Wenjing Tao

The blackchin tilapia (Sarotherodon melanotheron) is an aquaculture species in Southeast Asia, recognized for its adaptability to diverse environmental conditions. Genomic resources for this species remain limited, hindering progress in genetic research and breeding programs. In this study, we generated a high-quality, chromosome-level genome assembly of blackchin tilapia by utilizing Illumina short reads, ONT long reads, Hi-C, and RNA sequencing data. The final assembly spans 1,027.41 Mb (scaffold N50 = 38.87 Mb), with 93.42% of the assembly anchored to 22 chromosomes. Genome completeness, assessed using BUSCO, reached 99.50%. We predicted 27,896 protein-coding genes, of which 90.87% were functionally annotated. Repetitive elements accounted for approximately 42.62% of the genome. This chromosome-scale genome assembly provides a reference for comparative genomic and genetic analyses of blackchin tilapia, supporting investigations into the genetic basis of salinity tolerance and traits relevant to aquaculture breeding.

Heat stress induces metabolic adaptations in fish, including the regulation of triglyceride (TG) synthesis/degradation to preserve cellular lipid balance and energy homeostasis. Diacylglycerol acyltransferase (DGAT) catalyzes the final step in TG synthesis. However, the molecular mechanisms by which DGAT regulates TG metabolism in heat-stressed fish remain unexplored. Our previous study suggested that miR-10c regulates dgat2 expression in genetically improved farmed tilapia (GIFT, Oreochromis niloticus) under heat stress. Here, we characterized the GIFT miR-10c precursor as a 65-nucleotide transcript yielding a 22 nt mature miRNA (oni-miR-10c). A phylogenetic analysis revealed a high level of miR-10c sequence conservation across species. A dual-luciferase reporter assay confirmed dgat2 as a direct target of miR-10c. Overexpression of miR-10c in vivo down-regulated dgat2 transcripts and DGAT2 protein. SiRNA-knockdown of dgat2 resulted in upregulation of cpt1α, fas, and lpl and downregulation of hsl, thereby reprogramming lipid metabolism in GIFT hepatocytes. Thus, the miR-10c-dgat2 regulatory axis facilitates TG hydrolysis and promotes fatty acid metabolism under heat stress. Our findings highlight miR-10c’s potential as a dgat2 inhibitor and its function in regulating lipid metabolism in heat-stressed GIFT. Our study reveals a key molecular pathway mediating thermal adaptation of energy metabolism in fish, providing novel targets for preventing heat-induced metabolic disorders.

Growth traits are the most important economic traits in red tilapia (Oreochromis spp.) production, and are the main targets for its genetic improvement. Increasing salinity levels in the environment are affecting the growth, development, and molecular processes of aquatic animals. Red tilapia tolerates saline water to some degree. However, few credible genetic markers or potential genes are available for choosing fast-growth traits in salt-tolerant red tilapia. This work used genome-wide association study (GWAS) and RNA-sequencing (RNA-seq) to discover genes related to four growth traits in red tilapia cultured in saline water. Through genotyping, it was determined that 22 chromosomes have 12,776,921 high-quality single-nucleotide polymorphisms (SNPs). One significant SNP and eight suggestive SNPs were obtained, explaining 0.0019% to 0.3873% of phenotypic variance. A significant SNP peak associated with red tilapia growth traits was located on chr7 (chr7-47464467), and plxnb2 was identified as the candidate gene in this region. A total of 501 differentially expressed genes (DEGs) were found in the muscle of fast-growing individuals compared to those of slow-growing ones, according to a transcriptome analysis. Combining the findings of the GWAS and RNA-seq analysis, 11 candidate genes were identified, namely galnt9, esrrg, map7, mtfr2, kcnj8, fhit, dnm1, cald1, plxnb2, nuak1, and bpgm. These genes were involved in ‘other types of O-glycan biosynthesis’, ‘glycine, serine and threonine metabolism’, ‘glycolysis/gluconeogenesis’, ‘mucin-type O-glycan biosynthesis’ and ‘purine metabolism signaling’ pathways. We have developed molecular markers to genetically breed red tilapia that grow quickly in salty water. Our study lays the foundation for the future marker-assisted selection of growth traits in salt-tolerant red tilapia.

