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

{"title":"A sex-determining loci in koi carp(Cyprinus carpio) based on whole genome resequencing technology","authors":"Xu Zhuang ,&nbsp;Bin Wen ,&nbsp;Zaizhong Chen","doi":"10.1016/j.cbd.2025.101647","DOIUrl":"10.1016/j.cbd.2025.101647","url":null,"abstract":"<div><div>The recent resolution of the koi carp (<em>Cyprinus carpio</em>) genome framework through high-throughput sequencing has enabled novel insights into sex determination mechanisms. Whole-genome resequencing (WGS) was performed on koi carp, yielding 1,341,975 high-quality SNPs. Integrated analyses, including gene annotation, GO functional classification, and KEGG pathway enrichment, identified four core genes (<em>sox6</em>, <em>wnt7ba</em>, <em>gnrhr4,</em> and <em>mrps30</em>) significantly associated with vertebrate sex-determination pathways. Validation through PCR-RFLP and Sanger sequencing confirmed that SNP3, a sexually dimorphic locus within the exon region of <em>gnrhr4</em>, demonstrated a sex identification accuracy of 100 % (<em>n</em> = 20).This study not only provides a practical molecular marker for sex-controlled breeding but also advances the theoretical understanding of epigenetic regulatory networks underlying sex determination in teleost fishes.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101647"},"PeriodicalIF":2.2,"publicationDate":"2025-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145219275","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":"Investigating the molecular basis of cleptobiosis in eusocial stingless bees (Apidae: Hymenoptera)","authors":"Paulo Cseri Ricardo ,&nbsp;Natalia de Souza Araujo ,&nbsp;Maria Cristina Arias","doi":"10.1016/j.cbd.2025.101645","DOIUrl":"10.1016/j.cbd.2025.101645","url":null,"abstract":"<div><div>Cleptobiosis, the act of raiding other species to obtain food or resources, is widespread among animals but rarely obligatory. The eusocial stingless bee <em>Lestrimelitta limao</em> is one of the few species that depend entirely on cleptobiosis, raiding other stingless bee colonies for survival. To investigate the molecular basis and putative evolutionary adaptations associated with this specialized lifestyle, we compared the transcriptomes of non-raiding foragers of <em>L. limao</em> and of three non-robber stingless bees – <em>Nannotrigona testaceicornis</em>, <em>Scaptotrigona</em> aff. <em>depilis</em>, and <em>Tetragonisca angustula</em>.</div><div>Our analysis revealed that differentially expressed orthologs were predominantly downregulated in <em>L. limao</em> workers, suggesting reduced transcriptional activity during foraging in this species. These downregulated genes fall into three major functional categories potentially linked to cleptobiotic adaptations: (1) detoxification and chemoreception genes, including cytochrome P450s and odorant receptors, indicating decreased exposure to phytochemicals; (2) neuronal and synaptic genes, such as <em>para</em> and <em>Dys</em>, possibly reflecting neurophysiological modifications; and (3) mitochondrial and carbohydrate metabolism genes, suggesting lower energetic demands. These findings provide novel insights into the molecular mechanisms associated with cleptobiotic behavior in eusocial bees.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101645"},"PeriodicalIF":2.2,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145219180","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":"Multi-omics analysis of gut-liver axis reveals the mechanism by which sulforaphane alleviates liver injury in Cyprinus carpio exposed to triphenyltin","authors":"Chunnuan Zhang ,&nbsp;Huajuan Shi ,&nbsp;Bingke Wang ,&nbsp;Jianshuang Ma ,&nbsp;Xiaohui Sun ,&nbsp;Yajuan Liu ,&nbsp;Juan Du","doi":"10.1016/j.cbd.2025.101642","DOIUrl":"10.1016/j.cbd.2025.101642","url":null,"abstract":"<div><div>This study investigates the protective effects of sulforaphane (SFN) against triphenyltin (TPT)-induced hepatotoxicity, immune dysfunction and gut microbiota dysbiosis in <em>Cyprinus carpio</em>. <em>Cyprinus carpio</em> were divided into three groups and exposed for 8 weeks, including control, 10 μg/L TPT and 10 μg/L TPT + 10 mg/kg SFN group. This result showed that TPT exposure induced significantly (<em>P</em> &lt; 0.05) hepatotoxicity, evidenced by increasing hepatic total bile acid (TBA) and