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

{"title":"Comparative analyses of the transcriptome among three development stages of Zeugodacus tau larvae (Diptera: Tephritidae)","authors":"","doi":"10.1016/j.cbd.2024.101333","DOIUrl":"10.1016/j.cbd.2024.101333","url":null,"abstract":"<div><div>Studying differences in transcriptomes across various development stages of insects is necessary to uncover the physiological and molecular mechanism underlying development and metamorphosis. We here present the first transcriptome data generated under Illumina Hiseq platform concerning <em>Zeugodacus tau</em> (Walker) larvae from Nanchang, China. In total, 11,702 genes were identified from 9 transcriptome libraries of three development stages of <em>Z. tau</em> larvae. 7219 differentially expressed genes (DEGs) were screened out from the comparisons between each two development stages of <em>Z. tau</em> larvae, and their roles in development and metabolism were analyzed. Comparative analyses of transcriptome data showed that there are 5333 DEGs between 1-day and 7-day old larvae, consisting of 1609 up-regulated and 3724 down-regulated genes. Expressions of DEGs were more abundant in L7 than in L1 and L3, which might be associated with metamorphosis. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested the enrichment of metabolic process. KOG annotation further confirmed that 20-hydroxyecdysone (20E) pathway related genes <em>Cyp4ac1_1</em>, <em>Cyp4aa1</em>, <em>Cyp313a4_3</em> were critical for the biosynthesis, transport, and catabolism of secondary metabolites and lipid transport and metabolism. Expression patterns of 8 DEGs were verified using quantitative real-time PCR (RT-qPCR). This study elucidated the DEGs and their roles underlying three development stages of <em>Z. tau</em> larvae, which provided valuable information for further functional genomic research.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142318584","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-based study on the response mechanism of juvenile golden cuttlefish (Sepia esculenta) to benzo[a]pyrene exposure","authors":"","doi":"10.1016/j.cbd.2024.101331","DOIUrl":"10.1016/j.cbd.2024.101331","url":null,"abstract":"<div><p>Benzo[<em>a</em>]pyrene (BaP), a polycyclic aromatic hydrocarbon from incomplete combustion, builds up in coastal regions through river runoff, atmospheric deposition, and coastal activities. BaP's lipophilicity and stability lead to persistent environmental impacts due to its resistance to degradation. The economically valuable golden cuttlefish, <em>Sepia esculenta</em>, often spawns and hatches in shallow waters, making it prone to BaP exposure. This study employs transcriptomic analysis to initially investigate juvenile golden cuttlefish's response to BaP. The results indicate that BaP exposure significantly affects various physiological and molecular functions of the juveniles, particularly affecting pathways related to immune and inflammatory responses, metabolic regulation, and nervous system functions. Functional enrichment and PPI network analyses identified key genes such as HSGALT-like, ASAH1-like, and GTL-like in the BaP response. These genes exhibited a suppressive trend during short-term exposure, indicating that BaP exposure may influence lipid metabolism, energy conversion, and digestive functions at the genetic level, which could further disrupt the overall physiological state and developmental processes of juvenile golden cuttlefish. The study offers novel insights into BaP's effects on juvenile golden cuttlefish and marine life, aiding marine ecosystem and biodiversity conservation.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274396","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":"Comprehensive transcriptome analysis unravels the perturbated cardiovascular-related molecular mechanisms of tilapia under high-temperature stress","authors":"","doi":"10.1016/j.cbd.2024.101324","DOIUrl":"10.1016/j.cbd.2024.101324","url":null,"abstract":"<div><p>With the ongoing intensification of global warming, thermal stress poses significant challenges to tilapia aquaculture. However, the molecular mechanisms underlying the cardiac response of tilapia to high temperatures remain largely unexplored. To address this knowledge gap, we investigated the effects of high-temperature stress on the transcriptomic landscape of the tilapia heart. RNA sequencing was performed