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

{"title":"An integrated transcriptome, proteome and targeted metabolome analysis reveals genes and steroids related to gonadal development in Ruditapes philippinarum","authors":"Kaiyue Huang,&nbsp;Yimeng Chen,&nbsp;Yijin Gao,&nbsp;Haichun Liu,&nbsp;Zhiying Gao,&nbsp;Yang Liu,&nbsp;Zhongming Huo,&nbsp;Yanjie Qin","doi":"10.1016/j.cbd.2025.101587","DOIUrl":"10.1016/j.cbd.2025.101587","url":null,"abstract":"<div><div>Gonadal development in <em>Ruditapes philippinarum</em> involves germ cell formation, sex differentiation, vitellogenesis, and maturation, regulated by complex genes-hormone interactions. To elucidate these mechanisms, multi-omics analyses (transcriptomics, proteomics, and steroid targeted metabolomics) and qPCR were applied to gonads across developmental stages in clams. Differential expression analysis revealed 332 testicular and 560 ovarian genes, alongside 174 testicular and 107 ovarian proteins. Integrated omics identified 12 concordantly annotated gene-protein pairs. Expressed levels for 14 genes (8 transcriptome only, 6 multi-omics) demonstrated that <em>Cyclin B2</em> (<em>CCNB2</em>), <em>Moloney sarcoma oncogene</em> (<em>MOS</em>), and <em>Glutaminase</em> (<em>GLS</em>) peaked during the maturation stage and significantly declined during the partially spent stage (<em>P</em> &lt; 0.05). These three genes were also more highly expressed in the ovary compared to the testis (<em>P</em> &lt; 0.05). <em>Cell Division Cycle 20</em> (<em>CDC20</em>), Atrial Natriuretic Peptide Receptor Type A (<em>ANPRA</em>), and Rpsr-1 showed highest levels during both maturation and partially spent stage (<em>P</em> &lt; 0.05), with <em>ANPRA</em> predominantly expressed in the testis, and <em>CDC20</em> and Rpsr-1 in the ovary; <em>Calmodulin</em> (<em>CALM</em>), <em>Glutamine Synthetase</em> (<em>GLUL</em>), Sushi Domain Containing 2 (SUSD2), Rpsr-2, Rpsr-3, Rpsr-4 and CD151 Molecule (Raph Blood Group) (CD151) attained their highest values in the partially spent stage (<em>P</em> &lt; 0.05), where Rpsr-3, Rpsr-4 and CD151 expressed higher in the testis (<em>P</em> &lt; 0.05), and <em>CALM</em>, <em>GLUL</em>, SUSD2 and Rpsr-2 were more pronounced in the ovary (<em>P</em> &lt; 0.05); <em>Phospholipase A2 Group IVA</em> (<em>PLA2G4</em>) exhibited its highest expression during the growing stage, gradually declining as development progressed, which was significantly higher in the testis than in the ovary (<em>P</em> &lt; 0.05). Targeted metabolomics identified 14 steroids in clam gonads, with five steroids—Pregnenolone, 5α-Pregnane-3,20-dione, 17α-Hydroxypregnenolone, 25-Hydroxycholesterol, and 24-dehydro Cholesterol—elevated during the gonadal growing phase (no sex differences). Intriguingly, 17β-estradiol (typically reported in bivalve gonad development) was undetected. Integrated transcriptomic/proteomic analyses confirmed absence of its synthesis pathway, including key enzymes like cytochrome P450 aromatase (CYP19A1). This study established a multi-omics platform to detect the genes-hormone interactions, and evaluate expression dynamics of 14 key regulators across gonadal stages and sexes in <em>R philippinarum</em>, concurrently evaluating steroid hormones roles. These findings provide valuable resources for further research into the comprehensive regulatory mechanisms governing gonad development in clams.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101587"},"PeriodicalIF":2.2,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144695239","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":"Gonadal sex differentiation in Eleutheronema tetradactylum: Histological features and transcriptomic insights from mature gonads","authors":"Evodia Moses Mkulo ,&nbsp;Lukman Iddrisu ,&nbsp;Salifu Ibrahim ,&nbsp;Jiansheng Huang ,&nbsp;Linjuan Wang ,&nbsp;Anna Zheng ,&nbsp;Happiness Moses Mwemi ,&nbsp;Jin Minxuan ,&nbsp;Huijuan Zhang ,&nbsp;Baogui Tang ,&nbsp;Qian Ma ,&nbsp;Kwaku Amoah ,&nbsp;Bei Wang ,&nbsp;Zhongliang Wang","doi":"10.1016/j.cbd.2025.101586","DOIUrl":"10.1016/j.cbd.2025.101586","url":null,"abstract":"<div><div>Plasticity