Sex chromosomes display remarkable diversity and variability among vertebrates. Compared with research on the X/Y and Z/W chromosomes, which have long evolutionary histories in mammals and birds, studies on the sex chromosomes at early evolutionary stages are limited. Here, we precisely assembled the genomes of homozygous XX female and YY male Lanzhou catfish (Silurus lanzhouensis) derived from an artificial gynogenetic family and a self-fertilized family, respectively. Chromosome 24 (Chr24) was identified as the sex chromosome based on resequencing data. Comparative analysis of the X and Y chromosomes showed an approximate 320 kb Y-specific region with a Y-specific duplicate of anti-Mullerian hormone type II receptor (amhr2y), which is consistent with findings in 2 other Silurus species but on different chromosomes (Chr24 of Silurus meridionalis and Chr5 of Silurus asotus). Deficiency of amhr2y resulted in male-to-female sex reversal, indicating that amhr2y plays a male-determining role in S. lanzhouensis. Phylogenetic analysis and comparative genomics revealed that the common sex-determining gene amhr2y was initially translocated to Chr24 of the Silurus ancestor along with the expansion of transposable elements. Chr24 was maintained as the sex chromosome in S. meridionalis and S. lanzhouensis, whereas a sex-determining region transition triggered sex chromosome turnover from Chr24 to Chr5 in S. asotus. Additionally, gene duplication, translocation, and degeneration were observed in the Y-specific regions of Silurus species. These findings present a clear case for the early evolutionary trajectory of sex chromosomes, including sex-determining gene origin, repeat sequence expansion, gene gathering and degeneration in sex-determining region, and sex chromosome turnover.

Oyster pompano (Trachinotus anak) is currently the highest-yielding marine aquaculture fish species in China. However, previously available genome assemblies were fragmented and incomplete, hindering advances in genomic research and breeding applications. Here, we generated two haplotype-resolved, telomere-to-telomere (T2T) genome assemblies for a female T. anak using PacBio HiFi, ONT ultra-long, and Hi-C data. The resulting assemblies (haplotype A and B) span 663.78 Mb and 661.09 Mb with contig N50 of 28.62 Mb and 29.02 Mb, respectively. Both haplotypic assemblies were anchored into 24 gap-free chromosomes, each comprising a complete set of 48 telomeres. The quality value (QV) scores were 70.45 and 68.66, and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness scores were 98.9% and 99.0% for haplotype A and B, respectively. Genome annotation identified 187.94 Mb and 178.63 Mb of repetitive sequences, and predicted 23,118 and 23,119 protein-coding genes in haplotypes A and B, respectively, with 99.79% and 99.78% functionally annotated. These two high-quality T2T assemblies provide invaluable resources for molecular breeding and advancing biological and evolutionary research in T. anak.

Background Golden pompano (Trachinotus ovatus) is a commercially important aquaculture species in southern China. However, its delayed sexual maturation hampers breeding efficiency. Nell2 interacting cell ontogeny regulator 1 (Nicol1) is a novel peptide implicated in reproductive regulation in mammals and growth-related processes in fish, but its molecular mechanisms in teleosts remain poorly understood. Results This study investigated the effects of Nicol1-17, the biologically active form of Nicol1, on hepatic gene expression and metabolism in golden pompano. RNA-Seq analysis identified 59 differentially expressed (DE) long non-coding RNAs (lncRNAs) and 305 DE mRNAs following Nicol1-17 treatment. Functional enrichment analysis revealed significant involvement of these transcripts in steroid biosynthesis, MAPK signaling, and energy metabolism pathways. Protein-protein interaction and lncRNA-mRNA co-expression analyses revealed interconnected networks linking hepatic metabolism with downstream growth and reproductive regulation, suggesting a coordinated regulatory role of Nicol1. Co-expression network analysis highlighted three candidate lncRNAs (MSTRG.29233.1, MSTRG.29362.4, and MSTRG.29409.9), which were highly expressed in the brain, pituitary, liver, and gonads, and potentially regulate key genes associated with reproduction and growth. In addition, biochemical assays showed that Nicol1-17 significantly increased hepatic levels of high-density lipoprotein cholesterol and free fatty acids, as well as the activities of lipid synthesis enzymes (fatty acid synthase, malic enzyme), β-oxidation enzyme (acyl-CoA oxidase), and glucose metabolism enzyme (glucose-6-phosphate dehydrogenase). Conclusions These findings suggest that Nicol1 participates in regulating hepatic metabolic remodeling and gene expression to coordinate growth-and reproduction-related pathways in golden pompano. This work provides a molecular framework for understanding how endocrine peptides integrate hepatic metabolism with growth and reproductive processes in teleosts and lays the groundwork for future functional and applied research in aquaculture.

Aromatase inhibitor letrozole (LZ) and 17α-methyltestosterone (MT) are commonly used for sex control breeding to induce female-to-male sex reversal in aquaculture. However, studies on the molecular regulatory mechanisms of LZ and MT are still limited. Here, a comparative transcriptome analysis was conducted on the hypothalamus, the gonad, and the liver of golden pompano (Trachinotus ovatus) after 30 days of LZ and MT treatment, which demonstrated significant sexual size dimorphism. Following LZ treatment, the transcriptome data identified 156, 890, and 1286 different expression genes (DEGs) in the hypothalamus, the liver, and the gonad, respectively. After MT treatment, the transcriptome data identified 114, 876, and 950 DEGs in the hypothalamus, the liver, and the gonad, respectively. Functional enrichment analysis revealed that DEGs were involved in oocyte meiosis and steroid-hormone synthesis following LZ treatment. Similarly, the analysis indicated that DEGs were associated with cysteine and methionine metabolism and steroid-hormone synthesis after MT treatment. Further analysis showed that LZ treatment can promote the first meiotic division but inhibit the second meiotic division of the oocyte. MT treatment promotes polyamine synthesis to induce oocyte apoptosis, both of which affect the trajectory of ovarian differentiation in golden pompano. However, LZ and MT have converse effects in sex hormone synthesis. LZ inhibits estrogen metabolism but promotes cholesterol synthesis by regulating sqle, cyp3a40, ugt1a1, and ugt2a1, while MT promotes estrogen metabolism but inhibits the conversion of cholesterol to pregnenolone by regulating cyp19a1, cyp1a, and hsd17b7. This study reveals that both LZ and MT may inhibit the ovarian differentiation and induce masculinization through different regulatory mechanisms, which provides a fundamental insight into the sex control breeding in aquaculture.