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

{"title":"Comparative transcriptome sequencing of two shell colour variants of Haliotis discus hannai identifying genes involved in shell formation and photosensitivity","authors":"Mengqiang Yuan,&nbsp;Kun Liu,&nbsp;Tianshuo Liu,&nbsp;Qianqian Li,&nbsp;Wenjian Guo,&nbsp;Meiwei Zhang,&nbsp;Xiaona Wang,&nbsp;Xuekai Zhang,&nbsp;Xiaotong Wang","doi":"10.1016/j.cbd.2025.101461","DOIUrl":"10.1016/j.cbd.2025.101461","url":null,"abstract":"<div><div>Shell colour variation in <em>Haliotis discus hannai</em> is a complex trait influenced by genetic, physiological, and environmental factors. This study investigates the molecular mechanisms underlying shell colour formation, with a focus on the roles of biomineralisation, photosensitivity, and stress resistance. Using transcriptome analysis and microstructural observations, we compared red-shelled (RS) and green-shelled (GS) variants to identify key genes and pathways associated with shell colour. The results reveal that GS variants exhibit higher expression of visual protein genes (e.g., <em>RHO-opnGq</em>), which are linked to light sensitivity and pigment synthesis. Additionally, RS variants show upregulated chitin biosynthesis genes (e.g., <em>CHs-IA</em>), potentially influencing shell structure and pigmentation. These findings suggest that these genes play a critical role in regulating pigment deposition and shell colour formation, while biomineralisation genes contribute to shell integrity. This study provides new insights into the genetic basis of shell colour variation and its ecological significance, offering valuable information for selective breeding programs.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101461"},"PeriodicalIF":2.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562127","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":"Analysis of intestinal metabolites in Litopenaeus vannamei infected with white faeces syndrome based on untargeted metabolomics","authors":"Tingting Wang ,&nbsp;Aobo Pang ,&nbsp;Kangze Xv ,&nbsp;Xin Zhang ,&nbsp;Adinda Luthfiah ,&nbsp;Yongjie Jiang ,&nbsp;Haitao Zhang ,&nbsp;Beiping Tan ,&nbsp;Wei Zhang","doi":"10.1016/j.cbd.2025.101462","DOIUrl":"10.1016/j.cbd.2025.101462","url":null,"abstract":"<div><div>White faeces syndrome (WFS) has always been one of the main intestinal diseases of <em>Litopenaeus vannamei</em>, which has caused huge economic losses to shrimp farming. WFS infection is known to result from a combination of pathogens, but the changes in intestinal metabolites following WFS infection are unknown. In this study, morphological sections of the hepatopancreas and intestine of WFS infected shrimp were analyzed, and lesions were found in the hepatopancreas and intestine of infected shrimp. The hepatopancreatic bodies of shrimp infected with WFS were arranged and scattered, and the stellate cavity was deformed. The connective tissue within the intestinal fold's atrophies to the point where the muscular layer almost disappeared. The enzyme linked kit results showed that lysozyme activity in hepatopancreas was significantly increased, total antioxidant capacity was significantly decreased, intestinal total antioxidant capacity and superoxide dismutase activities were significantly decreased in WFS infected shrimp, indicating that the antioxidant capacity of hepatopancreas and intestine were impaired. The intestinal metabolites of WFS shrimp and healthy shrimp were analyzed by non-targeted metabolic technology, and 10 differential metabolites and 7 differential metabolic pathways were screened. Among them, arginine, a significant differential metabolite, may positively activate the mTOR pathway, leading to the high expression of mTOR pathway, which is closely related to intestinal health. This indicates that when <em>L. vannamei</em>. is infected with WFS, the arginine content in the intestine is up-regulated, which positively activates the mTOR signaling pathway leading to pathway disorder, thereby destroying the intestinal health of <em>L. vannamei</em>. Through this study, we can not only understand the intestinal metabolic characteristics of WFS, but also provide a theoretical reference for the prevention and treatment of WFS in <em>L. vannamei</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101462"},"PeriodicalIF":2.