in teleosts is a fascinating evolutionary strategy enables species to acclimate to environmental changes. However, the molecular mechanisms that underlie gonadal differentiation and reversal remain incompletely understood. The four-finger threadfin (<em>Eleutheronema tetradactylum</em>), a protandrous hermaphrodite belonging to the Polynemidae family, serves as an excellent model for studying genes and molecules involved in gonadal transformation. In this study, we used de novo transcriptome sequencing of the male and female gonads to identify key regulatory genes and pathways involved in sex differentiation. A total of 12,034 DEGs were identified, with 7567 upregulated and 4467 downregulated between testes and ovaries. GO and KEGG enrichment analyses identified steroid hormone biosynthesis as the key pathway in gonadal differentiation. Several novel sex biased genes DEGs were identified, including testis-biased genes <em>nefl</em>, <em>rfesd</em>, and <em>gpatch8</em>, and ovary-biased genes <em>ift57</em>, <em>hoxb5a</em>, <em>naxd</em>, and <em>tgfbr3</em>. furthermore, clusters of testis-specific genes, including <em>dnah7</em>, <em>tspan1</em>, <em>hspa8</em>, <em>dnah3</em>, <em>dnah6</em>, <em>dnah17</em>, <em>myo10</em>, <em>kcnq3</em>, <em>dnaaf11</em>, <em>rtase</em>, <em>dmrt1</em>, <em>smcl1b</em>, <em>slc44a5b</em>, <em>tex11</em>,<em>cyp51</em> and ovary-biased genes, such as <em>cd9</em>, <em>zp2</em>, <em>ccnp</em>, <em>cldnd</em>, <em>znf622</em>, <em>tc1a</em>, <em>hsd17b7</em>, foxl2, <em>sox3</em>, and <em>sox19a</em> were identified, emphasizing their crucial roles in gonadal differentiation. This in-depth transcriptomic study sheds light on the molecular foundations of reproductive adaptability, offering novel insights for disciplines such as aquaculture, conservation and evolutionary biology.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101586"},"PeriodicalIF":2.2,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144679447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic profiling reveals sex-specific gene expression patterns in Eriocheir sinensis gonads","authors":"Feng Zhao ,&nbsp;Haoyu Liu ,&nbsp;Yaxuan Shi ,&nbsp;Longlong Fu ,&nbsp;Huixia Feng ,&nbsp;Cong Zhang ,&nbsp;Kai Zhang ,&nbsp;Shaowu Yin ,&nbsp;Xianhui Ning","doi":"10.1016/j.cbd.2025.101584","DOIUrl":"10.1016/j.cbd.2025.101584","url":null,"abstract":"<div><div>The Chinese mitten crab (<em>Eriocheir sinensis</em>) exhibits prominent sexual dimorphism with important economic implications, yet the molecular mechanisms underlying its sex determination and regulation remain poorly characterized. Here, we present the first comparative gonadal transcriptome analysis of <em>E. sinensis</em> to identify sex-related genes. High-throughput sequencing of testicular and ovarian tissues identified 5894 differentially expressed genes (DEGs), including 2581 female-related and 3313 male-related DEGs. Functional enrichment analyses revealed critical pathways governing crustacean sexual regulation, such as Steroid hormone biosynthesis pathway and GnRH signaling pathway. Moreover, a protein-protein interaction (PPI) network of 65 sexual regulation-related DEGs was constructed. Accordingly, Estradiol 17-beta-dehydrogenase 8 (<em>HSD17B8</em>), a dual-function enzyme in estrogen/testosterone metabolism, and Heat shock protein 90 (<em>HSP90</em>), a molecular chaperone stabilizing estrogen receptors, were identified as hub genes. In addition, experimental validation via RT-qPCR showed strong concordance with transcriptomic data, confirming the reliability of sex-biased expression patterns. The results of this study provide valuable resource of target genes for future studies on the molecular mechanisms underlying sex determination and regulation in <em>E. sinensis</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101584"},"PeriodicalIF":2.2,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144670788","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 and characterization of heat shock protein superfamily in the cotton aphid Aphis gossypii: phylogenetic, structural, and expression profiles analyses","authors":"Tianxing Jing ,&nbsp;Chenyang Li ,&nbsp;Yanjin Zhang ,&nbsp;Peixuan Li ,&nbsp;Jin Yang ,&nbsp;Honghua Su ,&nbsp;Shuai Zhang","doi":"10.1016/j.cbd.2025.101583","DOIUrl":"10.1016/j.cbd.2025.101583","url":null,"abstract":"<div><div>The cotton aphid, <em>Aphis gossypii</em>, belonging to Hemiptera Aphididae is a worldwide pest on various plants. This pest is particularly notorious for its high tolerance to both temperature and insecticides. Heat shock proteins (HSPs), which have been recognized as molecular chaperones, play pivotal roles in the response of insects to environmental stress. However, information on <em>HSP</em> genes in <em>A. gossypii</em> and their expression response remain limited. In this study, 50 <em>HSP</em> genes were identified in the <em>A. gossypii</em> genome, including 3 <em>HSP90s</em>, 15 <em>HSP70s</em>, 11 <em>HSP60s</em>, 19 <em>HSP40s</em> and 2 <em>sHSPs</em>. Phylogenetic analysis strongly supported the family classification of <em>A. gossypii HSP</em> genes. All of the <em>AgHSPs</em> were distributed across four chromosomes, and several gene duplication events were observed. Transcriptome data revealed that most <em>AgHSPs</em> could be induced by short-term high temperature treatment. Conversely, most <em>HSPs</em> decreased their transcription levels under long-term high temperature exposure. Notably, three <em>HSPs</em> (<em>AgHSP40-9-X2, AgHSP40-15</em> and <em>AgHSP70-8</em>) were consistently up-regulated after insecticide exposure in both susceptible and resistant populations. Moreover, the expressions of <em>HSPs</em> across several morphs of aphids were systematically evaluated for the first time. Our findings provide fundamental data for future studies and enhance our understanding of the roles of <em>HSPs</em> in environmental stress adaptation in <em>A. gossypii</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101583"},"PeriodicalIF":2.2,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144679448","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 characterization of three main ganglia in Patinopecten yessoensis provides novel insights into a monophyletic origin of the bilaterian central nervous system","authors":"Xianhui Ning ,&nbsp;Xiangchao Zhang ,&nbsp;Xue Li ,&nbsp;Jing Wang ,&nbsp;Lingling Zhang ,&nbsp;Xiaoli Hu ,&nbsp;Zhenmin Bao","doi":"10.1016/j.cbd.2025.101585","DOIUrl":"10.1016/j.cbd.2025.101585","url":null,"abstract":"<div><div>The question of whether the central nervous system (CNS) of bilaterians arose independently or has a monophyletic origin has been hotly debated. Increasing evidence supports the monophyletic origin of CNS across the three major bilaterian groups. However, in Mollusca, the second largest animal phylum, evolutional information of CNS was mainly obtained from cephalopods, of which the ganglionated cephalic neural system is under controversy to be homolog to vertebrate brain. Yesso scallop (<em>Patinopecten yessoensis</em>), a bivalve mollusk stands out with its slow-evolving genome and differential preservation of ganglia fusion trace. Here, we systematically analyzed the transcriptome of three main ganglia in Yesso scallop. We identified a ganglia-related module using gene co-expression network, and discovered the expansion of neurotransmitter receptors and hypothalamic hormone receptors, suggesting a complex CNS in scallops than we thought. Our analysis revealed predominant expression of expanded hypothalamic hormone receptors in ganglia. Furthermore, the repertoire of fundamental markers for vertebrate pituitary development was largely conserved in scallop ganglia, suggesting a shared evolutionary origin of the pituitary. Our investigation of specific ganglia characteristics demonstrated that ganglia fusion promotes both structural and functional complexity. Particularly, gene-set enrichment analysis (GSEA) demonstrated that gene sets of vertebrate pituitary or brain development are enriched by genes expressed in scallop ganglia, indicating the homolog between ganglionated neural system and vertebrate brain, which supporting the monophyletic origin of brain. Our findings provide new evidences to understand the monophyletic origin of the brain and pituitary in bilaterians.