Chromosome-Level Assembly of Male Opsariichthys bidens Genome Provides Insights into the Regulation of the GnRH Signaling Pathway and Genome Evolution

Abstract

The 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 the male O. bidens 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 female O. bidens genome, the number of annotated genes in males was much higher (23,992). The male chromosome LG06 exhibited over 97% identity with the female GH14/GH38. Male-specific genes were identified for LG06, where structural variation, 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 male O. bidens and grass carp, 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; GnRH signaling; comparative genomics; hook snout carp; sexual dimorphism.

Figure 1

The Hi-C heatmap, karyotypes, and exon length of the male O. bidens. (A) A Heat map generated by Hi-C technology presented contact matrices of thirty-eight chromosomes. The color bar indicates the logarithm of the strength of the contact density. (B) The karyotypes of male O. bidens’ genome. (C) The distributions of gene exon length in male O. bidens’ genome.

Figure 2

Gene annotation and function of male O. bidens’ genome. (A) Different database-annotated genes. (B) Gene functionally classification by GO analysis. (C) A Venn diagram showing the number of species-specific and shared gene orthogroups of O. bidens between D. rerio, L. rohita, C. carpio, and A. graham.

Figure 3

A phylogenetic tree based on single-copy genes from the nine genome sequences. (A) The number of orthologous for nine fish species. Names for species are abbreviated to Ag, Anabarilius grahami; Cc, Cyprinus carpio; Dr, Danio rerio; Ga, Gasterosteus aculeatus; Lr, Labeo rohita; Ob, Opsariichthys bidens; Ol, Oryzias latipes; Sr, Sinocyclocheilus rhinocerous; Tr, Takifugu rubripes. (B) A bayesian phylogenetic tree, gene families, and divergence time of male O. bidens. The bayesian posterior probability and the maximum likelihood bootstrap had support values of 100%. The numbers above the lines indicate gene family expansions (+ and red) and contractions (− and green).

Figure 4

GnRH signaling pathway of male O. bidens’ genome. The gene-marked colors indicate the gene copy number presented on this signaling pathway (KEGG ID: ko04912).

Figure 5

Physical distribution of GnRH signaling pathway-expanded genes in male O. bidens’ genome. The gene-marked colors indicate gene-expanded number (≥3, see Tables S5 and S6).

Figure 6

Genomic comparisons between female and male O. bidens. Genomic comparisons of whole genome sequences directly, and the majority of female and male O. bidens chromosomes exhibited 1:1 correspondence except for chromosomes LG06 in male and GH14 and GH38 in female.

Figure 7

Detail chromosome comparisons between LG06, GH14, and GH38, and structure variation between female and male O. bidens genomes. (A) The chromosome LG06 of male O. bidens genome showed significant synteny with GH14 and GH38 of female O. bidens genome. (B) Statistics of the structural variations in various regions of the male genome by alignment with female O. bidens genome.

Figure 8

Chromosome conserved synteny analysis between male O. bidens and grass carp genome. (A) The chromosomes in the two genomes showed multiple chromosomes breaking off in grass carps corresponding to chromosomes in male O. bidens. (B) Detail inter-genomic conserved blocks with 21,628 gene pairs between grass carp and male O. bidens genome.