on the hearts of <em>Oreochromis aureus</em> (AR), <em>Oreochromis niloticus</em> (NL), and hybrids (<em>O. niloticus</em> ♀ × <em>O. aureus</em> ♂, AN) under treatments of 28 °C, 36 °C, and 39 °C. Using a multi-method approach, including Differentially Expressed Genes analysis, Weighted Gene Co-expression Network Analysis, Fuzzy C-Means, Self-Organizing Map, and Support Vector Machine-Recursive Feature Elimination, we identified six marker genes at 39 °C (AR: <em>ptges3</em>, <em>tuba1a</em>; NL: <em>ran</em>, <em>tcima</em>; AN: <em>slc16a1</em>, <em>fam184b</em>). These genes exhibited strong positive correlations and increased expression under high-temperature conditions. Gene Set Enrichment Analysis and GENIE3 revealed that these marker genes closely regulate three cardiovascular-related pathways: adrenergic signaling in cardiomyocytes, vascular smooth muscle contraction, and cardiac muscle contraction. We hypothesize that the synergistic inhibition of these pathways by marker genes leads to the deterioration of cardiovascular function. In summary, thermal stress activates marker genes, which in turn inhibit cardiovascular pathways, impairing cardiac performance. We propose that these marker genes could serve as dynamic thermal indicators of cardiac performance in tilapia. Additionally, our findings provide theoretical support for improving the management of tilapia farming under high-temperature stress.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240490","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 variations in sea cucumbers: Insights from genome survey sequencing and comparative analysis of mitochondrial genomes","authors":"","doi":"10.1016/j.cbd.2024.101328","DOIUrl":"10.1016/j.cbd.2024.101328","url":null,"abstract":"<div><p>Sea cucumbers, marine benthic invertebrates, play crucial roles in maintaining the stability of marine ecosystems and hold key evolutionary positions. However, information regarding their genomes remains limited. Here, we conducted genome survey analyses on seven species from four orders. Results indicated that <em>Colochirus anceps</em>, <em>Colochirus quadrangularis</em>, and <em>Pseudocolochirus violaceus</em> within the order Dendrochirotida have significantly larger genomes (2238–3754 Mbp) compared to conventional sea cucumber genomes, accompanied by a very high proportion of repeat sequences (69.39–72.52 %). While <em>Holothuria edulis</em> and <em>Holothuria atra</em> exhibited similar genome sizes comparable to those of other species within the order Holothuriida, heterozygosity and repeat content varied among all the six species in this order. The representative species <em>Apostichopus californicus</em> of the order Synallactida possesses the smallest genome size (573.45Mbp) within its order, but its heterozygosity (2.24 %) is significantly higher than that of other species. The representative species <em>Synapta maculata</em> of the order Apodida exhibited a normal genome size (900.97 Mbp), lower proportion of repeat sequences (42.19 %), and lower heterozygosity (0.84 %), making it the species with the least challenges for genome sequencing and assembly in the future among all surveyed species. Subsequently, we compiled genomic information from a total of 19 sea cucumber genomes, both newly sequenced and previously reported, revealing a significant linear relationship (<em>P</em> = 0.0001) between genome size and the proportion of repeat sequences in sea cucumbers. Additionally, phylogenetic and comparative analysis of mitochondrial genomes among them indicated extensive rearrangements within the order Apodida, leading to significant discrepancies between mitochondrial and nuclear genome phylogenies.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274395","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 transcriptome analysis reveals molecular mechanisms of the effects of light intensity and photoperiod on ovarian development in Procambarus clarkii (Girard, 1852)","authors":"","doi":"10.1016/j.cbd.2024.101329","DOIUrl":"10.1016/j.cbd.2024.101329","url":null,"abstract":"<div><p><em>Procambarus clarkii</em> (Girard, 1852) has important economic value in China and internationally. In this research, the comparative transcriptome analysis was used to reveal molecular mechanisms of influences of photoperiod and light intensity on ovarian development in <em>P. clarkii</em> for the first time. Some genes (such as <em>laminin</em>, <em>collagen</em>, <em>integrin beta</em>, <em>catenin</em>) and pathways (including TGF-beta signaling pathway, focal adhesion, ECM–receptor interaction) associated with ovarian development and oocyte maturation were significantly upregulated. Some genes related to circadian clock (such as <em>CLK</em>, <em>PER</em>) were identified in this research. The results indicated that when light intensity or photoperiod increased, <em>P. clarkii</em> could up-regulate the expression levels of the <em>laminin</em> and <em>collagen</em>, thereby synthesizing related proteins, promoting meiosis of the oocytes, thus increasing the number of oocytes in the ovary. At the same time, <em>P. clarkii</em> could up-regulate the expression levels of <em>integrin beta</em>, <em>integrin alpha 6</em>, and <em>diacylglycerol</em> to synthesize related proteins, thereby promoting the formation of proteins and fats such as triglycerides, these proteins and fats can provide material basis for maturation and development of oocytes, resulting in oocyte maturation and ovarian development. <em>P. clarkii</em> could synthesize related proteins by upregulating expression levels of genes (such as <em>catenin</em>), these proteins or hormones can adhere to other actins (such as integrins), thereby stabilizing the morphology of the oocytes and ensuring normal development. Meantime, the increase in light intensity or photoperiod could cause release GSH and VTG, resulting in oocytes development and maturation. The data in this research can reveal molecular mechanisms of impacts of photoperiod and light intensity on oocyte maturation and ovarian development in <em>P. clarkii</em>, can offer crucial genomic data for studying developmental mechanisms of ovary and oocyte in crustacean.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240489","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":"Genetic dissection of crayfish (Procambarus clarkii) high temperature tolerance and assessment of the potential application in breeding of the HSP genes","authors":"","doi":"10.1016/j.cbd.2024.101330","DOIUrl":"10.1016/j.cbd.2024.101330","url":null,"abstract":"<div><p>Red swamp crayfish (<em>Procambarus clarkii</em>) is an important freshwater aquaculture species in China. In the process of crayfish aquaculture, high temperature stress is common, which seriously affects its yield and quality. It is urgently recommended to improve these traits in the breed. However, the application of high-temperature tolerance genes in molecular breeding of crayfish has not been reported. In this study, transcriptome analysis was used to explore the high-temperature tolerance genes of crayfish. The results showed that genes related to energy metabolism, antioxidant, immunity and body restoration were involved in high temperature adaptation of crayfish. Based on the selected high temperature tolerance genes <em>Heat Stress Protein 70</em> and <em>Heat Stress Protein 90</em> (<em>HSP70</em> and <em>HSP90</em>), the genetic variation of their open reading frames was investigated. Totally, three and four SNPs of <em>HSP70</em> and <em>HSP90</em>, were obtained respectively. In addition, three high-temperature stress experiments were conducted on crayfish to identify favoured haplotypes. HSP70–1 and HSP90–1 are the favoured haplotypes of <em>HSP70</em> and <em>HSP90</em>, respectively. Furthermore, a series of molecular markers were developed to identify the favoured haplotype combinations of <em>HSP70</em> and <em>HSP90</em>. Finally, we propose a molecular breeding strategy to improve crayfish tolerance to high temperature, thereby providing a potential to increase crayfish yield. Together, this study provides a theoretical basis and molecular markers for the breeding of high-temperature tolerant crayfish.