Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献

{"title":"Expression of Hox genes in embryogenesis of crucian carp (Carassius carassius) × common carp (Cyprinus carpio) hybrid","authors":"Rurong Zhao,&nbsp;Yi Zhou,&nbsp;Min Tao,&nbsp;Chun Zhang,&nbsp;Huan Zhong,&nbsp;Shaojun Liu","doi":"10.1016/j.cbd.2025.101605","DOIUrl":"10.1016/j.cbd.2025.101605","url":null,"abstract":"<div><div>Distant hybridization has been widely applied in fish breeding. Unfortunately, hybrid offspring often exhibit deformities and mortality during embryonic development. It has been demonstrated that the hybrid of the crucian carp (<em>Carassius carassius</em>) × common carp (<em>Cyprinus carpio</em>) can pass through reproductive isolation and generate fertile offspring. In the present study, we analyzed the transcriptomic changes during the embryonic developmental stages in red crucian carp (HJ), Koi carp (KOC) and the hybrid F₁. In addition, the expression of Hox genes in the three fishes was evaluated. The transcriptome expression analysis revealed that the greatest number of differentially expressed genes during the gastrula stage (GR) period was found among HJ, F₁, and KOC. Specifically, there were 3316 differentially expressed genes between KOC and F₁, 6027 differentially expressed genes between HJ and F₁, and 1232 differentially expressed genes between KOC and HJ. The identification of <em>cis</em>- and <em>trans</em>-regulatory patterns indicated that most genes subject to <em>cis</em>- and/or <em>trans</em>- were assigned to <em>cis</em>-<em>trans</em> compensating patterns, suggesting a complementary regulatory interaction between the subgenomes. The Hox gene expression comparison results indicated that the genes were low expressed in the GR stage and increased following somite formation. Although gene expression changes were found comparing the F₁ to its parents, the trend of expression changes is consistent in the three fishes. The knowledge about the transcriptomic changes and regulations in hybrids would aid to understand the interaction of subgenomes during embryonic development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101605"},"PeriodicalIF":2.2,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144841356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Toxic effects of trichlorfon on the hepatopancreas of Chinese mitten crab (Eriocheir sinensis): Tissue damage, oxidative stress, and Ferroptosis","authors":"Tian Zhu ,&nbsp;Yan Zhang ,&nbsp;Meiqi Song ,&nbsp;Yunyi Chen ,&nbsp;Norlaila Mohd Zanuri ,&nbsp;Gang Peng ,&nbsp;Tianheng Gao ,&nbsp;Qichen Jiang","doi":"10.1016/j.cbd.2025.101601","DOIUrl":"10.1016/j.cbd.2025.101601","url":null,"abstract":"<div><div>This study investigated the toxic effects and mechanisms of trichlorfon (TCF) on the hepatopancreas of Chinese mitten crabs (<em>Eriocheir sinensis</em>). The acute toxicity test results showed that the 96 h-LC₅₀ of TCF on <em>E. sinensis</em> was 4.853 mg/L. We conducted an 8-day short-term exposure experiment with TCF concentrations of 0, 0.061, 0.121, and 0.243 mg/L. The results showed that TCF exposure induces oxidative stress and causes tissue damage and lesions to the hepatopancreas, including hepatic tubules exhibiting disruption, swelling, necrosis, and an ill-defined structure. Transcriptomics revealed differentially expressed genes (DEGs) at the different concentrations, KEGG, and GO enrichment analysis showed that the DEGs were mainly involved in the bile secretion pathway and iron ion binding terms. GSEA was used for single-function enrichment analysis of cell growth and death. We found that DEGs at TCF concentrations of 0.121 and 0.243 mg/L were significantly enriched in the Ferroptosis pathway. Moreover, the synaptic vesicle cycle, GABAergic synapse, and serotonergic synapse were significantly enriched in DEGs at 0.243 mg/L, which indicated that TCF may pose a potential threat to the nervous system. The qPCR detection of Ferroptosis-related genes demonstrated that TCF induces hepatopancreatic Ferroptosis in <em>E. sinensis</em>. We hypothesized that lysosomal autophagy, mainly induced through FTH1 and NCOA4 interactions, released ferric ions, thereby indirectly contributing to Ferroptosis. In addition, WGCNA identified two key modules associated with the phenotype, and further identified the core hub genes were <em>MEX3</em>, <em>RBM46</em>, <em>SLC7A5</em>, and <em>TYR</em>. The results of this study can provide insights into the toxic effects of TCF on aquatic crustaceans.