Abstract: Hook snout carp Opsariichthys bidens is an
important farmed fish in East Asia that shows sexual dimorphism in
growth, with males growing faster and larger than females. To understand
these complex traits and improve molecular breeding, chromosome-level
genome assembly of male O. bidens was performed using Illumina,
Nanopore, and Hi-C sequencing. The 992.9 Mb genome sequences with a
contig N50 of 5.2 Mb were anchored to 38 chromosomes corresponding to
male karyotypes. Of 30,922 functionally annotated genes, 97.5% of BUSCO
genes were completely detected. Genome evolution analysis showed that
the expanded and contracted gene families in male o.bedins genome
were enriched in 76 KEGG pathways, and 78 expanded genes were involved
in the GnRH signaling pathway that regulates the synthesis and secretion
of luteinizing hormone and glycoprotein hormones, further acting on male
growth by inducing growth hormone. Compared to the released femaleO. bidens genome, the number of annotated genes in males was much
higher than in females (23,992). The male chromosome LG06 exhibited over
97% of identity with the female’s GH14/GH38. Male-specific genes were
identified for LG06, where structural variety, including deletions and
insertions, occurred at a lower rate, suggesting a centric fusion of
acrocentric chromosomes GH14 and GH38. The genome-synteny analysis
uncovered significant inter-chromosome conservation between maleO. bidens and grass carp, and the former originating from
ancestral chromosome breakage to increase the chromosome number. Our
results provide a valuable genetic resource for studying the regulation
of sexual dimorphism, sex-determining mechanisms and molecular-guided
breeding of O. bidens .
Keywords: Cyprinid
fish, hook snout carp, sexual dimorphism, comparative genomics, GnRH
signaling