Comparative biochemistry and physiology. Part D, Genomics & proteomics最新文献

The leopard coral grouper (Plectropomus leopardus) is a reef-dwelling fish that is highly valued for its striking coloration. This coloration is affected by the expression of genes, which is, in turn, governed by chromatin structure. In this study, we characterized chromatin accessibility in black and red morphs to identify regulatory elements associated with pigmentation. Most accessible chromatin regions (ACRs) were located in non-coding regions, especially distal intergenic regions; the number of ACRs was 7.26% and 8.01% greater in distal intergenic regions than in promoters (≤1 kb) in black and red groups, respectively. Comparative analysis uncovered 3480 differentially accessible regions (DARs), including 2926 with increased and 554 with decreased accessibility. 1764 genes annotated from the identified DARs were subjected to functional enrichment analysis. Gene Ontology (GO) enrichment analysis of these genes derived from DARs revealed significant associations with pigmentation-related processes, including pigment granule formation, pigment biosynthesis, and melanin metabolism. Meanwhile, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that these genes were significantly enriched in multiple pathways, such as melanogenesis, the MAPK signaling pathway, lipid metabolism pathways (fatty acid, α-linolenic acid, and linoleic acid metabolism), and immune-related signaling pathways (TNF, IL-17, and C-type lectin receptor pathways). Integrated analysis of ATAC-seq and RNA-seq data revealed a positive association between chromatin accessibility and differential gene expression. Overall, these findings shed light on the regulatory landscape underlying body color variation in P. leopardus and provide valuable insights with implications for enhancing the coloration of fish via genetic approaches and selective breeding.

The sipunculid worm Sipunculus nudus is a dioecious marine invertebrate with ecological and aquaculture importance. To investigate the metabolic features underlying gamete specialization and thermal response, we performed untargeted metabolomic analysis of spermatozeugmata and oocytes under control conditions, as well as oocytes exposed to acute heat stress (37 °C for 24 h; n = 6 males, 6 females, and 4 heat-stressed females) using ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS). Combined multivariate and univariate statistical analyses, applied with fold-change and significance thresholds, revealed 894 putatively annotated metabolites that differed between oocytes and spermatozeugmata, and 1749 that changed significantly under heat stress. Oocytes were enriched in lipid species (e.g., phospholipids such as PI and LPC) and nucleotide derivatives (e.g., putatively annotated uridine monophosphate, deoxynucleosides), whereas spermatozeugmata showed higher levels of lipids (e.g., PE and PC species), amino acid derivatives (e.g., putatively annotated N-acetyl-DL-serine), and small peptides. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that metabolites mapped to neurotransmitter and energy metabolism pathways were more prominent in oocytes, while metabolites associated with antioxidant and nucleotide biosynthesis pathways were comparatively enriched in spermatozeugmata. Under heat stress, oocytes exhibited significant metabolic changes, with increased organic acids and lipid metabolites (fatty acids and glycerophospholipids) and decreased nucleotide- and amino acid-related compounds. Most KEGG-mapped metabolic pathways showed an overall reduction in associated metabolites, including amino sugar, nucleotide, and amino acid metabolism, whereas metabolites mapped to Fc epsilon RI signaling and bile secretion KEGG pathways were relatively enriched. This study provides the first comprehensive metabolomic profile of S. nudus germ cells, revealing sex-specific metabolic patterns and heat-induced reprogramming of oocyte metabolism. These findings enhance our understanding of gamete physiology and acute thermal stress responses in marine invertebrates and may contribute to the development of reproductive health biomarkers.

The Republic of Korea is the global leading producer of olive flounder (Paralichthys olivaceus), accounting for approximately 49% of national aquaculture production. Acute low-temperature stress poses a major challenge to this industry, causing substantial economic losses through impaired growth, increased mortality, and compromised immune function. This study aimed to identify genetic markers associated with acute low-temperature stress tolerance using a genome-wide association study (GWAS) and determine optimal genomic prediction parameters. A total of 576 healthy olive flounders (average weight 419.57 ± 9.56 g) were subjected to acute low-temperature stress at 9 °C for 20 min. Serum cortisol levels were measured and caudal fin samples were collected from 384 individuals for genomic DNA isolation. Genotyping using a 70 K single-nucleotide polymorphism (SNP) chip yielded 57,638 high-quality SNPs from 375 individuals, which were analyzed using a linear mixed model. Eighteen putative SNPs exhibiting suggestive significance level (p < 1 × 10^-5) were identified on chromosomes 8, 20, and 21; however, none surpassed the Bonferroni-corrected genome-wide significance threshold (p < 8.6 × 10^-7). These suggestive associations, therefore, require validation in independent populations. Among them, SNPs AX-419197258 and AX-419200963 explained 3.44% and 3.25% of the phenotypic variance, respectively. Functional annotation indicated that putative candidate genes, including gbe1, serta, lpgat1, and il20ra, are involved in key biological and immune-related pathways. Genomic prediction analyses demonstrated that the random forest model achieved the highest accuracy for predicting serum cortisol levels. Moreover, GWAS-based marker selection outperformed random marker selection, with approximately 1000 markers identified as optimal for reliable prediction. Collectively, these findings provide insights into the genetic architecture of low-temperature stress tolerance in olive flounder and support the application of genomic approaches in selective breeding programs to enhance resilience and sustainability in aquaculture.