The Scatophagus argus (S. argus) is a valuable aquaculture species in southern China, with females exhibiting significantly faster growth rates than males. However, the limited understanding of its sex determination and differentiation mechanisms poses challenges for sex-controlled breeding. MicroRNAs (miRNAs), key post-transcriptional regulators, are known to modulate critical pathways governing sex determination and differentiation across several vertebrates. However, there is currently no research on miRNAs related to sex determination and differentiation in S. argus. In this study, we analyzed the expression profiles of miRNA and mRNA in the gonads of adult S. argus using high-throughput sequencing. Our analysis identified 2210 miRNAs, including 482 differentially expressed miRNAs (DEMs) between sexes. These DEMs targeted 3340 differentially expressed genes (DEGs), generating 13,773 regulatory interaction pairs. The expression of some DEGs related to sex determination and differentiation was found to be either positively or negatively correlated with expression of DEMs that might regulate them. The novel_miR_110/Foxl2, novel_miR_802/Gdf9, and novel_miR_1263/Gdf9 show opposing differential expression trends, whereas sar-miR-143-5p-4/Gsdf, sar-miR-143-5p-5/Gsdf, and novel_miR_379/Sox3 show consistent trends. The regulatory relationship between miRNA and gene in the gonads does not seem to be conserved among different fish species. This work advances our understanding of the molecular mechanisms underlying the sexual dimorphism of gonadal gene expression in S. argus. The identified miRNA–gene interactions may serve as potential targets for future sex-control strategies, contributing to advancements in aquaculture practices for this species.

Fish sex is largely influenced by steroid hormones, especially sex hormones. Here, we established a steroid hormone-free genetic model by mutation of cyp11a1 in Nile tilapia, which was confirmed by EIA assay. Gonadal phenotype and transcriptome analyses showed that the XX mutants displayed sex reversal from female to male but with defective spermatogenesis. Despite the sex reversal, the aromatase encoding gene cyp19a1a was continuously expressed in the gonads of the XX mutants, which might be caused by androgen deficiency. Whole-mount fluorescence in situ hybridization and transcriptome analysis showed that the gonads of the XX mutants firstly developed towards ovary but shifted to testis between 10 to 15 days after hatching. Detailed expression analysis of key sex differentiation pathway genes foxl3 and dmrt1 combined with apoptosis analysis revealed transdifferentiation of germ cells from female to male during sex reversal. Rescue experiments showed that both P5 and E2 treatment rescued the sex reversal of cyp11a1 mutant XX fish. Overall, our results revealed a transient ovary-like stage and transdifferentiation of germ cells from female to male in the early gonads of the steroid hormone-deprived cyp11a1 mutant XX fish.

The role of glucocorticoids in oogenesis remains to be elucidated. cyp11c1 encodes the key enzyme involved in the synthesis of cortisol, the major glucocorticoid in teleosts. In our previous study, we mutated cyp11c1 in tilapia and analyzed its role in spermatogenesis. In this study, we analyzed its role in oogenesis. cyp11c1^+/− XX tilapia showed normal ovarian morphology but poor egg quality, as indicated by the mortality of embryos before 3 d post fertilization, which could be partially rescued by the supplement of exogenous cortisol to the mother fish. Transcriptome analyses revealed reduced expression of maternal genes in the eggs of the cyp11c1^+/− XX fish. The cyp11c1^−/− females showed impaired vitellogenesis and arrested oogenesis due to significantly decreased serum cortisol. Further analyses revealed decreased serum E2 level and expression of amh, an important regulator of follicular cell development, and increased follicular cell apoptosis in the ovaries of cyp11c1^−/− XX fish, which could be rescued by supplement of either exogenous cortisol or E2. Luciferase assays revealed a direct regulation of cortisol and E2 on amh transcription via GRs or ESRs. Taken together, our results demonstrate that cortisol safeguards oogenesis by promoting follicular cell survival probably via Amh signaling.