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101585"},"PeriodicalIF":2.2,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144680008","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":"Biochemistry and metabolomics revealed the regulation mechanism of osmolality in Sinonovacula constricta under salinity stress","authors":"Sudong Xia ,&nbsp;Jianing Yu ,&nbsp;Yusong Geng ,&nbsp;Huaying Zhang ,&nbsp;Zheying Gao ,&nbsp;Zhihong Liu ,&nbsp;Biao Wu","doi":"10.1016/j.cbd.2025.101578","DOIUrl":"10.1016/j.cbd.2025.101578","url":null,"abstract":"<div><div>Salinity is a critical environmental factor that significantly influences the growth, development, survival, and reproduction of marine organisms. <em>Sinonovacula constricta</em>, an economically important bivalve in tidal flat and pond aquaculture, frequently encounters acute salinity fluctuations due to factors such as river runoff and precipitation. These abrupt changes in salinity can adversely affect its yield. However, the impacts of acute salinity stress on the osmolality and metabolic processes of <em>S. constricta</em> remain poorly understood. Therefore, this study investigates the impacts of acute salinity stress on hemolymph osmotic pressure, serum ion concentrations, and serum metabolites of <em>S. constricta</em> maintained at a salinity of 18 ppt to 22 ppt. Significant alterations in serum osmolality were observed (<em>P</em> &lt; 0.05), closely resembling seawater osmolality. The concentrations of Na⁺, K⁺, and Cl⁻ in serum also exhibited significant changes (<em>P</em> &lt; 0.05), stabilizing after 12 h, which is consistent with the trends in osmotic pressure. Metabolomics analysis identified differential metabolites primarily involved in phospholipid metabolism, carboxylic acid metabolism, and amino acid metabolism, indicating the activation of ion channels and energy metabolism pathways. <em>S. constricta</em> combats osmotic stress via coordinated ion channel regulation, neural-related metabolites，and amino acid catabolism, maintaining energy homeostasis through metabolic reprogramming. Specifically, <em>S. constricta</em> overcomes osmotic stress through ions (Na⁺, K⁺, Cl⁻) and key metabolites (e.g., glycerophosphate, taurine, proline, arachidonic acid), reveals novel signaling metabolites, highlighting the significant role of biomacromolecules and metabolites in assessing the health of bivalves in aquaculture.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101578"},"PeriodicalIF":2.2,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144633822","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":"A timecourse analysis of gonadal histology and transcriptome during the sexual development of yellow catfish, Pelteobagrus fulvidraco","authors":"Haijing Xu ,&nbsp;Wenkai Lin ,&nbsp;Xinlan Ma ,&nbsp;Muhammad Jawad ,&nbsp;Mengzhou Wu ,&nbsp;Junqiang Qiu ,&nbsp;Mingyou Li","doi":"10.1016/j.cbd.2025.101576","DOIUrl":"10.1016/j.cbd.2025.101576","url":null,"abstract":"<div><div>Yellow catfish (<em>Pelteobagrus fulvidraco</em>), as an important aquatic species, exhibiting pronounced sexually dimorphic growth patterns. However, the molecular mechanism underlying sexual differentiation in yellow catfish remains a mystery. In this study, we performed histological analysis to identify the critical period of gonadal sex differentiation in <em>P. fulvidraco</em>, Our results showed that the differentiation of male and female gonads did not occur synchronously. The ovarian cavities formation in female occurred at 7 days post-hatching (DPH), followed by the emergence of primordial glandular cells at 25 DPH, whereas male gonadal differentiation initiated later, at 35 DPH. Pseudotemporal analysis was used to infer the developmental trajectories of male and female yellow catfish, highlighting rapid differentiation of individual traits from 7 DPH to 30 DPH. Additionally, timecourse comparative transcriptomic analysis identified