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143686277","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":"Physiological analysis and transcriptome sequencing revealed that HSPA1 was involved in response to heat stress in thick-shell mussels, Mytilus coruscus","authors":"Huajian Lin ,&nbsp;Ronghui Yao ,&nbsp;Sisi Wei ,&nbsp;Wanliang Zhang ,&nbsp;Hao Wang ,&nbsp;Bingqi Wei ,&nbsp;Yingying Ye ,&nbsp;Zhi Liao ,&nbsp;Xiaojun Yan ,&nbsp;Weifeng Wang ,&nbsp;Baoying Guo","doi":"10.1016/j.cbd.2025.101449","DOIUrl":"10.1016/j.cbd.2025.101449","url":null,"abstract":"<div><div><em>Mytilus coruscus</em>, being sensitive to temperature variations, has developed a protective mechanism against heat stress through the upregulation of genes encoding heat shock proteins. Past research indicates that exposure to heat stress can activate <em>HSPA1</em> expression for protection, yet the underlying regulatory mechanisms governing this response are not fully clear. Therefore, the emphasis of this study lies on regulating the expression of <em>HSPA1</em> in mussels under high temperature stress. This study showed that high temperature could cause tissue damage and induce apoptosis in <em>M. coruscus</em>. Overexpression of <em>HSPA1</em> at high temperature can mitigate damage. Enzyme activity assays also found that after the overexpression of <em>HSPA1</em> at high temperature, the enzyme activity of SOD, CAT and GSH-PX increased to cope with the stimulation brought by high temperature, which suggests that the <em>HSPA1</em> gene plays a critical role in the antioxidant response. Transcriptome analysis showed that under high-temperature stress, key genes including <em>HSPA1S, HSP90, HSPA5, DnaJA1,</em> and <em>JUN</em> showed increased expression in <em>HSPA1</em>-knockdown treatments, with differential gene expression enriched in pathways associated with MAPK signaling, endoplasmic reticulum protein processing, TNF signaling, apoptosis, and cell apoptosis pathways. Based on this, we suggested that <em>M. coruscus</em> may counteract damage induced by high-temperature stress via the above key genes and biology processes, highlighting the crucial role of <em>HSPA1</em> in mitigating cell damage and apoptosis due to high temperature. Overall, our results revealed <em>HSPA1</em> regulatory relationship in <em>M. coruscus</em> treated with high temperature, and provided new insights for the conservation and environmental adaptive evolution of bivalve species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101449"},"PeriodicalIF":2.2,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562128","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":"Impact of gender and reproductive states on diets and intestinal microbiota in Pratt's leaf-nosed bats (Hipposideros pratti)","authors":"Sen Liu ,&nbsp;Jianying Du ,&nbsp;Yu Chen ,&nbsp;Qiaodan Fan ,&nbsp;Xinyu Yue ,&nbsp;Liming Zhao ,&nbsp;Dongge Guo ,&nbsp;Ying Wang","doi":"10.1016/j.cbd.2025.101459","DOIUrl":"10.1016/j.cbd.2025.101459","url":null,"abstract":"<div><div>Lactation represents a critical evolutionary adaptation in mammals, imposing heightened nutritional demands that drive shifts in foraging behavior and intestinal microbiota to optimize nutrient acquisition. In the sexually dimorphic Pratt's leaf-nosed bat (<em>Hipposideros pratti</em>), males exhibit enlarged transverse lobes posterior to the nasal leaf, a morphological trait may influence echolocation dynamics and dietary niche partitioning. This provides an opportunity to examine dietary and microbiota differences between genders and across various reproductive states. Using high-throughput sequencing of fecal samples from male (HPM), non-lactating female (HPF), and lactating female (HPFL) <em>H. pratti</em> collected in late June, we identified gender- and physiology-linked ecological strategies. While dietary diversity indices showed no significant intergroup differences, compositional analysis revealed distinct prey preferences: both HPM and HPFL predominantly consumed Coleoptera, whereas HPF favored Diptera. Coleoptera's larger size and nutrient profile—rich in