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

The response mechanism of high pH and alkalinity interactive stress on immune system and energy metabolism pathway of Litopenaeus vannamei 高pH和高碱度交互胁迫对凡纳滨对虾免疫系统和能量代谢途径的响应机制

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-13 DOI: 10.1016/j.cbd.2025.101531

Xue Mao, Ruiqi Zhang, Jianfu Wang, Baoyi Fan, Xiang Shi, Jintao Guo, Ziguo Wang

{"title":"The response mechanism of high pH and alkalinity interactive stress on immune system and energy metabolism pathway of Litopenaeus vannamei","authors":"Xue Mao, Ruiqi Zhang, Jianfu Wang, Baoyi Fan, Xiang Shi, Jintao Guo, Ziguo Wang","doi":"10.1016/j.cbd.2025.101531","DOIUrl":"10.1016/j.cbd.2025.101531","url":null,"abstract":"<div><div><em>Litopenaeus vannamei</em> is an important aquaculture species and faces complex stress challenges in saline-alkali water, such as high pH and alkalinity. In this study, the immune and metabolic responses of <em>L.vannamei</em> under acute interactive stress (pH 9.2, alkalinity 350 mg / L) were investigated by multi-omics analysis. The results showed that significant changes in antioxidant enzyme activity (e.g., increased SOD, decreased GSH-Px) and immune-related pathways (lysosomes, TGF-β, glutathione metabolism) were affected. Transcriptome analysis identified 1968 DEGs, which were mainly enriched in apoptosis, immune defense, and energy metabolism pathways. Metabolomics revealed the disorder of lipid, amino acid, and nucleotide metabolism, and key metabolites (such as arachidonic acid and sphingomyelin) were related to oxidative stress and membrane stability. Multi-omics integration showed that PI3K-AKT and TGF-β signaling pathways were coordinated and regulated under stress conditions. WGCNA analysis obtained a total of 19 co-expression modules. Among them, 13 hub genes related to saline-alkali stress were screened out in the turquoise and brown modules, and a transcriptional regulatory network was constructed. The expression patterns of five pairs of genes in four hot pathways under saline-alkali stress were verified. In summary, high pH and alkalinity interaction stress induces oxidative damage, disrupts metabolic homeostasis, and triggers adaptive responses through immune activation and energy redistribution. This study provides clues for exploring the molecular response mechanism of <em>L. vannamei</em> under saline-alkali stress and provides a theoretical basis for optimizing shrimp culture in saline-alkali waters.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101531"},"PeriodicalIF":2.2,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144084013","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}

引用次数: 0

Transcriptomic analysis reveals sexual dimorphism in lipid metabolism within largemouth bass (Micropterus salmoides) fed the high-fat diet 转录组学分析揭示了高脂肪饲料喂养的大口黑鲈（Micropterus salmoides）体内脂质代谢的性别二态性

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-10 DOI: 10.1016/j.cbd.2025.101533

Han Huang, Xianping Tian, Haijie Chen, Yuanfa He, Yongjun Chen, Shimei Lin

{"title":"Transcriptomic analysis reveals sexual dimorphism in lipid metabolism within largemouth bass (Micropterus salmoides) fed the high-fat diet","authors":"Han Huang, Xianping Tian, Haijie Chen, Yuanfa He, Yongjun Chen, Shimei Lin","doi":"10.1016/j.cbd.2025.101533","DOIUrl":"10.1016/j.cbd.2025.101533","url":null,"abstract":"<div><div>The study presented the differential responses of male and female largemouth bass fed a high-fat diet, focusing on growth performance, hepatic transcriptomics, and lipid metabolism. The high-fat diet, 50.23 % crude protein and 19.46 % crude fat, was formulated and fed to female and male largemouth bass for 73 days separately. Growth parameters, such as final weight, weight gain (WG) and specific growth rate (SGR), demonstrated superior performance in males compared to females fed the high-fat diet. Hepatic transcriptomic analysis between the sexes under high-fat diet revealed totally 267 differentially expressed genes (DEGs), of which 132 were up-regulated and 135 down-regulated. Notably, genes implicated in lipid biosynthesis, such as <em>elovl5</em>, <em>pap</em>, <em>aacs</em>, <em>hmgcra</em>, <em>fdft1</em>, <em>ebp</em>, and <em>dhcr24</em>, were found to be down-regulated in males and are enriched in metabolic pathways. This suggests a sex-dependent modulation of lipid metabolism. Furthermore, the study revealed a stark contrast in hepatic mRNA expression levels of genes pivotal for lipid anabolism, with <em>acc1</em>, <em>pparγ</em>, <em>srebf1</em>, <em>fasn</em>, and <em>scd</em> being more highly expressed in females compared to males. Conversely, genes associated with lipid catabolism, including <em>cpt1</em> and <em>hsl</em>, showed elevated expression in males. These findings underscore the interplay between sex, diet, and metabolic regulation in largemouth bass. The study's contributions to our understanding of physiological variances between male and female largemouth bass under high-fat diet are significant, offering valuable insights for the nutritional strategies to accommodate the metabolic needs of both sexes.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101533"},"PeriodicalIF":2.2,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143947207","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}