several female biased genes, including <em>Foxl2a</em>, <em>Foxl2b</em>, <em>Cyp19a1</em>, <em>zar1l</em>, <em>Rbpms2</em>, as well as chromosomal-structure related genes such as <em>Banf2</em>, <em>npm</em>, <em>Top1b</em>, and <em>H2AA</em>, suggesting a female specific differentiation pattern and ovarian development bias following maturation. In contrast, male-biased genes such as <em>dmrt1</em> show similar expression patterns in both sexes during the early stage of differentiation, but become male-specific in mature gonads, indicating a regulatory shift from post-transcriptional to expression regulation during sex differentiation. <em>In situ</em> hybridization analysis further confirms the localization of <em>Foxl2a</em> and <em>Foxl2b</em> in early-stage oocytes, and <em>Top1b</em> in early germ cells of mature gonads. This study systematically investigated the early gonadal differentiation process and provided fundamental data for future research on sex determination regulation mechanism in yellow catfish. These findings also offer valuable insight for industrial applications, including single-sex breeding and regulation of ovarian development in <em>Pelteobagrus fulvidraco</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101576"},"PeriodicalIF":2.2,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144614707","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":"Microgeographic variation in gene expression plasticity under osmotic stress in wild eastern oyster juveniles (Crassostrea virginica)","authors":"Avi Simon ,&nbsp;Harmony Borchardt-Wier ,&nbsp;Emily Manuel ,&nbsp;Daphne Munroe ,&nbsp;Matthew P. Hare","doi":"10.1016/j.cbd.2025.101577","DOIUrl":"10.1016/j.cbd.2025.101577","url":null,"abstract":"<div><div>Gene expression plasticity is an essential mechanism of physiological acclimation. In adult eastern oysters, <em>Crassostrea virginica</em> (Gmelin, 1791), transcriptomic responses to experimental osmotic stress differ between oyster bed sources within the estuarine salinity gradient. Here RNA-seq was used to characterize spatial variation in gene expression plasticity in wild oyster spat (juveniles), collected from upper and lower Delaware Bay oyster beds, and reciprocally exposed to moderate and low salinity experimental treatments. Low salinity conditions contribute significantly to mortality in the species and stressful upper bay episodes of extended hypo-salinity are expected to increase in frequency under future climate conditions. The spat collected at moderate salinity (lower bay) sites show more than twice as many differentially expressed transcripts between treatments, relative to their upper bay counterparts – a pattern of spatial variation in gene expression plasticity consistent with previous findings in adults. However, an alternate measure of gene expression plasticity, the log-fold degree of expression difference between treatments, was greater in oysters collected at low salinity (upper bay). Observed spatial differences in gene expression plasticity indicate that early pre- or post-settlement environmental conditions likely generated distinct transcriptome-wide osmotic stress responses between upper and lower bay populations of a single estuary.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101577"},"PeriodicalIF":2.2,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144631705","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 and characterization of IGF/IGFR/IGFBP gene families in spotted sea bass and their expression profiles in response to environmental stress","authors":"Chong Zhang ,&nbsp;Xinlin Yang ,&nbsp;Yonghang Zhang ,&nbsp;Shaosen Yang ,&nbsp;Cong Liu ,&nbsp;Pengyu Li ,&nbsp;Lingyu Wang ,&nbsp;Xin Qi ,&nbsp;Kaiqiang Zhang ,&nbsp;Haishen Wen ,&nbsp;Yun Li","doi":"10.1016/j.cbd.2025.101575","DOIUrl":"10.1016/j.cbd.2025.101575","url":null,"abstract":"<div><div>Insulin-like growth factor (IGF) signaling pathway constitutes an ancient regulatory network essential for neuroendocrine functions, significantly influencing developmental processes, reproductive activities, and adaptation to environmental