total cholesterol levels, while upregulating <em>Hsp70/90</em> and downregulating lysozyme gene expression. SFN supplementation reduced TBA accumulation, normalized <em>Hsp90</em> and <em>lysozyme</em> expression, mitigating TPT-induced lipid dysregulation and immunosuppression. Transcriptomic analysis revealed that TPT exposure activated lipid metabolism pathways (<em>PPAR</em> signaling and cholesterol metabolism), but suppressed immune-related pathways. SFN supplementation restored metabolic homeostasis by enriching glucose and amino acid metabolism pathways and activating AMPK signaling, while also modulating the expression of key genes (<em>PLIN1</em>, <em>ME1</em>, <em>CPT1B</em>). The microbiota composition were changed in SFN + TPT, including the increased of beneficial <em>Fusobacteriota</em> and <em>Cetobacterium</em>, and the decreased of pathogenic <em>Proteobacteria</em> and <em>Aeromonas</em>. The gut transcriptome dysregulation were restored in SFN + TPT by enhancing immune pathways in Toll-like/NOD-like receptors. The significant correlations linked were found in gut microbes (<em>Kaistia</em>, <em>Vagococcus</em>) to hepatic/intestinal gene expression in SFN + TPT. Overall, these findings elucidate novel mechanisms underlying TPT-induced immunotoxicity in liver and intestine and demonstrate the protective role of SFN, providing a theoretical foundation for its application in toxicity mitigation strategies.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101642"},"PeriodicalIF":2.2,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145202305","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":"Refeeding effects on physiological functions and gut microbiota composition in starved red swamp crayfish (Procambarus clarkii)","authors":"Xuhong Yang ,&nbsp;Ruijie Guo ,&nbsp;Kai Huang ,&nbsp;Shisong Jiang ,&nbsp;Yuxiao Luo ,&nbsp;Xiaohua Tang ,&nbsp;Kai Yu","doi":"10.1016/j.cbd.2025.101640","DOIUrl":"10.1016/j.cbd.2025.101640","url":null,"abstract":"<div><div>This study investigated the effects of starvation and refeeding on physiological responses and gut microbiota composition in <em>Procambarus clarkii</em>. Four treatment groups were established: a regular feeding group (RF), a 6-day starvation followed by 6-day refeeding group (SF6), a 12-day starvation followed by 12-day refeeding group (SF12), and a continuous starvation group (NS). A total of 360 healthy juvenile crayfish with intact appendages and uniform body size (mean weight: 9.25 ± 0.05 g) were randomly allocated to the four groups, with three replicates per group and 30 individuals per replicate. The feeding trial lasted 24 days. Starvation followed by refeeding significantly improved growth performance, restored physiological functions, and enhanced digestive capacity. Starvation increased body moisture and ash content, while decreasing crude protein and lipid levels. Energy utilization during starvation followed a sequential depletion of glycogen, lipids, and proteins. Elevated SOD activity post-starvation indicated enhanced antioxidative defense against reactive oxygen species and lipid peroxidation. Moreover, starvation markedly upregulated the expression of <em>TGF-β</em> and <em>Mstn</em>, while refeeding—particularly in the SF6 group—led to higher expression levels of <em>ACTL</em>, <em>TNT</em>, <em>Myhb</em>, and <em>MLC</em>. Histological analysis revealed that starvation induced degeneration of intestinal villi, thinning of intestinal walls, and atrophy of R-cells in the hepatopancreas. 16S rRNA gene sequencing showed that starvation significantly reduced gut microbial diversity and richness, increased the relative abundance of Bacteroidota, <em>Shewanella</em>, and <em>Citrobacter</em>, and decreased the Firmicutes/Bacteroidota (F/B) ratio. In contrast, refeeding reversed these changes, enriching the microbiota with Firmicutes, <em>Erysipelotrichaceae</em>, <em>Dysgonomonas</em>, and <em>Rhodobacter</em>. In conclusion, starvation imposed significant physiological and microbial alterations in <em>P. clarkii</em>, including impaired growth traits and increased abundance of potentially pathogenic bacteria. However, refeeding effectively mitigated these effects, demonstrating the resilience of <em>P. clarkii</em> to nutritional stress.