引用次数: 0

Transcriptome analysis and machine learning methods reveal potential mechanisms of zebrafish muscle aging

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-09 DOI: 10.1016/j.cbd.2025.101532

Jian Wang , Junwei Shan , Cheng Guo , You Duan , Feng Zhang , Weidong Ye , Yanxiao Liu

{"title":"Transcriptome analysis and machine learning methods reveal potential mechanisms of zebrafish muscle aging","authors":"Jian Wang , Junwei Shan , Cheng Guo , You Duan , Feng Zhang , Weidong Ye , Yanxiao Liu","doi":"10.1016/j.cbd.2025.101532","DOIUrl":"10.1016/j.cbd.2025.101532","url":null,"abstract":"<div><div>Muscle is one of the most abundant tissues in the human body, and its aging usually leads to many adverse consequences. Zebrafish is a powerful model used to study human muscle diseases, yet we know little about the molecular mechanisms of muscle aging in zebrafish. In this study, we determined the gene expression profiles of muscle tissues from male zebrafish of four different ages. Through differential expression analysis and expression pattern analysis, we identified a set of genes associated with muscle aging in zebrafish. Functional enrichment analysis revealed that several biological changes accompanied zebrafish muscle aging, including chronic inflammation, accumulation of sphingolipids, reduction of autophagy, and activation of the ferroptosis pathway. H&E staining showed that zebrafish muscle senescence leads to myofibrillar interstitial expansion and inflammatory cell infiltration. Furthermore, we screened zebrafish muscle aging related biomarkers by machine learning and verified the expression levels of some biomarkers by RT-qPCR. Based on these biomarkers, we constructed a zebrafish muscle aging clock that can predict muscle age based on transcriptomic data. This study provides us with a new perspective to understand the molecular mechanism of muscle aging and a new tool for zebrafish-based anti-aging research.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101532"},"PeriodicalIF":2.2,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143943107","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}

引用次数: 0

Comparative analysis of gut microbiota-mediated bile acid profiles in Bufo gargarizans and Rana chensinensis tadpoles

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-08 DOI: 10.1016/j.cbd.2025.101530

Zhangying Xu , Yuebin Pei , Hongyuan Wang , Xinyi Li

{"title":"Comparative analysis of gut microbiota-mediated bile acid profiles in Bufo gargarizans and Rana chensinensis tadpoles","authors":"Zhangying Xu , Yuebin Pei , Hongyuan Wang , Xinyi Li","doi":"10.1016/j.cbd.2025.101530","DOIUrl":"10.1016/j.cbd.2025.101530","url":null,"abstract":"<div><div>Bile acids (BAs) are cholesterol derivatives synthesized by the liver, exhibit variation between different species. Researchers have long appreciated that microbiota play the roles in the biotransformation of BAs. However, relatively few studies have been reported on microbial-mediated production and transformation of BAs in amphibians. Our focus here is principally on difference of intestinal microbial diversity and BAs profiles between two common amphibians, <em>Bufo gargarizans</em> (<em>B. gargarizans</em>) and <em>Rana chensinensis</em> (<em>R. chensinensis</em>) tadpoles, through intestinal targeted BAs metabolomics and fecal metagenomic sequencing. The results demonstrated that <em>B. gargarizans</em> possessed higher levels of total BAs and higher ratio of unconjugated / conjugated BAs. In addition, the relative abundance of microbiota with bile salt hydrolase (BSH) activity in <em>B. gargarizans</em> was significantly higher than that of <em>R. chensinensis</em>, which may facilitate the conversion of conjugated to unconjugated BAs. Meanwhile the higher prevalence of bile-acid-induced (BAI) gene encoding microbiota in <em>R. chensinensis</em> may promote the synthesis of deoxycholic acid (DCA). Furthermore, discrepancies in virulence factors (VFs) and energy metabolism were observed between the two species, which may be linked to differences in the microbiota. This study revealed substantial differences in intestinal microbes and BAs across amphibian species, emphasizing the significant impact of intestinal microbes on BAs metabolism.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101530"},"PeriodicalIF":2.2,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143943108","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}

