Marine Biotechnology最新文献

{"title":"Establishment and Characterization of Bisexually Fertile Triploid Dwarf Surf Clam Mulinia lateralis","authors":"Ang Zhao,&nbsp;Zujing Yang,&nbsp;Haoran Wang,&nbsp;Hao Wang,&nbsp;Shuai Zhong,&nbsp;Chenhui Li,&nbsp;Yuehuan Zhang,&nbsp;Jingjie Hu,&nbsp;Zhenmin Bao,&nbsp;Xiaoting Huang","doi":"10.1007/s10126-024-10406-9","DOIUrl":"10.1007/s10126-024-10406-9","url":null,"abstract":"<div><p>Triploids are widely used to rapidly achieve genetic improvements of organisms due to their fast growth and enhanced environmental adaptability. Artificially induced triploids are generally considered to be infertile owing to the obvious inhibition of gonadal development. Recently, some fertile individuals with reduced advantages have been found in triploid bivalves, which is a notable deviation from the original intention of artificially inducing triploids. This study utilized dwarf surf clams (<i>Mulinia lateralis</i>), a promising model organism of bivalves, to develop a model for exploring the potential mechanism of triploid reproduction. The results showed that the optimal induction condition for triploid <i>M. lateralis</i>, determined by orthogonal experiments, was 0.5 mg/L cytochalasin B (CB) to inhibit PB2 for 20 min, resulting in a triploidy rate of 95.57% and a hatching rate of 60.25%. By tracking the development of <i>M. lateralis</i>, we found that the induced triploids could develop normally to maturity and exhibited significant growth and survival advantages post-metamorphosis. Although the triploidy rate exhibited a slight decline overtime, it remained high, with a ratio of 90.63% at 120 dpf. Histological observation confirmed that the gonadal development pattern of triploid <i>M. laterali</i> was similar to that of diploids, but it also showed characteristics such as developmental retardation, few mature gametes, and gamete gigantism. The dynamic expression of genes related to gonadal development provided further molecular evidence for this phenomenon. Additionally, 82.6% of triploid <i>M. laterali</i> exhibited normal spawning behavior, produced fewer but larger viable gametes, and could generate offspring with full developmental potential. Flow cytometry analysis revealed that sperm of triploid <i>M. laterali</i> was aneuploid, with a DNA content of about 1.5 times that of diploid sperm, and the ploidy levels of mating offspring were 2N (DD, diploid female × diploid male), 2.5N (DT, diploid female × triploid male), 2.5N (TD, triploid female × diploid male), and 3N (TT, triploid female × triploid male), respectively. Overall, the artificially induced triploid <i>M. laterali</i> has been confirmed to be bisexually fertile, which will provide a unique model for exploring the underlying mechanisms of advantageous trait formation and fertility regulation in triploids, and offer a valuable platform for the study of ploidy control and polyploidization in bivalves. Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary. Yes, i have checked and it is OK. </p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142889722","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}

{"title":"Rapid Sex Identification in Spotted Knifejaw (Oplegnathus punctatus) Using tmem88 Gene Structural Variation Markers","authors":"Pingrui Xu,&nbsp;Yongshuang Xiao,&nbsp;Junde Dong,&nbsp;Zhizhong Xiao,&nbsp;Jun Li,&nbsp;Yanfeng Wang","doi":"10.1007/s10126-024-10403-y","DOIUrl":"10.1007/s10126-024-10403-y","url":null,"abstract":"<div><p>Spotted knifejaw (<i>Oplegnathus punctatus</i>) is an economically important marine cultured species exhibiting a unique complex sex chromosome system (X₁X₁X₂X₂ in females and X₁X₂Y in males), with males possessing one fewer chromosome (2n = 47) than females (2n = 48) and an abnormally large Y chromosome. Additionally, males demonstrate significant growth advantages over females. Rapid and accurate sex identification is essential for effective culture management, selective breeding, and population control. In this study, we identified a homologous region of the <i>tmem88</i> gene containing large DNA insertion markers on the X and Y chromosomes through whole-genome sequencing of <i>O. punctatus</i>. The X₁ chromosome harbors a 278 bp DNA fragment, whereas the Y chromosome contains a 1472 bp fragment, resulting in a 1194 bp size difference indicative of structural variation in the non-coding region of the <i>tmem88</i> gene. We developed a rapid detection method based on this variation, utilizing a pair of primers that amplify two distinct bands (278 bp and 1472 bp) in male (X₁X₂Y) individuals and a single 278 bp band in female (X₁X₁X₂X₂) individuals when analyzed by agarose gel electrophoresis. This method enables efficient and accurate sex differentiation in <i>O. punctatus</i>, significantly reducing the time required for identification and enhancing detection efficiency. This study provides a valuable tool for the rapid identification of sex in <i>O. punctatus</i>, facilitating improved breeding strategies and supporting the large-scale production of high-quality fry.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s10126-024-10403-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142859454","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}

