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De novo Genome Assembly, Annotation, and Comparative Analysis of the Lined Sole Achirus lineatus as a Resource for Evolutionary and Environmental Genomics 作为进化和环境基因组资源的线形鳎基因组组装、注释和比较分析。
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-30 DOI: 10.1007/s10126-026-10665-8
Mercedes Quintanilla-Mena, Elsa B. Góngora-Castillo, Rossanna Rodriguez-Canul, Rafael Rivera-Bustamante
{"title":"De novo Genome Assembly, Annotation, and Comparative Analysis of the Lined Sole Achirus lineatus as a Resource for Evolutionary and Environmental Genomics","authors":"Mercedes Quintanilla-Mena,&nbsp;Elsa B. Góngora-Castillo,&nbsp;Rossanna Rodriguez-Canul,&nbsp;Rafael Rivera-Bustamante","doi":"10.1007/s10126-026-10665-8","DOIUrl":"10.1007/s10126-026-10665-8","url":null,"abstract":"<div><p>The lined sole, <i>Achirus lineatus</i>, is a widely distributed species in the Gulf of Mexico. This basin is constantly exposed to hydrocarbon contamination due to natural oil seeps, oil extraction and oil spills. Previous studies suggest the line sole <i>A. lineatus</i> as a possible sentinel species for oil spills; but the overall landscape of xenobiotic metabolism in this species remains poorly understood. Access to high-quality reference genomes will improve this situation. Here, we report the first whole-genome sequence, assembly, and annotation of the lined sole <i>A. lineatus</i>. We generated 132 Gb of PacBio High-Fidelity (HiFi) reads, which were filtered to retain 93 Gb of ultra-high-quality data. The assembly resulted in a mitogenome of 16,579 bp and a nuclear genome of 486.3 Mb distributed across 199 contigs, with a contig N50 of 9.87 Mb. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis based on the <i>actinopterygii</i>_odb10 database (3,640 orthologs) identified 3,611 (99.2%) complete BUSCOs. Genome annotation strategy resulted in the identification of 22,412 protein-coding genes with a high percentage (95.94%) of functional annotation. The genome of <i>A. lineatus</i> revealed 693 expanded and 3349 contracted gene families. We also identified 123 genes involved in the xenobiotics biodegradation and metabolism pathways, as well as neuroplasticity-related genes that may be associated with responses to environmental toxicants, providing baseline genomic information that suggests an integrated adaptive strategy involving both metabolic and nervous system processes. This assembly represents a valuable genomic resource for future toxicological and ecological studies of this species.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 4","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10126-026-10665-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148350249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Proteomic and Small RNA Characterization of Extracellular Vesicle-enriched Particles Released from Cultured Host-isolated Symbiodiniaceae 共生菌科细胞外囊泡富集颗粒的蛋白质组学和小RNA表征。
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-29 DOI: 10.1007/s10126-026-10661-y
Tzu–Yuan Sung, Pei-Chi Shih, Bonien Chen, Ming–Chang Hong
{"title":"Proteomic and Small RNA Characterization of Extracellular Vesicle-enriched Particles Released from Cultured Host-isolated Symbiodiniaceae","authors":"Tzu–Yuan Sung,&nbsp;Pei-Chi Shih,&nbsp;Bonien Chen,&nbsp;Ming–Chang Hong","doi":"10.1007/s10126-026-10661-y","DOIUrl":"10.1007/s10126-026-10661-y","url":null,"abstract":"<div><p>Extracellular vesicles and EV-enriched extracellular particles are increasingly recognized as potential mediators of intercellular communication. In coral reef ecosystems, dinoflagellate symbionts of the family Symbiodiniaceae play central roles in host metabolism, environmental acclimation, and stress responses; however, the molecular composition of extracellular particles released by cultured Symbiodiniaceae remains poorly understood. In this study, a host-isolated Symbiodiniaceae culture derived from the sea