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101601"},"PeriodicalIF":2.2,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144841348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide analysis reveals expansion and structural rearrangements of the attacin gene family in saturniid silkmoths","authors":"Indumathi Kamatchi Balakrishnan ,&nbsp;Himanshu Dubey ,&nbsp;Rajal Debnath ,&nbsp;Vanitha C ,&nbsp;Kallare P. Arunkumar ,&nbsp;Gangavarapu Subrahmanyam ,&nbsp;Manthira Moorthy ,&nbsp;Vikram Kumar ,&nbsp;Abhishek Singh ,&nbsp;K.M. Ponnuvel","doi":"10.1016/j.cbd.2025.101597","DOIUrl":"10.1016/j.cbd.2025.101597","url":null,"abstract":"<div><div>Antimicrobial peptides (AMPs) are essential components of insect immunity, yet the <em>attacin</em> gene family remains poorly studied in Saturniidae. Despite comprehensive functional studies on AMPs across various lepidopteran taxa, the <em>attacin</em> gene family remains insufficiently characterized in <em>Antheraea assamensis</em> (<em>A. assamensis</em>) and related saturniid silkmoths. Here, we present a comprehensive genome-wide analysis across five saturniid silkmoths, identifying 10 <em>attacin</em> genes in <em>A. assamensis</em>, 9 in <em>Antheraea pernyi</em> (<em>A. pernyi</em>), 5 in <em>Antheraea mylitta</em> (<em>A. mylitta</em>), 4 in <em>Antheraea yamamai</em> (<em>A. yamamai</em>), and 10 in <em>Samia ricini</em> (<em>S. ricini</em>). Domain analysis revealed that while most Attacins possess both N- and C-terminal glycine-rich domains, several encode truncated isoforms and some with extended polypeptide lengths. Phylogenetic analysis demonstrated lineage-specific expansions, and aBSREL analysis identified positive selection acting on certain clades, particularly those encoding C-terminal-only isoforms. Conserved microsynteny with <em>Bombyx mori</em> (<em>B. mori</em>) supports a shared evolutionary origin despite scaffold variation. In silico structural modelling and molecular docking predicted high-affinity interactions between Attacin peptides and bacterial lipopolysaccharides (LPS), implicating their role in membrane disruption. Finally, qRT-PCR analysis revealed that several <em>attacin</em> paralogs, particularly <em>attacin</em>5 to <em>attacin</em>8, were significantly upregulated in both the fat body and midgut of <em>A. assamensis</em> following <em>E. coli</em> infection. Notably, <em>attacin</em>2 and <em>attacin</em>10 exhibited higher expression levels in the midgut, highlighting their potential roles in both systemic and gut-localized immune responses.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101597"},"PeriodicalIF":2.2,"publicationDate":"2025-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144829325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic and proteomic insights into the growth-promoting mechanisms of dietary γ-aminobutyric acid (GABA) in tawny puffer (Takifugu flavidus)","authors":"Xiaowen Yu ,&nbsp;Zhilong Xie ,&nbsp;Wenjie Hou,&nbsp;Benwei Liu,&nbsp;Yuhua Zhou,&nbsp;Tiannan Chen","doi":"10.1016/j.cbd.2025.101603","DOIUrl":"10.1016/j.cbd.2025.101603","url":null,"abstract":"<div><div>γ-aminobutyric acid (GABA) has been shown to promote growth in certain aquatic species, yet the molecular mechanisms remain unclear. This study investigated the effects of GABA in juvenile tawny puffer (<em>Takifugu flavidus</em>) via growth performance, liver transcriptomic and proteomic analyses, and plasma stress indices. Dietary supplementation with 100 mg/kg GABA for 50 days significantly improved weight gain rate (WGR) and specific growth rate (SGR), alongside higher feeding rate (FR) and hepatosomatic index (HSI). Transcriptomic profiling identified DEGs predominantly enriched in growth-related signal pathways (MAPK, TGF-β), and anabolic processes: lipid metabolism (fatty acid elongation, fatty-acyl-CoA and fatty acid derivative biosynthetic), nucleic acid synthesis (nucleotide, purine), and nutrient metabolism (vitamin B6, tryptophan). Proteomic analysis revealed DEPs primarily enriched in regulatory processes: nitrogen metabolism, nicotinate/nicotinamide metabolism, and arachidonic acid metabolism. Both omics datasets confirmed GABA's stress mitigation—transcriptomic downregulation of stress pathways (cortisol synthesis, oxytocin signaling, Cushing syndrome) and proteomic enrichment of neuroactive ligand-receptor interactions, validated by lower plasma stress indices in the GABA group. PPI analysis revealed that GABA promotes growth in <em>T. flavidus</em> by activating growth-related proteins [e.g., Actin, alpha skeletal muscle A (ACTA1B)], inhibiting ubiquitin-like protein 7B (UBL7B), and coordinating four growth and development functional subnetworks. In conclusion, GABA promotes the growth of <em>T. flavidus</em> by activating growth-related signal pathways and anabolic/regulatory metabolism, mitigating stress, and regulating growth-related and ubiquitin-like proteins. This is the first study to unravel GABA's liver-mediated growth-promoting mechanisms in <em>T. flavidus</em> via comprehensive approaches, providing a basis for developing GABA as a functional feed additive.