引用次数: 0

Corrigendum to “Whole transcriptomic analysis reveals the lncRNA-miRNA-mRNA regulatory mechanism underlying the heat-hardening formation in Mytilus coruscus” [Comp. Biochem. Physiol. Part D Genomics Proteomics (2025) 101468] “全转录组学分析揭示了Mytilus coruscus热硬化形成的lncRNA-miRNA-mRNA调控机制”的勘误表[Comp. Biochem.]。杂志。Part D Genomics Proteomics (2025) 101468]

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-07 DOI: 10.1016/j.cbd.2025.101521

Hao Wang , Bingqi Wei , Zhenyu Dong , Zhenqi Xin , Huajian Lin , Wanliang Zhang , Yingying Ye , Zhi Liao , Weifeng Wang , Xiaojun Yan , Mingshan Song , Baoying Guo

引用次数: 0

Comparative analysis of different Phyllostachys species on gut microbiome and fecal metabolome in giant pandas (Ailuropoda melanoleuca) 不同毛竹属物种对大熊猫肠道微生物组和粪便代谢组的比较分析

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-07 DOI: 10.1016/j.cbd.2025.101529

Jingle Jiang, Haili Wu, Yaohua Yuan

{"title":"Comparative analysis of different Phyllostachys species on gut microbiome and fecal metabolome in giant pandas (Ailuropoda melanoleuca)","authors":"Jingle Jiang, Haili Wu, Yaohua Yuan","doi":"10.1016/j.cbd.2025.101529","DOIUrl":"10.1016/j.cbd.2025.101529","url":null,"abstract":"<div><div>The influences of different bamboo species on the microbiome and metabolome of giant pandas (<em>Ailuropoda melanoleuca</em>) remain understudied. The aim of this study was to investigate the effects of different <em>Phyllostachys</em> species on the gut microbial communities and fecal metabolite profiles in giant pandas. Metagenome and metabolome were performed on the feces of giant pandas fed with different <em>Phyllostachys</em> species (<em>P. edulis</em>, <em>P. iridescens</em>, <em>P. glauca</em>, and <em>P. violascens</em>). The results of metagenome showed that dietary with <em>P. glauca</em> could notably decrease the microbial Shannon index. The relative abundances of both <em>Cellulosilyticum</em> and <em>Pseudomonas</em> were enhanced after dietary with <em>P. iridescens</em>, suggesting <em>P. iridescens</em> could enhance the cellulose-degrading function in giant pandas. However, dietary with <em>P. glauca</em> or <em>P. violascens</em> could increase the relative abundances of certain pathogenic bacteria (<em>Escherichia</em>, <em>Shigella</em>, and <em>Klebsiella</em>). Metabolomics analysis further revealed that all experimental groups exhibited notably elevated levels of fecal flavonoids and fatty acids. In addition, the correlation analysis showed that certain nutrients of bamboo leaves (mainly crude protein and Cu) were significantly correlated with several differential gut bacteria and fecal metabolites. Based on the present results, <em>P. iridescens</em> might be a substitute for the routinely used <em>Phyllostachys</em> species (<em>P. edulis</em>) in the captive management of giant pandas. The results have revealed that bamboo species is an important factor affecting the gut microbiota and fecal metabolites in giant pandas. Our results could provide important information about bamboo species-induced alterations on the microbiome and metabolome in giant pandas.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101529"},"PeriodicalIF":2.2,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143928401","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}

引用次数: 0

Sequence characteristics, evolutionary history and expression pattern of BCO2 in Chinese mitten crab Eriocheir sinensis 中华绒螯蟹BCO2序列特征、进化历史及表达模式

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-03 DOI: 10.1016/j.cbd.2025.101524

