Comparative Biochemistry and Physiology D-Genomics & Proteomics最新文献_第5页

Multi-organ transcriptomics provide insights into growth regulation in the Dongtingking crucian carp (Carassius auratus indigentiaus) 多器官转录组学研究洞庭湖鲫鱼生长调控机制

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-16 DOI: 10.1016/j.cbd.2025.101538

Dan Zeng , Yunsheng Zhang , Hu Xia , Liangguo Liu , Yangyang Tu , Mengying Chen , Pinghong Yang

{"title":"Multi-organ transcriptomics provide insights into growth regulation in the Dongtingking crucian carp (Carassius auratus indigentiaus)","authors":"Dan Zeng , Yunsheng Zhang , Hu Xia , Liangguo Liu , Yangyang Tu , Mengying Chen , Pinghong Yang","doi":"10.1016/j.cbd.2025.101538","DOIUrl":"10.1016/j.cbd.2025.101538","url":null,"abstract":"<div><div>To investigate the key regulatory genes and pathways related to growth traits in the Dongtingking crucian carp (<em>Carassius auratus indigentiaus</em>), the transcriptomes of brain, intestine, and muscle tissues were sequenced at early juvenile stage using RNA-Seq from two groups with extreme growth rates (fast-growing and slow-growing). A total of 65, 184, and 130 differentially expressed genes (DEGs) were detected in the brain, intestine, and muscle, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted that the PPAR signaling pathway, Insulin/PI3K/Akt/mTOR/FoxO/AMPK pathway, and Protein digestion and absorption pathways are crucial for growth in this species. Based on the transcriptome data, 32 key DEGs were identified, mainly participating in processes such as cell proliferation and differentiation, growth, development, and metabolism. Prominent examples are cyclic AMP-responsive element-binding protein 5 (<em>creb5b</em>), forkhead box protein O1-A (<em>foxo1a</em>), transcription factor AP-1-like (<em>jun</em>), lipoprotein lipase-like (<em>lpl</em>), angiopoietin-like 4 (<em>angptl4</em>), and egl nine homolog 3-like (<em>egln3</em>). This study enhances the understanding of the genetic factors and regulatory mechanisms responsible for variations in growth rates and provides a valuable basis for further studies on the regulatory mechanisms of growth in <em>C. auratus indigentiaus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101538"},"PeriodicalIF":2.2,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144090069","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

Papillae growth and molecular responses in sea cucumber (Apostichopus japonicus) exposed to light spectra 光照条件下海参乳突生长及分子响应

IF 2.2 2区生物学

Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-05-14 DOI: 10.1016/j.cbd.2025.101536

Ziyu Liu , Shuchao Ruan , Junhui Wang , Weiyan Li , Ye Tian , Chong Zhao , Lingshu Han , Luo Wang , Yaqing Chang , Jun Ding

{"title":"Papillae growth and molecular responses in sea cucumber (Apostichopus japonicus) exposed to light spectra","authors":"Ziyu Liu , Shuchao Ruan , Junhui Wang , Weiyan Li , Ye Tian , Chong Zhao , Lingshu Han , Luo Wang , Yaqing Chang , Jun Ding","doi":"10.1016/j.cbd.2025.101536","DOIUrl":"10.1016/j.cbd.2025.101536","url":null,"abstract":"<div><div>This study primarily investigated the light spectra that increased the number of papillae in sea cucumbers and the molecular pathways that contributed to the growth of papillae under these light conditions. At 8.0—15.0 °C, sea cucumbers were subjected to a 60-day indoor experiment under different lighting environments (normal, dark, blue light, yellow light, green light, red light, and white light). The number of papillae was analyzed using repeated measures ANOVA, and transcriptome sequencing data of the papillae were subsequently analyzed. The analysis revealed that there were significant differences in the number of papillae within each group at the beginning of the experiment and on days 15, 30, and 45 of light exposure (<em>p</em> < 0.05), while no significant differences were observed within each group between days 45 and 60 of light exposure (<em>p</em> > 0.05). Under blue light exposure, the number of papillae and the increase in the number of papillae in sea cucumbers showed significant differences compared to the control group (<em>p</em> < 0.05). The pathways related to the increase in the number of papillae in sea cucumbers include phenylalanine, tyrosine, and tryptophan biosynthesis and phenylalanine metabolism. The number of papillae increased the most after 45 days of blue light exposure, after which it stabilized. It was speculated that the increase in the number of papillae might be related to amino acid metabolism and collagen synthesis.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101536"},"PeriodicalIF":2.2,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144089954","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

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

Comprehensive analysis of the transcriptome implicated in the immune response of Procambarus clarkii to Aeromonas hydrophila 与克氏原螯虾对嗜水气单胞菌免疫反应相关的转录组综合分析

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.2025.101528

Xi-Rong Zhu , Wen-Hui Tang , Qin Peng , Rui Zhang , Yao-Hui Chen , Qiu-Ning Liu , Bo-Ping Tang , Li-Shang Dai

{"title":"Comprehensive analysis of the transcriptome implicated in the immune response of Procambarus clarkii to Aeromonas hydrophila","authors":"Xi-Rong Zhu , Wen-Hui Tang , Qin Peng , Rui Zhang , Yao-Hui Chen , Qiu-Ning Liu , Bo-Ping Tang , Li-Shang Dai","doi":"10.1016/j.cbd.2025.101528","DOIUrl":"10.1016/j.cbd.2025.101528","url":null,"abstract":"<div><div>In order to better understand the immune response of <em>Procambarus clarkii</em> to <em>Aeromonas hydrophila</em> injection, the transcriptome data of the gill tissue of <em>P. clarkii</em> were compared and analyzed. 1008 significant DEGs were identified in <em>A. hydrophila</em> infected and PBS control groups, including 411 up-regulated genes and 597 down-regulated genes. Endocytosis, phagocyte and lysosome were the most clustered pathways of DEGs in KEGG database. RNA-Seq results were validated through the verification of immune-related differentially expressed genes (DEGs), whose expression levels were assessed using quantitative real-time PCR (qRT-PCR). With the increase of treatment time of <em>A. hydrophila</em>, the total protein in gill of the treatment group showed a trend of increasing first, then decreasing and then increasing and decreasing. ACP and AKP both show a trend of rising first, then falling and then rising. The results of comprehensive research showed that crayfish infected with <em>A. hydrophila</em> caused damage to gill tissue, and the related immune genes were up-regulated and the immune mechanism was operated to protect the body from <em>A. hydrophila</em>. The differential gene <em>MRC1</em> was screened through the transcriptome, and to further understand its impact, it was disrupted by RNAi technology, which showed a significant down-regulation of immune genes (<em>TAB2</em>, <em>TLR3</em>, <em>ALF6</em>, <em>Lyso3</em>, <em>clotting factor G beta subunit-like</em> and <em>coagulation factor X-like</em>) as well as genes downstream of the pathway (<em>AP4E1</em>, <em>ARSB</em> and <em>TUBA1A</em>). This study provides a theoretical basis for further exploring the immune adaptability of aquatic animals under bacterial infection.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101528"},"PeriodicalIF":2.2,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144105322","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 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