actinopterygii_odb10 database as a reference (Simao,
Waterhouse, Ioannidis, Kriventseva, & Zdobnov, 2015). This step ensured
that the resulting genome was both comprehensive and accurate, laying a
solid foundation for further analysis and applications.