challenges. In this study, we detected 3 <em>IGF</em> genes, 3 <em>IGFR</em> genes and 11 <em>IGFBP</em> genes in spotted sea bass genome. The annotation accuracy and evolutionary conservation of identified genes were confirmed through phylogenetic, syntenic and copy number analyses. Molecular basis of gene functions, and protein interaction relationships were investigated by gene structure and protein-protein interaction (PPI) network analyses. Moreover, selective pressure analysis revealed that most genes primarily underwent purifying selection during evolution. Furthermore, RNA-Seq datasets were utilized to analyze tissue expression profiling for <em>IGF</em>/<em>IGFR</em>/<em>IGFBP</em> genes, along with documentation of their environmental stress-responsive transcriptional dynamics in targeted tissues. Our results demonstrated that <em>IGF</em>/<em>IGFR</em>/<em>IGFBP</em> genes were widely expressed in different tissues, with several genes exhibiting high expression levels in specific tissues. Additionally, the stress response mechanisms of IGF signaling system mainly involve IGFs functions regulated by IGFBPs and IGF-independent functions of IGFBPs. Notably, <em>igf1</em>, <em>igf2</em>, <em>igfbp1a</em>, <em>igfbp3b</em> and <em>igfbp4</em> were pinpointed as key functional genes of environmental challenge adaptation in this species. This investigation provides foundational insights into the <em>IGF</em>/<em>IGFR</em>/<em>IGFBP</em> gene families in spotted sea bass, delivering the first comprehensive genomic resource for these gene families while clarifying their functional contributions to environmental stress adaptation.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101575"},"PeriodicalIF":2.2,"publicationDate":"2025-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144580916","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":"Genomic resources and transcriptomic evidence of thermal stress in the southern saucer scallop (Ylistrum balloti)","authors":"Sharon E. Hook ,&nbsp;Alistair J. Hobday ,&nbsp;Ryan J. Farr ,&nbsp;Jenny Su ,&nbsp;Leon Court ,&nbsp;Gunjan Pandey ,&nbsp;Rahul V. Rane ,&nbsp;Mervi Kangas ,&nbsp;Michel Bermudes ,&nbsp;Aisling Fontanini ,&nbsp;Thomas Walsh","doi":"10.1016/j.cbd.2025.101571","DOIUrl":"10.1016/j.cbd.2025.101571","url":null,"abstract":"<div><div>Marine heatwaves can lead to mass mortality events, affecting bivalves. The saucer scallop (<em>Ylistrum balloti</em>) is an important commercial species found in Western Australia (WA) and central Queensland. The largest fishery for this species in WA is at Shark Bay, on the central WA coastline. The fishery has been impacted by heatwaves in the recent past and has yet to fully recover. Whether thermal pressures are influencing the fishery's recovery is uncertain, as other factors, including larval advection, could also influence recovery. A functional genomics approach was used to address this uncertainty. Scallops were collected from multiple locations in Shark Bay with different water temperatures and from a small, more southerly fishery adjacent to Perth. A full genome was assembled. The genome contains comparatively few gene copies of heat shock protein 70, an important indicator of thermal stress, particularly from class 12, which has been highly duplicated in other heat tolerant bivalves. Transcriptomic profiles in scallops collected from the different locations were compared, with the greatest differences observed in scallops collected from an area of Shark Bay with the warmest water temperatures. Some transcripts with altered abundance encoded heat shock proteins, proteins involved in macromolecule repair, and those with a primary metabolism role. Although this study is a snapshot of a few individuals at a single time point, it adds to the weight of evidence that extreme heatwave events and climate change impacts the recruitment of this commercially important species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101571"},"PeriodicalIF":2.2,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144614708","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}