{"title":"Correction to: Differentially Expressed Genes and Alternative Splicing Analysis Revealed the Difference in Virulence to American Eels (Anguilla rostrata) Infected by Edwardsiella anguillarum and Aeromonas hydrophila","authors":"Peng Lin,&nbsp;Zihao Chen,&nbsp;Guanghua Sun,&nbsp;Songlin Guo","doi":"10.1007/s10126-024-10400-1","DOIUrl":"10.1007/s10126-024-10400-1","url":null,"abstract":"","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142859455","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}

{"title":"Functional Characterization of Galectin-8 from Golden Pompano Trachinotus ovatus Reveals Its Broad-Spectrum Antimicrobial Activity","authors":"Jin-Min Pan,&nbsp;Jie Gao,&nbsp;Ming Jian Liu,&nbsp;Ke-Cheng Zhu,&nbsp;Hua-Yang Guo,&nbsp;Bao-Suo Liu,&nbsp;Nan Zhang,&nbsp;Dian-Chang Zhang","doi":"10.1007/s10126-024-10393-x","DOIUrl":"10.1007/s10126-024-10393-x","url":null,"abstract":"<div><p>Galectins exhibit a variety of biological functions through interactions with their ligands, including galactose and its derivatives. Tandem-repeat galectins, such as Galectin-8, can act as pattern recognition receptors to aggregate and neutralize bacterial pathogens. In this study, <i>Galectin-8</i> was identified in <i>Trachinotus ovatus</i> (golden pompano). Galectin-8 consists of two carbohydrate recognition domains (CRDs) connected by a linker region. Furthermore, molecular docking analysis suggests that the C-terminal CRD can bind galactose, mannose, and <i>N</i>-acetylglucosamine at similar binding sites. ToGal-8 expression levels were highest in the brain and blood of healthy <i>T. ovatus</i>. However, following infection with <i>Streptococcus agalactiae</i>, expression levels in the spleen and head kidney surged at 48 h, while liver expression significantly decreased by 96 h. Cytoplasmic Galectin-8 expression was upregulated after stimulation by peptidoglycan compared with lipopolysaccharide. Recombinant ToGal-8 (rToGal-8) was produced using a prokaryotic expression system. This protein could agglutinate red blood cells from rabbits, carp, and <i>T. ovatus</i> independently of Ca²⁺. Moreover, it was also effective in aggregating and eliminating several bacterial strains, such as <i>Staphylococcus aureus</i>, <i>Bacillus subtilis</i>, <i>Vibrio vulnificus</i>,<i> S. agalactiae</i>, <i>Pseudomonas aeruginosa</i>, and <i>Aeromonas hydrophila</i>. Therefore, this study provides an in-depth analysis of the function of <i>T. ovatus</i> Galectin-8 for the first time, offering guidance for the healthy aquaculture of <i>T. ovatus</i>.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142833384","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}

{"title":"Comparative Analysis of Promoter Activity in Crassostrea gigas Embryos: Implications for Bivalve Gene Editing","authors":"Yongzhen Yu,&nbsp;Qian Li,&nbsp;Hong Yu,&nbsp;Qi Li","doi":"10.1007/s10126-024-10398-6","DOIUrl":"10.1007/s10126-024-10398-6","url":null,"abstract":"<div><p>In recent years, CRISPR/Cas9 gene editing technology has emerged as a powerful genetic tool with potential application in aquaculture. <i>Crassostrea gigas</i>, as a valuable species in aquaculture, holds promising potential for genetic enhancement and breeding through gene editing. However, the lack of efficient promoters for driving exogenous gene expression poses a major obstacle in bivalve gene editing. In this study, we isolated the promoter sequences of the β-tub and histone H3.3A genes from <i>C</i>. <i>gigas</i>. DNA expression constructs were generated by linking the promoters with the enhanced green fluorescent protein (EGFP) reporter and compared with the promoter activity of the endogenous EF-1α gene and an exogenous OsHV-1 promoter in <i>C</i>. <i>gigas</i> embryos. All four promoters effectively drive the expression of EGFP during early embryonic development in <i>C</i>. <i>gigas</i>. Among these four promoters, the β-tub promoter is the most potent promoter in driving EGFP expression in <i>C. gigas</i> embryos as early as 4.5 h after fertilization. The OsHV-1 promoter showed similar activity as β-tub promoter and appeared to be more active than the EF-1α and histone H3.3A promoters in <i>C</i>. <i>gigas</i> embryos. Furthermore, we assessed their performance in other three <i>C</i>. <i>gigas</i> relatives (<i>Crassostrea ariakensis</i>, <i>Crassostrea nippona</i>, and <i>Crassostrea sikamea</i>) and similar results were found. Collectively, these data suggest that the β-tub promoter is an effective promoter in directing gene expression in directing gene expression in oyster embryos, thus offering a potential application for gene editing in bivalves.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142810995","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}