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101640"},"PeriodicalIF":2.2,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145157161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated application of transcriptomics and metabolomics provides insights into sexual dimorphism in Apostichopus japonicus","authors":"Jingjing Cong ,&nbsp;Abudula Abulizi ,&nbsp;Yue Li ,&nbsp;Rui Gao ,&nbsp;Zhihui Sun ,&nbsp;Yaqing Chang","doi":"10.1016/j.cbd.2025.101643","DOIUrl":"10.1016/j.cbd.2025.101643","url":null,"abstract":"<div><div>Sea cucumber (<em>Apostichopus japonicus</em>) is a commercially important aquaculture species in China. Research findings have indicated that adult male sea cucumbers with differentiated gonads have a greater growth advantage compared to females. Understanding the molecular basis of sexual dimorphism in <em>A. japonicus</em> is critical for developing sex control breeding strategies in aquaculture. In this study, we integrated transcriptomic and metabolomic analyses of testes and ovaries to elucidate differences in gene expression and metabolite profiles. Key sex-biased genes, including <em>cyp2</em> subfamily members, <em>cpeb1</em>, and <em>sult1e1</em>, were predominantly expressed in the ovaries, whereas <em>sac</em> and <em>catsper4</em> showed specific expression in the testes, suggesting their potential roles in sex development. Moreover, compared to the ovaries, the testes exhibited significantly higher expression of immune-related genes (<em>myosin-9</em>, <em>formin-like</em>, and <em>vwde</em>), along with greater abundance of metabolites such as astaxanthin and ferulate, suggesting that males may possess stronger immune capacity than females. Higher expression levels of <em>ugts</em> in differentiated ovaries compared to testes suggest that female gonads may possess greater nutritional value due to their role in saponin biosynthesis. Additionally, pathway enrichment analyses revealed that ovaries exhibited enhanced carbon metabolism, amino acid biosynthesis, and purine and pyrimidine metabolism, suggesting that the higher energy demands of oogenesis compared to spermatogenesis may contribute to sexual dimorphism in growth. These findings provide novel insights into sex-biased metabolic and regulatory mechanisms and lay a foundation for future studies aimed at elucidating the regulatory mechanisms of gonadal development in sea cucumbers.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101643"},"PeriodicalIF":2.2,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145219276","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 analysis of the PLP_deC genes involved in taurine synthesis in bivalves","authors":"Meiqian Pang ,&nbsp;Haigang Qi ,&nbsp;Min Wang ,&nbsp;Mingyang Du ,&nbsp;Jincheng Chen ,&nbsp;Rihao Cong ,&nbsp;Li Li ,&nbsp;Guofan Zhang","doi":"10.1016/j.cbd.2025.101641","DOIUrl":"10.1016/j.cbd.2025.101641","url":null,"abstract":"<div><div>Bivalves, such as oysters and scallops, are rich in taurine and play crucial roles in marine ecosystems as well as in aquaculture. However, mechanisms governing the taurine biosynthesis in bivalves remain poorly understood. Cysteine sulfinic acid decarboxylase (CSAD) and glutamate decarboxylase-like 1 (GADL1), as members of pyridoxal phosphate-dependent decarboxylase (PLP_deC) family, catalyze the decarboxylation step in taurine synthesis. To investigate their evolution and function in bivalves, a genome-wide identification of these genes was conducted in five bivalve species. A total of 61 <em>PLP_deC</em> genes were identified, of which 23 were predicted to be involved in taurine synthesis. Phylogenetic analysis revealed that these genes cluster into two distinct groups: CSAD/GADL1-like and GAD-like. Notably, bivalves possess only one <em>Gad</em> gene, in contrast to the two typically found in vertebrates, whereas they harbor three to five <em>Csad/Gadl1</em> genes, compared with just two in vertebrates. Three bivalve <em>Csad</em> genes exhibited high expression levels across most of developmental stages and adult tissues, suggesting their essential roles in development and the maintenance of normal physiological activities. Molecular docking analysis revealed that oyster CSADs exhibit higher substrate-binding specificity for cysteine sulfinic acid, while GAD shows higher specificity for glutamate. Heterologous overexpression assays demonstrated that oyster CSAD and GAD can significantly increase cellular taurine levels. This study is the first to provide evidence of the expansion of <em>Csad</em> genes in bivalve genomes and their involvement in taurine synthesis, offering novel insights into understanding the molecular mechanisms underlying the high taurine content in bivalves.