anemone <i>Exaiptasia diaphana</i> was established under host-free laboratory conditions for EV-enriched particle isolation and characterization. Physicochemical analysis of the recovered extracellular particle fraction showed an average diameter of 534.1 ± 63.9 nm, a polydispersity index of 0.733 ± 0.08, and an average zeta potential of − 14.57 ± 1.55 mV, indicating a heterogeneous and negatively charged extracellular particle suspension. Small RNA analysis showed that the EV-associated RNA fraction contained multiple RNA biotypes, with rRNA- and tRNA-derived reads representing the dominant annotated components, whereas miRNA-like sequences accounted for only a minor fraction of the annotated small RNA pool. Comparison against an antisense <i>Exaiptasia diaphana</i> CDS dataset further identified retained EV-associated small RNAs showing sequence complementarity to host coding transcripts, including cytohesin-1 and EPG5. These matches are interpreted as candidate sequence-level observations rather than evidence of functional host regulation. In parallel, miRNA-oriented analysis identified candidate miRNA-like sequences after downstream filtering. Proteomic profiling by LC–MS/MS generated 4,086 accession-level matches. After removal of uninformative entries and consolidation of duplicate protein names, 834 non-redundant named proteins were retained and classified into nine functional groups, including proteins involved in metabolism and energy production, transport and membrane trafficking, photosynthesis and chloroplast function, and signal transduction and regulation. Representative annotations included 14-3-3-related proteins, Rab/ARF family proteins, Hsp70, Hsp90, and oxygen-evolving enhancer protein. These results provide an initial qualitative molecular characterization of EV-associated molecules released by a host-isolated Symbiodiniaceae culture and serve as a baseline for future studies of algal extracellular communication and cnidarian–dinoflagellate symbiosis.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 4","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148343632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Exosome-Secreted Tropomyosin and Gigasin-6 Roles in Biomineralization Divergence Between Estuarine and Coastal Oysters 外泌体分泌的原肌球蛋白和Gigasin-6在河口和海岸牡蛎生物矿化分化中的作用。
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-23 DOI: 10.1007/s10126-026-10658-7
Qi Yang, Shentong Wang, Wei Wang, Guofan Zhang, Li Li
{"title":"Exosome-Secreted Tropomyosin and Gigasin-6 Roles in Biomineralization Divergence Between Estuarine and Coastal Oysters","authors":"Qi Yang,&nbsp;Shentong Wang,&nbsp;Wei Wang,&nbsp;Guofan Zhang,&nbsp;Li Li","doi":"10.1007/s10126-026-10658-7","DOIUrl":"10.1007/s10126-026-10658-7","url":null,"abstract":"<div><p>Biomineralization in mollusks, a fundamental process in marine ecosystems, is highly sensitive to anthropogenic stressors. Exosome-secreted species-specific shell matrix proteins (SMPs) are essential in biomineralization adaptation but remain understudied. Estuaries are considered unfavorable for biomineralization compared to open coastal zones and serve as an ideal research location to explore the roles of exosome-secreted species-specific SMPs in biomineralization adaptation under future rapid environmental change. Here, combining proteomics of shell matrix and mantle-derived exosomes, the high-abundance species-specific SMPs <i>Car-TPM</i> (tropomyosin from estuarine oyster <i>Crassostrea ariakensis</i>) and <i>Cgi-GIGA6</i> (gigasin-6 from coastal oyster <i>Crassostrea gigas</i>) were taken as representatives to decipher the roles of exosome-secreted species-specific SMPs in oyster biomineralization adaptation. Tissue expression profiles and in situ hybridization revealed that <i>Car-TPM</i> was highly expressed in the adductor muscle and mantle, while <i>Cgi-GIGA6</i> predominated in the mantle. Post-injury experiments demonstrated that <i>Car-TPM</i> expression upregulated quickly at 6 h, and <i>Cgi-GIGA6</i> continued to be down-regulated. Knockdown of <i>Car-TPM</i> suppressed shell repair, whereas silencing <i>Cgi-GIGA6</i> enhanced it. In vitro assays revealed that <i>Car-TPM</i> significantly promoted calcium carbonate precipitation and aggregation of rhombohedral calcite crystals, whereas <i>Cgi-GIGA6</i> suppressed crystallization and eroded the original flat edges. These findings indicate that <i>Car-TPM</i> is a positive regulator of biomineralization in <i>C. ariakensis</i> inhabiting harsh estuarine environments, while <i>Cgi-GIGA6</i> exerts a negative regulatory effect to optimize energy allocation by restraining excessive biomineralization in <i>C. gigas</i>. This study reveals the essential role of species-specific SMPs secreted via exosomes in the biomineralization adaptation and adaptive potential of mollusks in future marine environments.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 4","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Integrated Environmental and Molecular Mechanisms of Navicula sp. Biofilm Induced Settlement and Metamorphosis in Mizuhopecten yessoensis Larvae Navicula sp.生物膜诱导Mizuhopecten yessoensis幼虫沉降和变态的综合环境和分子机制。
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-16 DOI: 10.1007/s10126-026-10634-1
Xiaoyan Xu, Meirong Du, Zengjie Jiang, Jianfu Lyu, Weiwei Jiang, Jinghan Zhang, Chao Sun, Yitao Zhang, Junwei Wang
{"title":"Integrated Environmental and Molecular Mechanisms of Navicula sp. Biofilm Induced Settlement and Metamorphosis in Mizuhopecten yessoensis Larvae","authors":"Xiaoyan Xu,&nbsp;Meirong Du,&nbsp;Zengjie Jiang,&nbsp;Jianfu Lyu,&nbsp;Weiwei Jiang,&nbsp;Jinghan Zhang,&nbsp;Chao Sun,&nbsp;Yitao Zhang,&nbsp;Junwei Wang","doi":"10.1007/s10126-026-10634-1","DOIUrl":"10.1007/s10126-026-10634-1","url":null,"abstract":"<div><p>Many marine invertebrate larvae are influenced by environmental factors during development, with diatom biofilms playing a crucial role in the settlement and metamorphosis of bivalve larvae. This study found that <i>Navicula</i> sp. biofilms alter the larval microenvironment by increasing dissolved oxygen levels through photosynthesis and decreasing nitrate, ammonium, and phosphate levels in the surrounding water. Exposure to Navicula sp. biofilms induced directional swimming in larvae and significantly shortened the time required for settlement and metamorphosis. Biofilms formed by <i>Navicula</i> sp. contained effective substances and key infochemicals that promoted the settlement and metamorphosis of <i>Mizuhopecten yessoensis</i> larvae. Soluble polysaccharides containing β-1,4-glycosidic bonds secreted by the biofilm were recognized by the larvae, triggering settlement and metamorphosis signaling. Untargeted and targeted metabolomic analyses revealed increased levels of cGMP (Cyclic guanosine monophosphate), and GMP (Guanosine monophosphate), suggesting that larval settlement and metamorphosis may be associated with cGMP regulation. Based on these results, cGMP was selected for subsequent functional analyses. Treatments with the NO donor SNAP, the cGMP analog 8-Br-cGMP, and the sGC activator BAY 41-2272 significantly promoted metamorphosis, whereas the sGC inhibitor ODQ suppressed metamorphosis in a dose-dependent manner. These findings demonstrate that the NO–sGC–cGMP pathway positively regulates the settlement and metamorphosis of <i>M. yessoensis</i> larvae, with cGMP serving as a key effector. This study provides new insights into the mechanisms underlying larval settlement and metamorphosis in bivalves.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 4","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148256709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Network Clustering Approach Reveals Key Proteins and Biological Functions in the Response of Whiteleg Shrimp (Penaeus vannamei) to Acute Hepatopancreatic Necrosis Disease 网络聚类方法揭示凡纳滨对虾(Penaeus vannamei)对急性肝胰腺坏死病反应的关键蛋白和生物学功能