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101603"},"PeriodicalIF":2.2,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144810586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary supplementation of selenium nanoparticle improves the vitellogenesis and fecundity of female zebrafish","authors":"Siqiu Chen ,&nbsp;Yufeng Song ,&nbsp;Meixuan Lei ,&nbsp;Fenfei Liang ,&nbsp;Guosong Zhang ,&nbsp;Kejun Cai ,&nbsp;Shaowu Yin ,&nbsp;Cheng Zhao ,&nbsp;Tao Wang","doi":"10.1016/j.cbd.2025.101604","DOIUrl":"10.1016/j.cbd.2025.101604","url":null,"abstract":"<div><div>Selenium (Se) is an essential micronutrient that plays a critical role in supporting growth and reproductive function in fish. Nano‑selenium (nano-Se), characterized by its higher bioavailability and lower toxicity, has emerged as a promising alternative for dietary Se supplementation. Female zebrafish were fed diets containing 0, 10, or 20 μg/g nano-Se (O_0, O_10, O_20) to examine its impact on ovarian function. After 60 days of feeding, nano-Se supplementation significantly improved growth performance and fecundity, as indicated by increased body weight, gonadosomatic index (GSI), ovulated egg number, and upregulated expression of <em>lhb</em>. Histological analysis revealed a higher proportion of vitellogenic follicles in the ovaries of nano-Se-treated fish. Transcriptomic profiling revealed significantly enrichment in Gene Ontology (GO) terms with cellular response to estrogen stimulus and response to estrogen, which both observed in the O_0 vs. O_10 and O_10 vs. O_20 comparison groups. A series of critical genes related to gonad development and steroidogenesis were significantly up-regulated, such as <em>vtgs</em>, <em>foxl2</em>, <em>cyp11a</em> and <em>hsd17b3</em>. In conclusion, dietary nano-Se supplementation promotes ovarian development and enhances fecundity in female zebrafish, offering novel insights into improving reproductive performance in economically important aquaculture species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101604"},"PeriodicalIF":2.2,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144841357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering multi-organ protein regulatory strategies in the Asian frog, Pelophylax nigromaculatus during hibernation to elucidate energy homeostasis maintenance mechanisms","authors":"Jiaxuan Han ,&nbsp;Ziheng Zhao ,&nbsp;Ningmei Wang ,&nbsp;Bofang Zhang ,&nbsp;Panyi Yang ,&nbsp;Zhijun Yu ,&nbsp;Kenneth B. Storey ,&nbsp;Yuhong Hu ,&nbsp;Hui Wang","doi":"10.1016/j.cbd.2025.101602","DOIUrl":"10.1016/j.cbd.2025.101602","url":null,"abstract":"<div><div>Hibernation is a low-energy consumption survival strategy adopted by organisms to cope with adverse environments such as low temperatures and food scarcity. This study used the <em>Pelophylax nigromaculatus</em> as the model organism, and for the first time comprehensively analyzed the proteomic and phosphoproteomic regulatory networks in its kidneys, liver, and lungs through DIA quantitative proteomics technology, revealing specialized organ protection mechanisms under the hypometabolic state of hibernation. The research found that the regulation of these proteins relates to glycolysis and glycogenolysis, enhanced intracellular substance transport, membrane repair and energy buffering, rapid degradation of glycation end products, mitigation of inflammatory responses, and maintenance of signal transduction and cellular morphology. Using the glycogenolysis inhibitor CP-91149 to block glycogen breakdown, the study investigated frog hibernation status when glycogenolysis was inhibited to a certain extent, with results showing these frogs exhibited higher mortality during hibernation. This research not only provides substantial reliable data for elucidating the molecular mechanisms of amphibian hibernation but also establishes a foundational framework for understanding the molecular regulation of animal low-energy metabolism.