leucine, isoleucine, and chitin—likely optimize energy efficiency for HPFL, reducing foraging effort while supplying amino acids critical for mammary gland function and immunity. Gender-based differences were observed in intestinal microbiota diversity, with females demonstrating higher diversity indices compared to males. Males showed a notable abundance of <em>Clostridium</em> sensu stricto <em>1</em>, a proteolytic genus associated with Coleoptera digestion but linked to inflammatory risks via pathogenic strains. The HPFL group exhibited microbiota enriched in <em>Lactococcus</em> (chitinolytic taxa) and lactation-adapted symbionts: <em>Lachnoclostridium</em> may suppress pro-inflammatory responses via acetate production, while <em>Pseudonocardia</em> may enhance calcium homeostasis and antimicrobial defense. This study advances understanding of host-microbe coadaptation in mitigating life-history trade-offs and highlights ecological drivers of microbiota plasticity in insectivorous bats.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101459"},"PeriodicalIF":2.2,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143535119","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":"Comparative analysis of the heart histological structure, metabolic enzyme activities and transcriptome profiles of juvenile and adult yellowfin tuna (Thunnus albacares) in the South China Sea","authors":"Xu Ji ,&nbsp;Ying Zou ,&nbsp;Wanlin Guan ,&nbsp;Xiameng Su ,&nbsp;Jigui Yuan ,&nbsp;Qian Li ,&nbsp;Zhiyuan Lu ,&nbsp;Juan Xiao ,&nbsp;Hai Huang ,&nbsp;Mei Wang ,&nbsp;Zhiqiang Guo","doi":"10.1016/j.cbd.2025.101460","DOIUrl":"10.1016/j.cbd.2025.101460","url":null,"abstract":"<div><div>The yellowfin tuna is a large marine carnivorous fish with high commercial value. It is known for its unique physiological characteristics and holds significant potential for aquaculture. However, research on this species' developmental biology and physiology remains limited, particularly regarding the structural characteristics and functional changes in the developing heart. To investigate the differences in cardiac tissue structure and function at different developmental stages in yellowfin tuna, we conducted comparative analyses of histology, metabolic enzyme activity, and transcriptomes. Hematoxylin and eosin (H&amp;E) and Masson staining revealed that cardiac muscle fibers were thicker and more compact, and the area of collagen fibers was significantly increased in adult fish compared to juvenile fish (<em>p</em> &lt; 0.001). Additionally, the enzyme activities of Na⁺K⁺-ATPase, Ca²⁺Mg²⁺-ATPase, carnitine palmitoyltransferase 1 (CPT-1), lactate dehydrogenase (LDH), succinate dehydrogenase (SDH), and malate dehydrogenase (MDH) were notably greater in adult fish compared to juvenile fish (<em>p</em> &lt; 0.05). Comparative transcriptome analysis identified 1293 differentially expressed genes (DEGs) between juvenile and adult fish. Functional enrichment analyses indicated that these differential genes are primarily closely associated with heart development and metabolic regulation pathways. Furthermore, key metabolism-related DEGs, such as <em>acsl3b</em>, <em>acsbg2</em>, <em>acsl1a</em>, and <em>cpt1ab</em>, were further identified, and quantitative real-time PCR (qRT-PCR) validated the accuracy of the results. In conclusion, this study provides a systematic analysis of the differences in histology, metabolic enzyme activities, and transcriptomics between the hearts of juvenile and adult yellowfin tuna, providing foundational data for future research on heart development in the later stages of yellowfin tuna and contributing to the advancement of aquaculture practices for this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101460"},"PeriodicalIF":2.2,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143534364","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 identification of FTZ-F1 genes in Chlamys farreri and analysis of ChIP-seq-based binding sites and potential target genes","authors":"Qichao Fan ,&nbsp;Peipei Liu ,&nbsp;Jingjing Miao ,&nbsp;Lianxue Han ,&nbsp;Kexin Lei ,&nbsp;Ruifeng Fu ,&nbsp;Xiuru Li ,&nbsp;Luqing Pan","doi":"10.1016/j.cbd.2025.101458","DOIUrl":"10.1016/j.cbd.2025.101458","url":null,"abstract":"<div><div>FTZ-F1 (<em>Fushi tarazu</em> factor-1) is a crucial member of the monomeric orphan nuclear receptor family, playing essential roles in reproductive development, steroidogenesis, and metabolism. However, studies on the function of FTZ-F1 and its target genes in bivalve mollusks remain limited. In this study, we conducted a genome-wide analysis of <em>Chlamys farreri</em> and identified two FTZ-F1 family members, designated as <em>Cf FTZ-F1</em> and <em>Cf FTZ-F1b</em>. We characterized their sequence features, evolutionary relationships, and protein structures. To elucidate its potential regulatory roles, we employed chromatin immunoprecipitation sequencing (ChIP-seq) to identify potential target genes, revealing 22,570 binding peaks. Motif analysis identified three conserved motifs consistent with the known binding characteristics of FTZ-F1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that the target genes associated with these motifs are primarily involved in phospholipid metabolism, carbohydrate metabolism, steroid hormone biosynthesis, and key signaling pathways such as the PI3K-Akt pathway. Notably, genes involved in steroid hormone biosynthesis (<em>CYP17A1</em>, <em>Srd5a1</em>), gonadal differentiation (<em>DAX-1</em>, <em>Dmrta2</em>), and metabolic regulation (<em>fumA</em>, <em>Adcy1</em>) were identified as putative targets, suggesting that Cf FTZ-F1 may play a crucial role in these physiological processes. ChIP-qPCR further validated the binding sites of several target genes. This study sheds insights into the regulatory roles of FTZ-F1 in <em>C. farreri</em>, particularly its potential involvement in steroidogenesis, gonadal development, and metabolic regulation, laying the foundation for future functional investigations.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101458"},"PeriodicalIF":2.2,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143578410","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":"Silymarin mediates the gut-liver axis pathway to alleviate Carassius auratus hepatic lipid metabolism disorders caused by carbonate exposure","authors":"Xin-yu Lei,&nbsp;Xin Wang,&nbsp;Xue Cao,&nbsp;Yue-hong Li","doi":"10.1016/j.cbd.2025.101457","DOIUrl":"10.1016/j.cbd.2025.101457","url":null,"abstract":"<div><div>An 8-week feeding trial was conducted to investigate the mechanism of silymarin alleviating the abnormal lipid metabolism of Hefang Crucian Carp (HCC) (13.43 ± 0.059 g) liver caused by carbonate exposure. The fish were randomly divided into three groups: Control group (group B, 0 g/L carbonate, 0 mg/kg silymarin), carbonate stress group (group CA, 3 g/L carbonate, 0 mg/kg silymarin) and silymarin group (group SI, 3 g/L carbonate, 60 mg/kg silymarin). The results showed that the growth performance of group CA was significantly increased compared with group B. Compared with CA group, brush villi in SI group recovered significantly, and the width of submucosa decreased. Compared with group B, the intestinal barrier was damaged and permeability increased in group CA, while the damage was alleviated in group SI. Intestinal microbiota analysis showed that the bacterial community function genes related to lipopolysaccharide biosynthesis protein and lipopolysaccharide biosynthesis in CA group were higher than those in B and SI groups, and it was found that the change of LPS content in fish was echoed by the results of intestinal microflora. Compared with group B, the liver of group CA was damaged and the lipid metabolism process was abnormal, resulting in lipid metabolism disorder. SI group alleviated the liver damage caused by carbonate exposure, promoted the process of liver lipid synthesis, and balanced the body's lipid metabolism. More than 50 % of the metabolites are closely related to lipids and lipid molecules. The most metabolites in metabolism are oxidative phosphorylation and pyruvate metabolism. In summary, this study demonstrated that silymarin alleviating carbonate exposure altered intestinal microbiota homeostasis in HCC, leading to intestinal inflammation and increased mucosal barrier permeability, inhibiting LPS synthesis and absorption, preventing it from entering the liver through the intestinal liver, and increasing oxidative stress in the liver and abnormal lipid metabolism in the liver, thereby leading to liver injury. To provide theoretical basis for the development and utilization of silymarin functional feed additives and the mitigation strategy of carbonate exposure to liver damage in fish.