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-16 DOI: 10.1007/s10126-026-10655-w
Noorul Darlina Edlin Abd Rahim, Khor Waiho, Min Pau Tan, Yeong Yik Sung, Md. Altaf-Ul-Amin, Shigehiko Kanaya, Zeti-Azura Mohamed-Hussein, Nor Afiqah-Aleng
{"title":"Network Clustering Approach Reveals Key Proteins and Biological Functions in the Response of Whiteleg Shrimp (Penaeus vannamei) to Acute Hepatopancreatic Necrosis Disease","authors":"Noorul Darlina Edlin Abd Rahim,&nbsp;Khor Waiho,&nbsp;Min Pau Tan,&nbsp;Yeong Yik Sung,&nbsp;Md. Altaf-Ul-Amin,&nbsp;Shigehiko Kanaya,&nbsp;Zeti-Azura Mohamed-Hussein,&nbsp;Nor Afiqah-Aleng","doi":"10.1007/s10126-026-10655-w","DOIUrl":"10.1007/s10126-026-10655-w","url":null,"abstract":"<div><p>Whiteleg shrimp, <i>Penaeus vannamei</i>, is the most cultured shrimp species worldwide and plays an important role in global aquaculture production, food security, and economic growth. Nonetheless, infectious diseases, including acute hepatopancreatic necrosis disease (AHPND), can severely threaten the sustainability of shrimp production. These impacts may also be exacerbated by climate-related environmental stressors, such as temperature and salinity, which further disrupt host metabolism and immunity. Although many shrimp genes have been reported in AHPND studies, the molecular interactions underlying host responses to this disease remain unclear. Therefore, this study aims to investigate the potential molecular mechanisms of AHPND by identifying sets of interacting proteins and associated biological functions using network clustering. The <i>P. vannamei</i> AHPND-related proteins (<i>Pv</i>AHPNDrp) were identified via bibliomic analysis and used to construct the AHPND protein-protein interaction (PPI) network. The network was clustered using the DPClusO algorithm, and statistically enriched clusters were identified using the <i>Pv</i>AHPNDrp distribution. Functional enrichment analysis was subsequently performed to determine the potential biological functions associated with AHPND mechanisms. The analysis identified significant clusters with interactions of <i>Pv</i>AHPNDrp and non-<i>Pv</i>AHPNDrp, including glutamine-, proline-, and tyrosine-tRNA ligases, and alpha-1,4-N-acetylglucosaminyltransferase. Enriched biological functions, such as aminoacyl-tRNA ligase activity and lipid metabolic process, may be associated with <i>P. vannamei’s</i> response to AHPND. Collectively, this study provides a systems-level perspective on the molecular interaction networks associated with AHPND and identifies candidate proteins and functions for future experimental validation, contributing to improved understanding of disease mechanisms and supporting climate-resilient shrimp health management strategies.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 4","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148256726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Identification of Growth-Related SNPs and Genes Through Genome-Wide Association Studies in Pseudobagrus ussuriensis 通过全基因组关联研究鉴定乌苏里假袋生长相关snp和基因。
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-15 DOI: 10.1007/s10126-026-10656-9
Chuankun Zhu, Jingyuan Zhu, Yu Wang, Chao Lu, Zhishang Ouyang, Zhengjun Pan, Shuchu Li, Yanhong Sun, Guoliang Chang, Haitao Zhao, Lei Zhang, Haiyang Liu
{"title":"Identification of Growth-Related SNPs and Genes Through Genome-Wide Association Studies in Pseudobagrus ussuriensis","authors":"Chuankun Zhu,&nbsp;Jingyuan Zhu,&nbsp;Yu Wang,&nbsp;Chao Lu,&nbsp;Zhishang Ouyang,&nbsp;Zhengjun Pan,&nbsp;Shuchu Li,&nbsp;Yanhong Sun,&nbsp;Guoliang Chang,&nbsp;Haitao Zhao,&nbsp;Lei Zhang,&nbsp;Haiyang Liu","doi":"10.1007/s10126-026-10656-9","DOIUrl":"10.1007/s10126-026-10656-9","url":null,"abstract":"<div><p><i>Pseudobagrus ussuriensis</i> is a widely cultured bagrid fish known for its delicious tastes and high nutrition values in China. As growth performances