DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in multiple important biological processes in fish, such as gonadal development. The cellular DNA methylation level is tightly regulated by DNA methyltransferases (Dnmt). However, detailed investigations of this family in fish are very scarce. In this study, our results confirmed that teleost genomes contain 4 to 16 Dnmt genes, with diversity likely resulting from a combination of whole-genome duplication (WGD), tandem duplication, and gene loss. Differences were observed in tissue distribution, transcription abundance, and protein structure of Dnmt duplicates, supporting their subfunctionalization or neofunctionalization after duplication. Interestingly, we found that fish Dnmt3b duplicates likely have acquired the functions of mammalian Dnmt3l, which may compensate for the absence of fish Dnmt3l. Furthermore, transcriptome analysis and qPCR results indicated that DNA methyltransferase genes (Dnmt1, Dnmt3aa, Dnmt3ab, Dnmt3ba, and Dnmt3bb.1) possibly play important roles in the natural sex change of protandrous hermaphrodite blackhead seabream (Acanthopagrus schlegelii) and inferred that global remodeling of gonadal DNA methylation, regulated by DNA methyltransferase genes, was closely associated with sex change in sequentially hermaphroditic fishes. Overall, our results may help provide a better understanding of the evolution and function of DNA methyltransferases in fish.

The greater amberjack (Seriola dumerili) is a globally important pelagic fish valued for its rapid growth, superior flesh quality, and high aquaculture potential. Here, we report the first telomere-to-telomere (T2T) chromosome-level genome assemblies for male and female S. dumerili generated through an integrated sequencing strategy combining Pacific Biosciences High-Fidelity (PacBio HiFi) long reads, MGI (MGI Technology, Inc.) short reads, and Hi-C (chromosome conformation capture) data.The assemblies spanned 685 Mb (female) and 683 Mb (male), each anchored to 24 chromosomes and exhibiting near-complete continuity and accuracy. Both genomes achieved exceptional completeness, with over 99.3% of the BUSCO genes identified, and contained 22,352 and 22,325 annotated protein-coding genes, respectively. The availability of these T2T genomes provides a comprehensive resource for investigating sex-specific genomic features, evolutionary adaptation, and functional mechanisms underlying growth and disease resistance, thereby advancing molecular breeding and sustainable aquaculture of the greater amberjack.

This study investigates the genomic basis of immune adaptation in the transparent glass catfish (Kv: Kryptopterus vitreolus), focusing on the loss of the Toll-like receptor 21 (TLR21) gene. Comparative genomic analysis with closely related non-transparent North African catfish (Cg: Clarias gariepinus) revealed 11 TLR genes in the latter, while only 8 TLR genes (KvTLR1, 2, 3, 5, 7, 9, 13, and 20) were retained in the glass catfish, with TLR21 specifically absent. Collinearity analysis confirmed that the genomic region containing TLR21 is conserved across eight siluriform species, with loss exclusively in the glass catfish, supporting its lineage-specific absence. Structural expansion was notable in KvTLR5, KvTLR7, and KvTLR20. Molecular docking indicated that binding stability between CpG oligonucleotides and TLR21 varies significantly, with CpG-B 1681 showing the strongest interaction, which highlights sequence-dependent ligand recognition. Interestingly, absence of the TLR1 gene in another transparent teleost, the X-ray tetra (Pristella maxillaris), suggests that transparent fishes may share an evolutionary trend of lineage-specific TLR gene loss. Together, these findings reveal a distinctive evolutionary trajectory in the innate immune receptor family of transparent fishes and provide new molecular insights into their adaptive immune strategies. These insights will benefit the academic community by improving comparative frameworks for fish innate immunity, and they may inform disease prevention and health management strategies in aquaculture and the ornamental fish trade.

Acyl-CoA thioesterase 9 (ACOT9), a member of the type II hot-dog fold thioesterase superfamily, play important roles in regulating the balance between intracellular acyl-CoA and free fatty acids. Although its functions have been extensively studied in vertebrates, its evolutionary diversification and physiological roles in Diptera, particularly in the economically important insect black soldier fly (Hermetia illucens), remain largely unclear. In this study, ACOT9 homologs were identified from 93 representative dipteran species, and H. illucens was used as a model to investigate phylogenetic re-lationships, synteny, domain architecture, expression profiles, and RNA interference (RNAi)-based functional analysis. The results showed that ACOT9 underwent lineage-specific duplications in the suborder Brachycera, giving rise to four paralogs (ACOT9.1–9.4), accompanied by lineage-specific gene losses. Synteny and conserved domain analyses suggested potential functional divergence among these paralogs. In contrast, the ancestral single-copy ACOT9 retained a catalytically con-served domain (e.g., d1lo7a) shared between vertebrates and insects. We cloned the full-length open reading frame (ORF) of H. illucens ACOT9. Transcript abundance peaked on day 12 of larval devel-opment (pre-pupation), with higher expression in males than in females, and predominant localiza-tion in the Malpighian tubules. RNAi-mediated knockdown in 6- to 7-day-old larvae significantly altered fatty acid composition: total saturated fatty acids increased by 13.35%, while monounsatu-rated and polyunsaturated fatty acids decreased by 5.39% and 14.27%, respectively, with relative abundances of lauric acid and linoleic acid changing by more than 10%. Transcriptomic analysis revealed that ACOT9 knockdown significantly upregulated genes involved in de novofatty acid synthesis (FAS1/2/3, ACC, MAT, KAS, ACP) and acyl-CoA activation (ACSM1/2, ACSL4/6), down-regulated the lipolysis gene LIP, and induced expression of the mitochondrial β-oxidation trans-porter genes CPT1/2. These findings indicate that ACOT9 deficiency triggers compensatory lipid synthesis and β-oxidation activation, ultimately leading to saturated fatty acid accumulation. In summary, this study elucidates the evolutionary diversification of ACOT9 in Diptera and demon-strates its pivotal role in lipid homeostasis in H. illucens, providing important insights into insect thioesterase function and endogenous lipid metabolic networks.