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101641"},"PeriodicalIF":2.2,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145152220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of the SR gene family in Procambarus clarkii and their expression responses to Vibrio parahaemolyticus under non-lethal heat shock","authors":"Zhangxuan Chen ,&nbsp;Xiuhong Cai ,&nbsp;Shirui Yue ,&nbsp;Shunchang Wang ,&nbsp;Xin Zhang","doi":"10.1016/j.cbd.2025.101638","DOIUrl":"10.1016/j.cbd.2025.101638","url":null,"abstract":"<div><div>Scavenger receptors (SRs) are key pattern-recognition receptors in immunity, with SRCR domain-containing members (SRCRs) playing vital roles. This study systematically analyzed <em>SRCR</em> genes in <em>Procambarus clarkii</em> via genome-wide screening and identified six family members. These genes exhibit diverse molecular characteristics, with their encoded proteins varying in length (535–2970 aa), molecular weight (60.13–333.02 kDa), and stability (mostly unstable). Structural analysis revealed diverse gene structures, conserved SRCR domains, and an even distribution across six chromosomes, with <em>Loxl2</em> showing evolutionary conservation with <em>Eriocheir sinensis</em>. Tissue-specific expression analysis by qPCR indicated high expression in hemocytes (immune relevance), gills (<em>Loxl2</em>, pathogen response), hepatopancreas (metabolism/detoxification), and intestine (<em>LOC123759426</em>, intestinal immunity). After non-lethal heat shock (NLHS) and bacterial challenge, LOC123770744 and LOC123759426 showed significant expression changes, indicating roles in stress responses, while the other genes exhibited varying degrees of differential expression. This study clarifies the characteristics and potential immune roles of SRCRs in <em>P. clarkii</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101638"},"PeriodicalIF":2.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145108769","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, docking and expression analysis of ATP-binding cassette gene family of Parnara guttata, a major rice pest (Insecta: Lepidoptera: Hesperiidae)","authors":"Xuan Zhang ,&nbsp;Mengfei Yi ,&nbsp;Yongliang Fan ,&nbsp;Yiping Li ,&nbsp;Xiangqun Yuan","doi":"10.1016/j.cbd.2025.101635","DOIUrl":"10.1016/j.cbd.2025.101635","url":null,"abstract":"<div><div>ATP-binding cassette (ABC) transporter family, is one of the largest and most ancient classes of transmembrane protein. Rice skipper, <em>Parnara guttata</em>, is a major rice pest distributed across China, Japan, and South Korea, and damages rice crop by rolling leaves into shelters, resulting in complicated pest control efforts. In this study, we performed genome-wide identification, docking and expression analysis of ABC transporters in <em>P. guttata</em>, and identified 47 ABC transporter genes. Phylogenetic analysis classified these genes into eight subfamilies (ABCA-H). Molecular docking revealed that transporters with the strongest binding affinities for <em>Bt</em> toxin Cry1Ac and chemical pesticides (cypermethrin, imidacloprid, malathion) predominantly belonged to the ABCC and ABCG subfamilies, suggesting these as potential pesticide targets. Transcriptomic data showed that all ABCD, ABCE, and ABCF genes were highly expressed in larval midguts, while other subfamilies exhibited partial high expression. These findings provide critical insights for toxicological studies and evolutionary analyses of ABC transporters in invertebrates.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101635"},"PeriodicalIF":2.