Yanan Gao , Maolei Wei , Jingyi Xiong , Min Zhang , Xugan Wu

{"title":"Sequence characteristics, evolutionary history and expression pattern of BCO2 in Chinese mitten crab Eriocheir sinensis","authors":"Yanan Gao , Maolei Wei , Jingyi Xiong , Min Zhang , Xugan Wu","doi":"10.1016/j.cbd.2025.101524","DOIUrl":"10.1016/j.cbd.2025.101524","url":null,"abstract":"<div><div>β-carotene 9’, 10’-oxygenase (BCO2) is a pivotal enzyme in the carotenoid cleavage. To fill the research gap of BCO2 in Chinese mitten crab <em>Eriocheir sinensis</em>, we first investigated <em>ESIN_BCO2</em> gene from its genome, revealing its evolutionary history, gene structure, and expression patterns. The results showed that E<em>SIN_BCO2</em> gene has a full-length open reading frame (ORF) of 1572 bp, encoding a protein of 523 amino acids. BCO2 was characterized by ten conserved motifs and an RPE65 domain, belonging to carotenoid cleavage oxygenase (CCO) family. Phylogenetic analysis revealed that <em>BCO1</em> was the ancestral gene, from which <em>BCO2</em> and <em>NinaB</em> diverged during evolution. Notably, the Ka/Ks ratios for BCO2 in Decapoda were approximately lower than BCO2 from other crustaceans (0.014 to 0.045 vs 0.112 to 0.185). <em>ESIN_BCO2</em> was predominantly expressed in the hindgut, with significantly higher expression levels in females than in males. It was predominantly localized near the nuclei (N) of <em>epi</em>thelial cells (epi) and basal cells (bc) in the hindgut. Moreover, dietary β-carotene supplementation significantly upregulated <em>BCO2</em> expression in the female hindgut. These findings provide valuable insights into the evolution and function of <em>BCO2</em> in <em>E. sinensis</em> as well as the other crustaceans, potentially shedding light on the conservation and divergence of carotenoid metabolism mechanisms across diverse crustaceans.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101524"},"PeriodicalIF":2.2,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144084187","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}

引用次数: 0

Association analysis reveals SNP markers associated with growth traits in swimming crabs (Portunus trituberculatus) 关联分析揭示游泳蟹（Portunus trituberculatus）生长性状相关SNP标记

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-02 DOI: 10.1016/j.cbd.2025.101527

Baohua Duan , Jishun Zhang , Tongxu Kang , Chen Zhang , Shumei Mu , Yueqiang Guan , Yuqin Ren , Zejian Li , Xianjiang Kang

{"title":"Association analysis reveals SNP markers associated with growth traits in swimming crabs (Portunus trituberculatus)","authors":"Baohua Duan , Jishun Zhang , Tongxu Kang , Chen Zhang , Shumei Mu , Yueqiang Guan , Yuqin Ren , Zejian Li , Xianjiang Kang","doi":"10.1016/j.cbd.2025.101527","DOIUrl":"10.1016/j.cbd.2025.101527","url":null,"abstract":"<div><div>The swimming crab (<em>Portunus trituberculatus</em>) is an economically important species in mariculture, widely distributed along the coastal areas of China. Due to its rapid growth and high nutritional value, it is a key target for selective breeding to enhance production efficiency and reduce costs. In this study, we conducted an association analysis between 233 high-quality SNPs and seven growth traits of 244 <em>P. trituberculatus</em> individuals: full carapace width (FCW), carapace width (CW), carapace length (CL), fixed length of the claw (FLC), meropodit length of the claw (MLC), body height (BH), and body weight (BW). The analysis identified 11 SNPs significantly associated with growth, which are distributed across multiple chromosomes, underscoring the polygenic nature of these traits. Multiple comparisons of diplotypes revealed that the diplotype D1 (AA-AT) exhibited a significant advantage for all seven growth-related traits. Additionally, we annotated 33 candidate genes located near these significant SNPs, including cytochrome <em>c</em> oxidase subunit (<em>COX</em>), NADH dehydrogenase subunit (<em>ND</em>), cytochrome <em>b</em> (<em>CYTB</em>), and 15-hydroxyprostaglandin dehydrogenase (<em>15-PGDH</em>). These genes play key roles in oxidative phosphorylation, ATP synthesis, and energy metabolism-key processes for cellular function and growth. These findings enhance our understanding of the genetic architecture underlying growth-related traits in <em>P. trituberculatus</em> and provide valuable SNP markers for marker-assisted selection to improve breeding efficiency in this economically important species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101527"},"PeriodicalIF":2.2,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912327","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}

引用次数: 0

Circular RNA transcriptome across various development periods of Paralichthys olivaceus reveal skeletal muscle-specific circchd6 regulating myogenesis 橄榄鲆不同发育时期的环状RNA转录组揭示了骨骼肌特异性circhd6调节肌肉发生