of this fish significantly declined in recent years, the breeding of new germplasm with excellent growth traits is urgently needed. In the present study, the genome-wide association study (GWAS) method was used to identify genetic sites significantly associated with five growth traits in a population with 183 individuals. A total of 2,408,557 high-quality SNPs were identified across the 26 chromosomes of the genome. Among these, 31 SNPs were found to be significantly associated with growth traits, including 12 SNPs on Chr08, Chr17 and Chr21 associated with body length, 9 SNPs from Chr07, Chr08, Chr16, Chr22 and Chr25 associated with head length, 8 SNPs on Chr03 and Chr08 associated with body weight, and 4 SNPs from Chr03, Chr04, Chr08 and Chr15 associated with condition factor. One SNP, Chr08:20667021, located at the upstream region of the <i>pld1</i> gene, was significantly associated with body length, head length and body weight, and it was also validated using Sanger sequencing in 100 individuals. Within a 50 kb range upstream and downstream of the 31 significant SNPs, 71 candidate genes were identified, with 28 of them being considered as more probable growth-associated candidate genes. The results of this study showed that the majority of growth related SNPs and candidate genes clustered on Chr08, which may be dominant in the process of growth regulation. These findings provide valuable insights into the genetic mechanisms of growth and useful tools for marker-assisted selection breeding in <i>P. ussuriensis</i>.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148248654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Correction to: Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins 修正:fucata Pinctada Shell珍珠的定量蛋白质组学分析定义了基于溶解度的壳基质蛋白类型分类
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-13 DOI: 10.1007/s10126-026-10650-1
Keisuke Oshima, Lumi Negishi, Takashi Atsumi, Hitoshi Atsumi, Michio Kurumizaka
{"title":"Correction to: Quantitative Proteomic Profiling of Pinctada fucata Shell Nacre Defines a Solubility-Based Type Classification of Shell Matrix Proteins","authors":"Keisuke Oshima,&nbsp;Lumi Negishi,&nbsp;Takashi Atsumi,&nbsp;Hitoshi Atsumi,&nbsp;Michio Kurumizaka","doi":"10.1007/s10126-026-10650-1","DOIUrl":"10.1007/s10126-026-10650-1","url":null,"abstract":"","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10126-026-10650-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148237133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic Insights into Genetic Diversity of Coilia nasus Across Wild Ecotypes and Farmed Populations in China 中国野生生态型和养殖群体鼻蝽遗传多样性的基因组学研究
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-13 DOI: 10.1007/s10126-026-10654-x
Jing Fan, Jipeng Zhang, Xiao Liang, Zhizhi Liu, Xianghan Liu, Kai Liu, Dong Liu
{"title":"Genomic Insights into Genetic Diversity of Coilia nasus Across Wild Ecotypes and Farmed Populations in China","authors":"Jing Fan,&nbsp;Jipeng Zhang,&nbsp;Xiao Liang,&nbsp;Zhizhi Liu,&nbsp;Xianghan Liu,&nbsp;Kai Liu,&nbsp;Dong Liu","doi":"10.1007/s10126-026-10654-x","DOIUrl":"10.1007/s10126-026-10654-x","url":null,"abstract":"<div><p><i>Coilia nasus</i> is a migratory fish in China, inhabiting oceanic waters and spawning in rivers and lakes, and exhibiting various ecotypes. Following a technological breakthrough in artificial breeding of this species from wild migratory form, a stock enhancement and release program was initiated to replenish its natural resources. However, comprehensive genomic comparisons among the migratory form and farmed populations remain limited. Here, we employed 2b-RAD sequencing to investigate genetic diversity of wild migratory form across marine, estuarine, migratory-route populations in comparison with the farmed populations. In total, 835 high-quality single nucleotide polymorphisms (SNPs) were detected, with the highest proportion (28.1%) located in exon regions. Significant genetic differences (<i>P</i> &lt; 