MicroRNAs (miRNAs) contribute to diverse biological functions and physiological mechanisms through the intricate regulation of their target genes. In this study, we investigated the influence of miR-182-5p on pigmentation in Crassostrea gigas. Differentially expressed miR-182-5p associated with melanin formation was successfully screened using small RNA sequencing. qRT-PCR revealed a higher expression level of miR-182-5p in the white mantle and lower expression in hemocytes and the black mantle across diverse tissues of C. gigas. Target prediction analyses identified microphthalmia-associated transcription factor (MITF) as a potential target of miR-182-5p. The relationship between MITF and miR-182-5p was further verified via the overexpression and inhibition of miRNAs, as well as by a dual-luciferase reporter assay. Masson-Fontana melanin staining revealed a marked decrease in pigment granules after injections of miR-182-5p mimics. Western blotting analyses revealed that changes in miR-182-5p levels could regulate MITF protein expression. Upon miR-182-5p overexpression, genes associated with melanin synthesis were markedly downregulated in the mantle tissue. In summary, miR-182-5p participates in the regulation of melanin formation in C. gigas through the regulation of MITF. These results are significant for elucidating the regulatory role of miRNAs in mollusk melanin synthesis and promoting comprehension of the molecular mechanisms underlying mollusk melanin formation.

This study systematically identified all six members of the soxE gene family (sox8a, sox8b, sox9a, sox9b, sox10a, sox10b) in Siniperca scherzeri for the first time. Their conserved HMG-box domains were confirmed through bioinformatics analysis. The expression patterns of these genes were analyzed across different tissues of adult fish and during various stages of gonad development. Additionally, the effects of 17α-methyltestosterone (MT) immersion treatment during the critical period of sex differentiation on soxE genes expression and gonad development were investigated. The results revealed that the expression levels of all soxE genes were significantly higher in male individuals, particularly in the testes, compared to females, indicating pronounced sexual dimorphism. Specifically, MT treatment significantly upregulated the expression of sox9a and sox9b, accompanied by an increase in the expression of the male-related gene dmrt1 and a decrease in the expression of the female-related gene cyp19a1a, thereby inducing sex reversal in genetic females. These findings suggest that the soxE gene family, particularly the two isoforms of sox9, may play crucial roles in male sex determination, gonad development, and the regulatory network of sex differentiation in Siniperca scherzeri, providing an important molecular foundation for understanding its sex determination mechanisms.

The Sox gene family plays a fundamental role in vertebrate reproductive processes, including sex determination, gonadal development, and steroidogenesis. In this study, 42 Sox genes were systematically identified in the genome of Spinibarbus hollandi and categorized into seven subfamilies (B1, B2, C, D, E, F, and H) based on phylogenetic and conserved domain analyses.Comparative genomics and gene structure evaluations demonstrated high evolutionary conservation alongside functional diversification, likely driven by teleost-specific whole-genome duplication (TS-WGD). Quantitative real-time PCR (qRT-PCR) across eight adult tissues revealed distinct expression profiles: 14 genes exhibited brain-predominant expression, with eight of these being the most abundant across all tissues. Notably, significant sexual dimorphism was observed in the gonads; Sox-3 and Sox-11b were characterized as female-biased (ovary-enriched), while Sox-9a/9b and Sox-30 were identified as male-biased (testis-enriched). Masculinization experiments induced by 17α-methyltestosterone (MT) demonstrated that exogenous androgens suppress female-biased Sox genes and activate male-biased ones, facilitating ovarian transformation into testis-like tissue via an androgen receptor-mediated regulatory cascade. Interestingly, Sox-17 and Sox-10 maintained stable expression across different gonadal states, suggesting their involvement in cellular homeostasis independent of hormonal fluctuations. Collectively, these findings elucidate the functional plasticity and endocrine-regulatory roles of Sox genes in teleost gonadal differentiation, providing a molecular basis for understanding sex determination mechanisms and enhancing sex-control technologies in aquaculture.