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240491","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 profiles of the skin associated with the color of the black and white coat of Angora goats","authors":"","doi":"10.1016/j.cbd.2024.101325","DOIUrl":"10.1016/j.cbd.2024.101325","url":null,"abstract":"<div><p>The coat color of mammals, determined by the distribution of melanin, particularly eumelanin and pheomelanin, reflects intricate genetic and molecular processes. However, our understanding of the relationship between coat color, gene expression, and polymorphisms in goats remains nascent. This study investigates transcriptomic differences between black and white Angora goats across three distinct hair growth phases. Skin tissue samples from both colored and white Angora goats were analyzed using mRNA expression profiling. Three skin samples were taken from each goat as biological duplicates at every stage of hair follicle growth (September, January, and March). In total, 36 samples were analyzed in this study, including samples from two Angora goat varieties, three developmental stages (three biological replicates), and two technical replicates for RNA sequencing. Significant differences in gene expression were observed between black and white goats at each growth phase, particularly in genes associated with the melanogenesis pathway. Specifically, several pigmentation genes were identified solely in black goats, indicating phase-specific and breed-specific regulation. Noteworthy genes, such as <em>SLC2A1</em>, <em>STAR</em>, and <em>SLC7A5</em>, exhibited differential expression patterns across growth phases in black goats, further highlighting the complexity of melanogenesis regulation. This is the first study to use mRNA expression profiling of skin tissues to analyze coat color differences between black and white coated Angora goats at the anagen, catagen, and telogen stages. The identification of phase-specific and black goat-specific pigmentation genes provides valuable insights into the complex mechanisms governing coat color formation.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240492","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":"Liver transcriptome and proteome are modulated by nutrient restriction in early lactation cows challenged with intramammary lipopolysaccharide","authors":"","doi":"10.1016/j.cbd.2024.101326","DOIUrl":"10.1016/j.cbd.2024.101326","url":null,"abstract":"<div><p>The objective was to evaluate the effects of nutrient restriction on liver function 24 h after an intramammary lipopolysaccharide (LPS) challenge in early lactation cows using transcriptomic and proteomic analyses. Multiparous Holstein cows were fed a lactation diet (CONT, n = 8) throughout the study or were switched to a diet diluted with barley straw (48 % DM) for 96 h (REST, n = 8) starting at 24 (18 to 30) days in milk. At 72 h, a healthy rear mammary quarter was infused with 50 μg of LPS in all cows. Blood and liver biopsies were collected at 96 h, corresponding to 24 h after LPS challenge. Liver transcriptome was analyzed with a 44 K bovine microarray and proteome by LC MS/MS. Transcriptomic and proteomic data were analyzed using GeneSpring (moderated <em>t</em>-test with Westfall-Young correction) and the “between subject design”, respectively. Data mining was performed using Panther and Pathway Studio software. By design, the negative energy balance was −68 and −37 MJ/d in REST and CONT, respectively. Plasma non-esterified FAs, and β-hydroxybutyrate were significantly greater in REST compared to CONT, which is consistent with 96 h of nutrient restriction in REST and ketosis induction. We detected 77 and 91 differentially expressed genes at mRNA and protein levels, respectively, between CONT and REST. Genes involved in fatty acid synthesis (<em>e.g.</em>: <em>ACAT</em>, <em>FASN</em>, <em>SCD</em>) were downregulated in REST, whereas those involved in fatty acid oxidation, detoxification, cholesterol synthesis, lipoprotein lipid secretion, and gluconeogenesis (<em>e.g.</em>: <em>ACAD</em>, <em>CPT1A</em>, <em>CPT1B</em>, <em>CPT2</em>) were upregulated. Differentially abundant mRNAs and proteins were consistent with negative energy balance and plasma metabolite concentrations, and reflected a state of intense lipomobilization, glucose deficit and ketogenesis in REST cows. Nutrient restriction did not change in deep liver expression of genes directly involved in immune function 24 h after an intramammary LPS challenge.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274394","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":"Exploring symbiont gene expression in two echinoid-associated shrimp species under host separation","authors":"","doi":"10.1016/j.cbd.2024.101327","DOIUrl":"10.1016/j.cbd.2024.101327","url":null,"abstract":"<div><p>Symbiotic relationships are omnipresent and particularly diverse in the marine world. In the Western Indian Ocean, the sea urchin <em>Echinometra mathaei</em> associates with two obligate ectosymbiotic shrimp species, <em>Tuleariocaris holthuisi</em> and <em>Arete indicus</em>. These shrimps are known for their host-dependent nature. <em>T. holthuisi</em>, for example, exhibits severe host separation syndrome, showing signs of stress and rapid mortality when isolated. Specific host pigments called spinochromes seem essential for <em>T. holthuisi</em> survival. Our study employs a transcriptomic approach to assess the stress induced by host separation on these shrimps.