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101602"},"PeriodicalIF":2.2,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144809960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic WGCNA analyses reveal sectional regulatory mechanisms in giant freshwater prawn Macrobrachium rosenbergii larvae under hypoxia-reoxygenation","authors":"Yaoran Fan ,&nbsp;Lei Cao ,&nbsp;Yaorui Liang ,&nbsp;Bingbing Feng ,&nbsp;Jinhua Gong ,&nbsp;Jiale Li ,&nbsp;Huangen Chen ,&nbsp;Min Zhang ,&nbsp;Jianbin Feng","doi":"10.1016/j.cbd.2025.101596","DOIUrl":"10.1016/j.cbd.2025.101596","url":null,"abstract":"<div><div>Hypoxia is a considerable challenge for the prawn culture, especially in high-density intensive aquaculture. The giant freshwater prawn, <em>Macrobrachium rosenbergii</em>, is an economically important species in Asia and South America. However, <em>M. rosenbgergii</em> larvae typically exhibit low resistance to hypoxic stress. To explore the molecular mechanism of hypoxia-reoxygenation on <em>M. rosenbergii</em> larvae, the transcriptomic WGCNA analysis was conducted to detect the dynamic regulatory mechanisms of <em>M. rosenbergii</em> larvae under 4, 8, 12, 24, 48, 72 h of hypoxia stress and 4, 12 h of reoxygenation stress. The results showed that a total of 3173 differentially expressed genes (DEGs) were identified in the gills (1812 up-regulated, 1361 down-regulated), 397 in the hepatopancreas (171 up-regulated, 226 down-regulated), and 768 in the muscle (374 up-regulated, 394 down-regulated). The gills were labeled as the primary functional organ by significantly abundant DEGs during hypoxia-reoxygenation. Additionally, 22 DEGs of 9 gene families were co-expressed during hypoxia-reoxygenation, including the cell protein (CP), cathelicidin associated protein (CAP), aminocyclopropane-1-carboxylate oxidase (ACO) families, etc. For the GO analysis during hypoxia-reoxygenation, the DEGs were mainly enriched in the cellular component and molecular function terms, including nucleolus, mitochondrion, and mRNA binding terms. Besides, the DEGs during hypoxia were significantly enriched in genetic and environmental information pathways involving the HIF-1 signaling pathway and ribosome. Additionally, the DEGs during reoxygenation were mainly associated with cellular processes, including lysosome, phagosome, and apoptosis. Furthermore, 30 candidate hypoxia-reoxygenation module-related DEGs were screened by WGCNA, involving <em>SpAN</em>, <em>TIF-2</em>, <em>Titin</em>, <em>ATP binding cassette</em>, <em>L-ThrDH</em>, <em>G6DP</em>, etc. Overall, these results may reveal the immunological regulatory mechanisms of <em>M. rosenbergii</em> larvae under hypoxia-reoxygenation stress and enrich practical reference materials underlying high-density intensive aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101596"},"PeriodicalIF":2.2,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144863841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Domestication traits and adaptive evolution in blunt snout bream (Megalobrama amblycephala) by artificial selection pressure","authors":"Yunwen Cui ,&nbsp;Xigeng Hu ,&nbsp;Huanshan Wang ,&nbsp;Chunling Wang ,&nbsp;Wenxuan Cao ,&nbsp;Futie Zhang","doi":"10.1016/j.cbd.2025.101594","DOIUrl":"10.1016/j.cbd.2025.101594","url":null,"abstract":"<div><div><em>Megalobrama amblycephala</em>, a herbivorous freshwater fish species native to China, has become an important aquaculture species in Chinese freshwater polyculture systems due to its high economic value. How morphological traits and gene expression of cultured populations are influenced by different artificial selection pressures compared to wild populations is still poorly understood. In the current study, a combination of morphological analysis, cytochrome <em>b</em> sequence characterization, and whole genome re-sequencing methods was employed to investigate the genetic differences caused by artificial selection, including the genetic diversity and differentiation of wild and cultured populations. The genetic diversity of the population was classified based on the cytochrome <em>b</em> gene as follows: wild population (WP) &gt; common breeding population (CP) &gt; artificially created strain (AS). Morphological traits showed that the values of head length, body depth, dorsal fin length and pelvic fin length were the largest in the WP, smaller in the CP and the smallest in the AS. But the largest body width was in the AS, smaller in the CP, and the smallest in the WP. A significant finding was the identification of several candidate genes involved in carbohydrate metabolism, including <em>Adcy9</em>, <em>Eif4ebp1</em>, <em>Gnai2b</em>, <em>Ppp1r3b</em>, <em>Ptprfa</em>, <em>Ptprfb</em> and <em>Slc8a2b</em>. The data generated by this research not only contribute to a deeper understanding of the molecular-level characteristics but