The sea urchin Strongylocentrotus intermedius is a commercially cold-water species in China, and is highly sensitive to temperature fluctuation. High temperatures from global warming pose a major threat to its survival and physiological homeostasis in summer. However, little is known about the molecular regulatory mechanisms of the heat stress response in the intestine of adult S. intermedius. In this study, RNA sequencing and data-independent acquisition (DIA)-based proteomics were applied to investigate intestinal transcriptomic and proteomic responses of adult S. intermedius following a 15 day high-temperature exposure (25 °C), compared with a control group maintained at 15 °C. Transcriptomic profiles showed that heat stress significantly suppressed the expression of COX and ATPase subunits in the oxidative phosphorylation pathway, potentially reducing energy synthesis efficiency. Meanwhile, the expression of heat shock proteins and molecular chaperones was upregulated to enhance misfolded protein repair. In the proteomic profile, high temperature upregulated LC3C and STK11 in autophagy pathway, which may promote the clearance of damaged components, while caspase-3 mediated apoptosis was also enhanced. Integrative analysis identified 20 co-upregulated DEGs/DEPs, mostly enriched in protein processing in the endoplasmic reticulum pathway, highlighting its key role in high temperature response. Additionally, cathepsins involved in immune-related pathways were downregulated, potentially affecting intestinal immunity. The present study enriches the current knowledge of the high temperature response in adult S. intermedius, and provides important insights into heat stress regulation in S. intermedius and other echinoderms.

Sea cucumber (Apostichopus japonicus) is of considerable commercial and ecological value, yet disease outbreaks substantially constrain the sustainable development of its aquaculture industry. The molecular mechanisms underlying A. japonicus's response to pathogenic bacterial invasion remain incompletely elucidated to date, particularly with respect to its differential response to peptidoglycans derived from distinct Gram-specific bacteria. In this study, the transcriptomes of A. japonicus coelomocytes were analyzed in response to challenges involving two different peptidoglycans: one from Gram-negative Escherichia coli (named "EK") and the other from Gram-positive Bacillus subtilis (named "BS"). Signal transduction, post-translational modification, and immune pathways were recognized as the dominant functions related to the identified transcripts. Significant variations in gene expression profiles were observed during the challenges, with tens of thousands of genes being expressed differently between the challenged and control groups. Further KEGG enrichment analyses revealed that the alternative complement pathway and apoptosis were the primary immune pathways, which were greatly up-regulated at 72 h after both challenges. Additionally, the enriched pathways revealed a distinct initial response of A. japonicus to different challenges, characterized by the upregulation of signal transduction pathways in the BS treatment group and stronger lipid and energy metabolism in the EK group. Furthermore, cell adhesion-related pathways were found to be enriched in A. japonicus at 96 h after the challenges. Moreover, according to the Venn diagram, the cytochrome c oxidase subunit I (CO1) and gag-pro-pol polyprotein transcripts were down-regulated throughout both challenges. Preliminary investigation of the function of the A. japonicus gag-pro-pol polyprotein was conducted using RNAi combined with RNA-Seq analysis. This revealed that four functional gene groups, including those responsible for vitamin transport, antioxidation and inflammation, cell adhesion, and complement activation, were positively regulated by this gene. Therefore, it can be speculated that the peptidoglycans from Gram-negative and -positive bacteria not only triggered differentiated immune reactions in A. japonicus, but also suppressed some immune response, nutrition absorption and energy delivery via the negative regulation of CO1 and gag-pro-pol polyprotein gene expression.

The spotted scat (Scatophagus argus), an economically valuable aquaculture species in southern China, exhibits a pronounced sexual dimorphism in growth performance, with females growing significantly faster than males. Nevertheless, progress in sex-controlled breeding remains limited due to limited understanding of its sex determination and differentiation mechanisms. To investigate sex-biased gene expression in this species, a comprehensive transcriptomic analysis was performed. A total of 62 transcriptomic libraries were analyzed, comprising 18 newly sequenced libraries derived from female gill, muscle, stomach, heart, and adipose tissue, and male adipose tissue, integrated with 44 publicly available libraries covering the brain, pituitary gland, liver, kidney, gonads, and other tissues. The analysis identified 33,214 unigenes, including 8958 novel genes, with 1724 receiving functional annotation. Principal component analysis (PCA) and heatmap clustering revealed distinct expression profiles in gonadal (ovary and testis) and somatic tissues. Differential expression analysis identified 2951 ovary-highly expressed and 1660 testis-highly expressed genes. Functional annotation revealed genes essential for folliculogenesis, spermatogenesis, and meiosis, including figla, gdf9, mos, amhr2, spata22, and dmc1. Additionally, 23 ovary-specific and 75 testis-specific genes were identified. KEGG enrichment analysis revealed significantly enriched pathways in the gonads, including oocyte meiosis, cell cycle, and DNA replication. RT-PCR and qRT-PCR validations confirmed the RNA-seq results, demonstrating consistent tissue-specific expression patterns of these genes. These findings advance the understanding of the molecular mechanisms of sex differentiation and gametogenesis in spotted scat and provided a foundation for studies of reproductive regulation and gonadal development in this species.