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

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.

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.

Ghrelin functions to stimulate appetite, promote the release of growth hormone, and regulate energy balance. Currently, research on the ghrelin is primarily focused on a single species, and there have been no systematic studies on the evolution of the ghrelin in fish. Therefore, this thesis conducts a comprehensive analysis of the ghrelin gene in 151 species of ray-finned bony fishes to reveal the universality and specificity of the ghrelin gene in the evolutionary history of fish, supplementing and perfecting the information on the ghrelin gene in Actinopterygii. The gene identification results show that the number of ghrelin genes varies among different fish species, 41 fish have lost the ghrelin gene, 98 fish having one ghrelin gene, and 12 fish having two ghrelin genes. Among the 110 fish species with the ghrelin gene, a total of 182 ghrelin gene sequences were identified, with transcript variant numbers ranging from 1 to 6, encoding 1 to 3 types of isoform proteins, and their mature peptides show a certain degree of similarity across different species. Phylogenetic analysis revealed that teleost ghrelin proteins segregate into three major evolutionary clades, with Salmoniformes orthologs comprising a distinct monophyletic cluster. The Cladistic and Chondrostei are clustered separately and then grouped with the more ancient Cypriniformes and Siluriformes species from the Neopterygii into a large group, while the other fish species from the Neopterygii form another large group. The Synteny analysis results indicate that the upstream gene of the ghrelin is CCDC174, and the downstream gene is TATDN2. The selection pressure analysis results show that there are no positive selection sites in the ghrelin gene, indicating that the ghrelin has been under strong functional constraint during the evolutionary process of fish. This study systematically investigates the evolutionary history of fish ghrelin, providing a theoretical basis for understanding the function and status of ghrelin in the feeding regulation system of fish, and deepening the recognition of its structural and functional evolution in the process of energy metabolism evolution.

The largefin longbarbel catfish (Hemibagrus macropterus) is an important commercially cultured fish in southwestern China, whose regulatory mechanism of gonad development remains unknown. In this study, the first gonadal transcriptome sequencing of immature male, female, and intersexual individuals were performed. A total of 28,543 genes was annotated, of which 12,028, 6283 and 8019 differentially expressed genes (DEGs) were detected by pairwise comparisons of ovary versus (vs.) testis, ovary vs. intersex, and testis vs. intersex. Besides, 26 male-biased, 24 female-biased, and 7 intersex-biased DEGs were screened. Representative pathways related to gonadal development and sex reversal were further enriched. Interestingly, apart from the reproduction-related genes and pathways, apoptosis-related DEGs (bcl2, myc, caspase3 and tp53) and pathways such as JAK-STAT signaling pathway and P53 signaling pathway, were suggested to be involved in the sexual reversal process. The intersexual gonad might be developed by the sex change from ovary to testis, with transcriptions of female-biased genes reduced and male-biased genes increased. Relative real time PCR results of 14 DEGs verified the reliability of transcriptome data. These results will benefit our understanding of gonad development regulations, and further be useful for the achievement of improved artificial propagation of largefin longbarbel catfish.

Salinity changes significantly impact fish physiology, requiring efficient osmoregulation for survival. The kidney is vital for maintaining ion and water balance, crucial for internal stability in varying salinity. This study used transcriptomic analysis to examine molecular responses in the kidneys of Takifugu obscurus, T. rubripes, and their hybrids (Tor1 and Tor2) in freshwater (0 ppt) and seawater (32 ppt). Following the transfer from seawater to freshwater, all four fish groups showed consistent expression trends of three genes in their kidneys-one downregulated gene (ca7) and two upregulated genes (MAP1B and MUC4)-indicating their pivotal roles in renal osmoregulation. Additionally, RNA sequencing unveiled distinct transcriptional profiles specific to each species T. obscurus displayed a limited number of DEGs (14 upregulated and 4 downregulated) in freshwater, suggesting streamlined regulatory mechanisms consistent with its broad salinity tolerance. In contrast, T. rubripes exhibited more extensive transcriptional adjustments (449 upregulated and 139 downregulated), involving ion transport genes and metabolic pathways. Moreover, we observed significant changes in the expression of immune-related genes, indicating that variations in ambient salinity affect the immune responses of the four fish species. Genetic correlation analysis indicated that Tor1 clustered with T. rubripes, while Tor2 grouped with T. obscurus, implying that hybrid offspring inherit adaptive strategies from both parental lineages. These findings shed light on the molecular mechanisms governing kidney function in euryhaline fish and provide a theoretical foundation for breeding aquaculture species with enhanced stress tolerance.