Silver arowana, Osteoglossum bicirrhosum, is sexually monomorphic, and its sex determination mechanism is still poorly understood, posing a significant challenge to its captive breeding efforts. To this end, we assembled two high-quality chromosome-level genomes for both female and male silver arowana, with scaffold N50 values of 10.6 Mb and 10.4 Mb for female and male individuals, respectively. Combining re-sequencing data of 109 individuals, we identified two sex-specific SNPs and confirmed a ZW model of sex-determination in this ancient species. Both sex-specific SNPs are located in about 26-kb upstream of foxl2 gene. We subsequently propose a complex gene network in the sex determination process of silver arowana, with foxl2 acting as the central player. The sex chromosomes are homomorphic with a potentially recent origin, as linkage disequilibrium analysis showed minor recombination suppression. Furthermore, we successfully developed accurate molecular markers for sex identification of silver arowana at each developmental stage, significantly improving the reproductive efficiency and further promoting the industrial development.

Abstract: Most grouper species are functional protogynous hermaphrodites, but the genetic basis and the molecular mechanisms underlying regulation of this unique reproductive strategy remain enigmatic. In this study, we reported a high-quality chromosome-level genome assembly of the representative orange-spotted grouper (Epinephelus coioides). No duplication or deletion of sex differentiation related genes was found in the genome, suggesting that sex development in this grouper may be related to changes in regulatory sequences or environmental factors. Transcriptomic analyses showed that aromatase and retinoic acid are probably critical to promote ovarian fate determination, and follicle-stimulating hormone triggers the female-to-male sex change. Socially controlled sex-change studies revealed that the brain of sex-changing fish in response to social environment may be mediated by activation of phototransduction cascade and the melatonin synthesis pathway. In summary, our genomic and experimental results provide novel insights into the molecular mechanisms of sex differentiation and sex change in the protogynous grouper.

Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of short reads from an Illumina Hiseq Xten platform, long reads from a Nanopore platform, and Hi-C sequencing data. This assembled genome is 731.7 Mb in length, with a scaffold N50 of 29.5 Mb and anchoring on 30 chromosomes. A total 18,895 protein-coding genes were predicted, among them 98.46% were functionally annotated. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be critical for molecular regulation of the high-fat trait in the striped catfish. Compared with Fabp1-1 (similar to the conserved Fabp1 in various vertebrate species), the R126T mutation may potentially affect the fatty acid binding capacity of the Fabp1 isotypes 2 and 3. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and laying a foundation for practical aquaculture and molecular breeding of this international teleost species.