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101457"},"PeriodicalIF":2.2,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143519820","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":"Transcriptomics, antioxidant enzyme activities, and immune-associated parameter analysis reveal the molecular responses of rainbow trout (Oncorhynchus mykiss) to transportation stress","authors":"Yueqing Wang,&nbsp;Yujun Kang,&nbsp;Zixuan Zhong,&nbsp;Jichang Liu,&nbsp;Jinlian Wu,&nbsp;Zhe Liu","doi":"10.1016/j.cbd.2025.101455","DOIUrl":"10.1016/j.cbd.2025.101455","url":null,"abstract":"<div><div>To explore how transportation stress affects the physiology of rainbow trout, we measure antioxidant and immunity-related indicators in spleen tissues of adult fish during transportation (at 0, 2, and 6 h) and 24 h following it (r24 h). We report a significant reduction in spleen catalase activity among the 2, 6, and r24 h groups compared with the 0 h group (<em>P</em> &lt; 0.05). Levels of glutathione peroxidase activity and total antioxidant capacity, and lipid peroxide, complement C4, and immunoglobulin M contents first decreased, then increased; complement C3 content and lysozyme activity first increased, then decreased; and tumor necrosis factor-α levels were relatively stable (<em>P</em> &gt; 0.05). Transcriptome sequencing of spleen samples at 0, 6, and r24 h using Illumina HiSeq6000 identified 4419, 2733, and 4375 differentially expressed genes (DEGs) in 0 vs 6, 6 vs r24, and 0 vs r24 h comparisons, respectively. Gene ontology annotation of these DEGs revealed them to function mainly in binding and catalytic activities, and to be significantly enriched in cellular processes and biological regulation terms. Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed DEGs in the 0 h vs 6 h comparison to be significantly enriched in cytokine–cytokine receptor interaction, C-type lectin receptor signaling pathway, in regulating actin cytoskeleton, lysosome (0 vs r24 h); and in the Toll-like and MAPK signaling pathways (6 vs r24 h). Several immune-related genes were identified from both the 0 h vs 6 h and 6 h vs r24 h comparisons. These findings lay a solid foundation for further research on understanding how fish respond to transportation stress at the molecular level.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101455"},"PeriodicalIF":2.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143478755","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":"Transcriptome analysis of different stages of testis development in Portunus trituberculatus","authors":"Kai-Di Ni,&nbsp;Chao-Guang Wei,&nbsp;Jun-Quan Zhu,&nbsp;Chang-Kao Mu,&nbsp;Chun-Lin Wang,&nbsp;Cong-Cong Hou","doi":"10.1016/j.cbd.2025.101453","DOIUrl":"10.1016/j.cbd.2025.101453","url":null,"abstract":"<div><div>The swimming crab (<em>Portunus trituberculatus</em>) is an important marine economic species, however its artificial breeding yield is relatively low. Currently, the main challenge faced by the swimming crab seed industry is the reliance on wild populations for seed cultivation, which results in unstable yield and quality, affecting the healthy development of the crab farming industry to some extent. The quality of germplasm resources depends on the quality of gametes, and the quality of sperm depends on the orderly genetic regulation process of spermatogenesis. Therefore, elucidating the genetic regulatory mechanisms of spermatogenesis is of great significance for improving the germplasm resources of <em>P. trituberculatus</em>. To gain a deeper understanding of this process, we conducted a comparative transcriptome study on the testis of the swimming crab at different developmental stages. This study aims to identify key genes that regulate testicular development. We performed paraffin section identification on the testicular tissue of male crabs and conducted transcriptome analysis on the testicular tissue at five different developmental stages and somatic cells. Through differential expression analysis, we screened a total of 31,788 differentially expressed genes (DEGs) from stages I to VI. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we found that these DEGs were significantly enriched in 15 pathways, including important functional pathways such as the adrenergic signaling pathway, HIF-1 signaling pathway, and TGF-β signaling pathway. GO analysis results showed that calcium ion homeostasis and cell skeleton-related activities were significantly enriched in stage II. Further protein-protein interaction network analysis revealed 68 hub genes, including 13 eukaryotic initiation factors, 6 Ras superfamily members, and 6 genes related to cell division. In addition, genes such as Actin, Myosin, and Nup50 consistently showed high expression at all developmental stages, while genes related to calcium ion homeostasis, such as CaM, significantly increased in expression during stage II. Hsp90 and apoptosis-related genes had higher expression in stage IV, while Smad4 had higher expression in stage V. These results suggest that stage II of the swimming crab sperm development may be a critical period for spermatogenesis, and stage IV may be an important period for regulating sperm quality and quantity. This study not only provides a foundation for further research on the molecular mechanisms of testicular development and spermatogenesis in the swimming crab but also offers theoretical support for improving breeding yield, which has significant practical application value.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101453"},"PeriodicalIF":2.2,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143478844","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":"Integrated transcriptomic and metabolomic analysis reveals the causes of mass mortality in juvenile pearl oysters (Pinctada maxima)","authors":"Jinfang Liu ,&nbsp;Qin Su ,&nbsp;Chuangye Yang ,&nbsp;Junpeng Luo ,&nbsp;Ruijuan Hao ,&nbsp;Yongshan Liao ,&nbsp;Robert Mkuye ,&nbsp;Qingheng Wang ,&nbsp;Yuewen Deng","doi":"10.1016/j.cbd.2025.101454","DOIUrl":"10.1016/j.cbd.2025.101454","url":null,"abstract":"<div><div><em>Pinctada maxima</em> is a pearl oyster species producing large, high-quality marine pearls. However, juvenile mortality (shell length &lt; 5 cm) in this species adversely affects commercial pearl production. Understanding the molecular mechanism and genes related to mass mortality will help mitigate this problem. Therefore, the present study investigated the transcriptomic and metabolic differences between pearl oysters during high mortality (HM) and after this period (PD) to shed light on the causes of juvenile mass mortality. Initial analysis of biochemical parameters revealed that protease, α-amylase, and catalase activities in the hepatopancreatic tissues of pearl oysters at the HM stage were significantly lower than at the PD stage. Conversely, glutathione and lysozyme contents, and superoxide dismutase, acid phosphatase, alkaline phosphatase activities were notably higher at the HM stage than at the PD stage. Metabolomic analysis identified 98 metabolites in the adductor muscle significantly different between the two stages, which enriched glycerophospholipid metabolism, glutathione metabolism, arachidonic acid metabolism, oxidative phosphorylation, and neuroactive ligand-receptor interaction pathways. Transcriptome analysis identified 677 differentially expressed genes in the adductor muscle between these stages, which enriched neuroactive ligand-receptor interaction, glutathione metabolism, and ECM-receptor interaction pathways. Finally, an integrated analysis of the metabolome and transcriptome suggested that pearl oysters at the HM stage experience oxidative stress, activate immune-related genes, and exacerbate the low energy status. These findings on the causes of mass mortality lay a theoretical foundation for improving the survival rate of juveniles and advancing the industrialization of <em>P. maxima</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101454"},"PeriodicalIF":2.2,"publicationDate":"2025-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143488431","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}