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-01 DOI: 10.1016/j.cbd.2025.101518

Hao Wang , Jingru Zhang , Guangling Li , Binghua Liu , Min Liu , Hengtai Tang , Haishen Wen , Feng He

{"title":"Circular RNA transcriptome across various development periods of Paralichthys olivaceus reveal skeletal muscle-specific circchd6 regulating myogenesis","authors":"Hao Wang , Jingru Zhang , Guangling Li , Binghua Liu , Min Liu , Hengtai Tang , Haishen Wen , Feng He","doi":"10.1016/j.cbd.2025.101518","DOIUrl":"10.1016/j.cbd.2025.101518","url":null,"abstract":"<div><div>The Japanese flounder (<em>Paralichthys olivaceus</em>) is greatly influenced in terms of muscle quality and quantity by the development of skeletal muscle. While the mechanisms underlying skeletal muscle development are well-studied, the role of non-coding RNAs, particularly circRNAs, in the skeletal muscle development of Japanese flounder remains unclear. To investigate the expression patterns of circRNAs during different developmental stages (JP1: 7 days, JP2: 90 days, JP3: 24 months (female), JP4: 24 months (male)) in Japanese flounder, we performed transcriptome sequencing analysis. We identified a total of 3523 circRNAs, of which 10.19 % were differentially expressed. These differentially expressed (DE) circRNAs were studied, and their impacts on muscle development were analyzed. The RNA interaction network revealed that skeletal muscle-specific circchd6 targeted novel-miR-508 and further regulated dual specificity tyrosine-phosphorylation regulated kinase 2 (<em>dyrk2</em>). Functional analysis showed that overexpressed circchd6 and <em>dyrk2</em> promoted myoblast proliferation and differentiation, while novel-miR-508 inhibited both. Our study identified the circchd6-novel-miR-508-<em>dyrk2</em> axis as a regulatory mechanism and provided new evidence for the use of epigenetic approaches in genetic breeding.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101518"},"PeriodicalIF":2.2,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912414","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}

引用次数: 0

Transcriptomic analysis reveals the molecular mechanisms of heterosis in low-temperature tolerance in the hybrids of Argopecten scallops 转录组学分析揭示了亚贝扇贝杂种耐低温优势的分子机制

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-04-30 DOI: 10.1016/j.cbd.2025.101526

Peican Zhu , Guizhen Wang , Yuan Liu , Lisen Wen , Qixiang Bo , Guilong Liu , Chunde Wang , Bo Liu

{"title":"Transcriptomic analysis reveals the molecular mechanisms of heterosis in low-temperature tolerance in the hybrids of Argopecten scallops","authors":"Peican Zhu , Guizhen Wang , Yuan Liu , Lisen Wen , Qixiang Bo , Guilong Liu , Chunde Wang , Bo Liu","doi":"10.1016/j.cbd.2025.101526","DOIUrl":"10.1016/j.cbd.2025.101526","url":null,"abstract":"<div><div>The F<sub>1</sub> hybrid of <em>Argopecten irradians irradians</em> (♀) × <em>A. purpuratus</em> (♂) exhibits significant heterosis in growth performance and mid-parent heterosis in low-temperature tolerance. This study presents a comparative transcriptomic analysis of <em>A. irradians irradians</em> (Ai), <em>A. purpuratus</em> (Ap), and the hybrid <em>A. irradians irradians</em>♀ × <em>A. purpuratus</em>♂ (Aip) to explore the mechanisms underlying low-temperature tolerance heterosis in Aip. A total of 33,376 differentially expressed genes (DEGs) were identified between F<sub>1</sub> hybrids and purebreds under cold stress. In Aip, 80.32 % of DEGs exhibited non-additive expression patterns, with over-dominant expression observed in 30.65 % of these genes. Pairwise comparisons among the transcriptomes of Ai, Ap, and Aip revealed 14,959 alternative splicing events, affecting 8169 genes. KEGG pathway analysis indicated substantial enrichment of overlapping genes from common DEGs and non-additively expressed genes (NAGs) in apoptosis, longevity regulation, ABC transporters, and spliceosome pathways. Furthermore, analysis of DEGs, DAGs (Differentially Alternative Splicing genes), and NAGs identified 6 genes undergoing alternative splicing. These pathways and genes may be crucial in Aip's response to low-temperature stress and offer insights for advancing scallop cross-breeding strategies.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"55 ","pages":"Article 101526"},"PeriodicalIF":2.2,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143895201","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}

引用次数: 0