0.01) were observed between the farmed and wild populations, corresponding to a moderate level of differentiation based on pairwise <i>F</i>st values (0.082–0.091). Population structure clearly separated the two groups: the farmed populations showed distinct genetic components, while the wild populations displayed only minor compositional differences. Phylogenetic analyses further distinguished the farmed from wild populations. Functional enrichment analyses revealed that elevated SNP frequencies in the farmed population were linked to genes related to growth, metabolism, and intestinal immunity, likely reflecting adaptation to nutrient-rich conditions and growth demands under captive environments. Additionally, 12 SNPs were validated for distinguishing farmed from wild individuals by PCR combined with sequencing. These findings provide genomic insights into the artificial breeding effects on <i>C. nasus</i> and offer practical tools for stock management and germplasm conservation of this ecologically important fish.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148237132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Characterization of the ctgf Promoter from Nibea coibor and its Response to TGF-β1 During Collagen Synthesis in Swim Bladder Cells Nibea coibor ctgf启动子的表征及其在鱼鳔细胞胶原合成过程中对TGF-β1的响应
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-13 DOI: 10.1007/s10126-026-10657-8
Ailing Zou, Yuying Yuan, Lingling Zhu, Yu Zhang, Lanfei Xiao, Xiaobo Wen, Fan Lin
{"title":"Characterization of the ctgf Promoter from Nibea coibor and its Response to TGF-β1 During Collagen Synthesis in Swim Bladder Cells","authors":"Ailing Zou,&nbsp;Yuying Yuan,&nbsp;Lingling Zhu,&nbsp;Yu Zhang,&nbsp;Lanfei Xiao,&nbsp;Xiaobo Wen,&nbsp;Fan Lin","doi":"10.1007/s10126-026-10657-8","DOIUrl":"10.1007/s10126-026-10657-8","url":null,"abstract":"<div><p>Connective tissue growth factor (<i>ctgf</i>) is a multifunctional protein that plays a crucial role in promoting collagen (the most abundant protein in organism) synthesis in vertebrates. However, its transcriptional regulation mechanism is poorly understood, especially in teleosts. In this study, we characterized the <i>ctgf</i> promoter (3,185 bp) from a marine teleost, the chu’s croaker (<i>Nibea coibor)</i>, and elucidated its response to TGF-β1 during collagen synthesis in swim bladder cells. Bioinformatics analysis revealed conserved cis-elements (TATA box, SP-1, Smad-3, NF-κB) within the promoter. Truncation assays identified a core functional region (-785 ~ + 166 bp). Notably, site-directed mutagenesis showed that mutation of SP-1 binding site enhanced the promoter activity, while mutations in binding sites of Smad-3 (-290 bp) and NF-κB (-262 bp) suppressed its activity. To demonstrate its correlation with collagen synthesis, swim bladder cells stably transfected with <i>ctgf</i> promoter drived EGFP vector (<i>pctgf</i>-EGFP) was constructed. It was further found that the promoter activity was up-regulated in concert with collagen synthesis promoted by TGF-β1 in swim bladder cells. These findings could advance our understanding of the transcriptional regulation of <i>ctgf</i>, and establish a technical platform for further screening natural compounds promoting collagen synthesis in fish.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"28 3","pages":""},"PeriodicalIF":2.8,"publicationDate":"2026-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148237131","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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
Novel Method for Preparing Pseudo-Male Common Carp by Inducing Secondary Female-to-Male Sex Reversal Under High Temperature Conditions 高温条件下诱导二次雌变雄制备伪雄鲤鱼的新方法
IF 2.8 3区 生物学
Marine Biotechnology Pub Date : 2026-06-13 DOI: 10.1007/s10126-026-10652-z
Yulai Wei, Yi Rong, Kuangxin Chen, Yongming Li, Yanlong Song, Binbin Tao, Ji Chen, Wei Hu
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