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145108770","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 sequencing reveals the molecular mechanisms of early malformations in the critically endangered Sichuan taimen (Hucho bleekeri)","authors":"Yeyu Chen ,&nbsp;Hua Li ,&nbsp;Qinyao Wei ,&nbsp;Guiliang Liu ,&nbsp;Zhao Liu ,&nbsp;Xiaoyun Wu ,&nbsp;Yanling Chen ,&nbsp;Yi Yu ,&nbsp;Quanyu Tu ,&nbsp;Huanchao Yang","doi":"10.1016/j.cbd.2025.101639","DOIUrl":"10.1016/j.cbd.2025.101639","url":null,"abstract":"<div><div><em>Hucho bleekeri</em> is a Class I protected species in China. In recent years, very few records of wild <em>H. bleekeri</em> have been documented. Therefore, artificial breeding has become the last resort to protect this species. However, during the larvae cultivation phase, a large number of individuals exhibit abnormal morphology, which constitute the majority of dead larvae. In this study, we conducted transcriptome sequencing on normal and malformed fish at three distinct developmental stages: 4 days post-hatching (dph), 15 dph, and 31 dph, and explored the expression patterns of key differentially expressed genes (DEGs) associated with skeletal development. Transcriptomic sequencing identified a total of 3024, 2678, and 7088 DEGs in the control versus malformed groups at 4 dph, 15 dph, and 31 dph, respectively. Gene Set Enrichment Analysis showed that cell development, regulation of cytoskeleton organization, TGF-β signaling pathway, and Wnt signaling pathway, had relatively high enrichment scores. Genes involved in skeletal development, including <em>shh</em>, <em>daam1</em>, <em>osteonectin</em>, <em>twist1</em>, <em>osteocalcin</em>, <em>col1a1</em>, <em>myod</em>, and <em>hox3</em>, were significantly down-regulated in malformed fish, while <em>mmp13</em> and <em>TGFβ</em> were significantly up-regulated. Notably, key genes in the Hedgehog signaling pathway were all inhibited in the malformed groups, indicating their crucial roles in the normal skeletal development of <em>H. bleekeri</em>. This study enhances our understanding of the underlying mechanisms of skeletal regulation in fish and may help reduce the incidence of malformations in <em>H. bleekeri</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101639"},"PeriodicalIF":2.2,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145104356","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 for identifying genes involved in reproduction of banana shrimp (Penaeus merguiensis)","authors":"Phimsucha Bunphimpapha ,&nbsp;Premruethai Supungul ,&nbsp;Sureerat Tang ,&nbsp;Kittanasan Inbumrung ,&nbsp;Sirawut Klinbunga","doi":"10.1016/j.cbd.2025.101637","DOIUrl":"10.1016/j.cbd.2025.101637","url":null,"abstract":"<div><div>Characterization of reproduction-related genes is crucial for comprehending molecular mechanisms involved in ovarian development of banana shrimp (<em>Penaeus merguiensis</em>). Here, genes expressed in different ovarian (immature, vitellogenic and mature) stages were characterized by RNA-Seq. In total, 12 libraries were established and 88.56 Gb (6.91–8.04 Gb/sample) clean data were obtained for overall samples. The Q30 values were between 94.14 and 94.86 %. The N50 values were 2763 bp for transcripts and 2536 bp for unigenes. A total of 2208 differentially expressed genes (DEGs) were identified, comprising 1203 up-regulated and 1005 down-regulated genes. Identified genes were annotated and functionally categorized. DEGs in protein synthesis, metabolism and biogenesis levels were abundant suggested that the development of immature ovaries to further stages requires energy and nutrient accumulation. Expression of DEGs in Cellular process, Environmental information processing, Genetic information processing, and Metabolism in immature ovaries increased in vitellogenic ovaries and decreased in mature ovaries. This reflects the rapid accumulation of various proteins during the vitellogenic stage. The identified DEGs in mature ovaries suggest that signal transduction pathways are crucial during the final ovarian maturation of <em>P. merguiensis</em>. Gene expression was further analyzed by qRT-PCR. <em>PmMknk1</em>, <em>PmTtc3</em> and <em>PmSult1C4</em> were upregulated in vitellogenic and mature ovaries (<em>P</em> &lt; 0.05). In addition, <em>PmCcnF</em>, <em>PmBmp2</em>, <em>PmFoxA1</em>, <em>PmChst5</em> and <em>PmVtg</em> were upregulated in mature ovaries (<em>P</em> &lt; 0.05). This suggested their important role in ovarian development and maturation. The information is crucial for further studies on reproductive maturation of <em>P. merguiensis</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"56 ","pages":"Article 101637"},"PeriodicalIF":2.2,"publicationDate":"2025-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145104348","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}