</p><p>Using paired-end Illumina HiSeq technology, we analyzed transcriptomes of both species under three conditions: (i) symbionts on their host (CC), (ii) isolated symbionts in seawater (IC), and (iii) isolated symbionts in spinochrome-enriched seawater (IC + S).</p><p>Sequencing revealed a total of 217,832 assembled unigenes, with an N50 value of 2061 bp. Isolated <em>T. holthuisi</em> showed 16.5 % DEGs (IC/CC), reduced to 8.5 % with spinochromes (IC + S/CC), both compared to the control condition (CC). Further analyses of stress-related genes show that <em>T. holthuisi</em> expressed stress-related genes when isolated in comparison to the control (IC/CC). Notably, heat shock proteins (HSPs) were significantly up-regulated in isolated <em>T. holthuisi</em>, especially without spinochromes. In contrast, <em>A. indicus</em> displayed differential expression of diverse genes, suggesting an adaptive micro-regulation mechanism to cope with isolation stress.</p><p>This study pioneers the use of NGS in exploring the transcriptomic responses of symbiotic shrimp species, shedding some light on the molecular impact of the host-separation syndrome and chemical dependencies.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274499","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":"Proteogenomic reconstruction of organ-specific metabolic networks in an environmental sentinel species, the amphipod Gammarus fossarum","authors":"","doi":"10.1016/j.cbd.2024.101323","DOIUrl":"10.1016/j.cbd.2024.101323","url":null,"abstract":"<div><p>Metabolic pathways are affected by the impacts of environmental contaminants underlying a large variability of toxic effects across different species. However, the systematic reconstruction of metabolic pathways remains limited in environmental sentinel species due to the lack of available genomic data in many taxa of animal diversity. In this study we used a multi-omics approach to reconstruct the most comprehensive map of metabolic pathways for a crustacean model in biomonitoring, the amphipod <em>Gammarus fossarum</em> in order to improve the knowledge of the metabolism of this sentinel species.</p><p>We revisited the assembly of RNA-seq data by de novo approaches to reduce RNA contaminants and transcript redundancy. We also acquired extensive mass spectrometry shotgun proteomic data on several organs from a reference population of <em>G. fossarum</em> males and females to identify organ-specific metabolic profiles.</p><p>The <em>G. fossarum</em> metabolic pathway reconstruction (available through the metabolic database GamfoCyc) was performed by adapting the genomic tool CycADS and we identified 377 pathways representing 7630 annotated enzymes, 2610 enzymatic reactions and the expression of 858 enzymes was experimentally validated by proteomics. To our knowledge, our analysis provides for the first time a systematic metabolic pathway reconstruction and the proteome profiles of these pathways at the organ level in this sentinel species. As an example, we show an elevated abundance in enzymes involved in ATP biosynthesis and fatty acid beta-oxidation indicative of the high-energy requirement of the gills, or the key anabolic and detoxification role of the hepatopancreatic caeca, as exemplified by the specific expression of the retinoid biosynthetic pathways and glutathione synthesis.</p><p>In conclusion, the multi-omics data integration performed in this study provides new resources to investigate metabolic processes in crustacean amphipods and their role in mediating the effects of environmental contaminant exposures in sentinel species.</p></div><div><h3>Synopsis</h3><p>This study provide the first evidence that it is possible to combine multiple omics data to exhaustively describe the metabolic network of a model species in ecotoxicology, <em>Gammarus fossarum</em>, for which a reference genome is not yet available.</p></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142229663","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}