also provide crucial scientific foundations for the conservation and genetic improvement of this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101594"},"PeriodicalIF":2.2,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144841349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic profiling reveals the adaptive mechanisms of Penaeus vannamei alkali-tolerant families under combined pH and alkalinity stress","authors":"Zhihang Zhu ,&nbsp;Xianke Huang ,&nbsp;Jiayan Wu ,&nbsp;Fang Li ,&nbsp;Kui Luo ,&nbsp;Min Zhang ,&nbsp;Wei Shi ,&nbsp;Maocang Yan","doi":"10.1016/j.cbd.2025.101595","DOIUrl":"10.1016/j.cbd.2025.101595","url":null,"abstract":"<div><div>Soil salinization is an increasingly critical global issue for which fishery-based utilization has emerged as a promising mitigation strategy. <em>Penaeus vannamei</em> is an ideal species for aquaculture in saline-alkali waters; however, the differences in alkali tolerance among various families and their underlying mechanisms remain largely unexplored. In this study, alkali-tolerant families were identified through median lethal time (LT₅₀) assays under high alkalinity and elevated pH. Comparative analyses with wild-type family revealed that alkali-tolerant families showed significant differences in energy metabolism and ion transport (Na⁺/K⁺-ATPase (NKA), carbonic anhydrase (CA), and cystic fibrosis transmembrane conductance regulator <strong>(</strong>CFTR)) Transcriptomic analysis showed that alkali-tolerant families had pathways related to cytoskeletal remodeling, including actin cytoskeleton organization (GO:0030029) and myosin complex (GO:0016459). KEGG analysis further revealed enrichment in cardiac muscle contraction (ko04260) and adrenergic signaling in cardiomyocytes (ko04261). We propose that CaCO₃ precipitation reduces extracellular Ca²⁺ levels and disrupts the carbonate buffering system under high pH and alkalinity. In response, alkali-tolerant families mitigate pH and alkalinity stress by enhancing ion regulation and energy efficiency while simultaneously downregulating high-energy Ca²⁺ regulatory pathways and remodeling gill microstructures. Collectively, these findings provide novel insights into the alkali adaptation mechanisms of <em>P. vannamei</em> and support selective breeding strategies to improve stress resilience in saline-alkali aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101595"},"PeriodicalIF":2.2,"publicationDate":"2025-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144780815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis unveils critical genes governing early development and sex differentiation in the Cipangopaludina chinensis (Gastropoda: Viviparidae)","authors":"Cheng Wang ,&nbsp;Zhijuan Bian ,&nbsp;Qiuting Ji ,&nbsp;Sisi Chen ,&nbsp;Yutong Shen ,&nbsp;Siyao Zhao ,&nbsp;Yiqi Sun ,&nbsp;Aobo Pang ,&nbsp;Dandan Tang ,&nbsp;Fujun Xuan ,&nbsp;Wu Jin ,&nbsp;Boping Tang ,&nbsp;Daizhen Zhang ,&nbsp;Kianann Tan ,&nbsp;Gang Wang","doi":"10.1016/j.cbd.2025.101590","DOIUrl":"10.1016/j.cbd.2025.101590","url":null,"abstract":"<div><div>The <em>Cipangopaludina chinensis</em> is a freshwater species of great economic value in the class Gastropoda. The research on the development of the larvae of this species and the subsequent sex differentiation mechanism is extremely limited. This study conducted transcriptome analysis on <em>C. chinensis</em> juveniles at various early developmental stages, as well as on their gonads before and after sexual maturity. The results indicated that during the early stages of juvenile development, key biological pathways associated with growth encompassed the meiotic cell cycle, mitotic cell cycle, and multicellular organism development. Differentially expressed genes in the pathway that were highly correlated with development include <em>DNMT1, OGG1, MCM, WDHD1</em> and <em>OGT</em>. Combining the results of protein-protein interactions and sex differentiation-related gene family analyses, we screened candidate genes <em>SYCP1</em>, <em>TUBGCP3</em>, <em>CDK1</em>, and <em>STMN1</em> associated with testis development, and candidate genes <em>DAX1</em>, <em>β-catenin</em>, <em>Foxl2</em>, and <em>CYP3A</em> associated with ovarian development<em>.</em> This study enhances our understanding of early development and sex differentiation mechanisms in <em>C. chinensis</em>, which provides basic research for subsequent use of molecular means to intervene in its sex ratio and improve reproductive efficiency.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101590"},"PeriodicalIF":2.2,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}