{"title":"Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste","authors":"Kanphorn Saeng-kla,&nbsp;Wuttichai Mhuantong,&nbsp;Teerasit Termsaithong,&nbsp;Onruthai Pinyakong,&nbsp;Prinpida Sonthiphand","doi":"10.1007/s10126-024-10399-5","DOIUrl":"10.1007/s10126-024-10399-5","url":null,"abstract":"<div><p>Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman’s correlation analysis suggested that <i>Myxococcales</i>, <i>Methyloligellaceae</i>, <i>Mycobacterium</i>, and <i>Micromonospora</i> were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through <i>catC</i>, <i>pcaD</i>, <i>pcaI</i>, <i>pcaF</i>, and <i>fadA</i>. Efficient bacterial isolates from the mangrove sediment, identified as <i>Gordonia</i> sp. and <i>Gordonia polyisoprenivorans</i>, were able to degrade DEHP (65–97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142762018","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}

{"title":"Transcriptome Reveals Molecular Mechanisms of Neuroendocrine Regulation of Allometric Growth in the Red Swamp Crayfish Procambarus clarkii","authors":"Zheyan Chen,&nbsp;Yongqing Wang,&nbsp;Xianji Tao,&nbsp;Yihai Qiao,&nbsp;Xilei Li,&nbsp;Jianbin Feng,&nbsp;Jiale Li","doi":"10.1007/s10126-024-10395-9","DOIUrl":"10.1007/s10126-024-10395-9","url":null,"abstract":"<div><p>Allometric growth is a typical characteristic of crustaceans, which mainly occurs among individuals, life stages, tissues, and between sexes. The red swamp crayfish <i>Procambarus clarkii</i> is an economically important crustacean species in the world. To date, the molecular regulatory mechanisms of neuroendocrine system in the allometric growth of <i>P. clarkii</i> remain unclear. In this study, <i>P. clarkii</i> exhibiting significant allometric growth among individuals were sampled from three full-sibling families. The brain, eyestalk, nerve cord, and Y-organ were dissected for transcriptome analysis. Key functional genes were identified by random forest and DESeq2 methods. The gene pathways were enriched utilizing Kyoto Encyclopedia Genes and Genomes (KEGG) analysis. Gene topological analysis was established through weighted gene co-expression network analysis (WGCNA), and hub genes were screened by protein–protein interaction (PPI) networks. Transcriptomic analysis results were validated via qRT-PCR. RNA-Seq identified 31 differentially expressed genes (DEGs) (7 up- and 24 downregulated); 301 DEGs (23 up- and 278 downregulated); 1308 DEGs (474 up- and 834 downregulated); and 64 DEGs (52 up- and 12 downregulated) in the brain, eyestalk, Y-organ, and nerve cord, respectively. Crucial functional genes such as <i>CHIA</i> in the brain and <i>perlucin-like</i> in the eyestalk were notably identified. WGCNA revealed two hub modules, while PPI networks identified neuroendocrine regulators module which hub genes mainly including <i>CP1876-like</i> and cuticle protein <i>AM1199-like</i>, and structural components module which hub genes mainly including <i>CUB&amp; CCP Domain-Containing Protein</i>, <i>ARRDC</i>, and <i>E3 Ubiquitin protein ligase MCYCBP2-like</i>. Correspondingly, the significant gene pathways such as amino sugar and nucleotide sugar metabolism (pcla00520) and insect hormone biosynthesis (pcla00981) were enriched. The results revealed the complex interactions and regulatory relationships of hub genes within hub modules to coordinate molting and growth. The results of RNA-Seq analysis were validated by the consistency of gene expression in qRT-PCR. In present study, key functional genes in the neuroendocrine system regulating allometric growth among individuals were identified, and significant pathways mainly include hormone synthesis were screened, thus constructing a neuroendocrine molecular regulatory network for the allometric growth of <i>P. clarkii</i>. Building on these investigations, a comprehensive mechanism whereby neuroendocrine regulators interact with structural components to coordinate molting and growth was proposed. The result would provide valuable insights into the molecular regulatory mechanisms of allometric growth, highlighting the interplay between the neuroendocrine system and relevant tissues.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758026","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}

{"title":"Establishment of Nile Tilapia Primary Cell Culture Methods and In Vitro Cell Knockdown Techniques","authors":"Siqi Huang,&nbsp;Shicen Wei,&nbsp;He Jiao,&nbsp;Songqian Huang,&nbsp;Qini Li,&nbsp;Zhe Wang,&nbsp;Yuhao Tang,&nbsp;Liangbiao Chen,&nbsp;Jigang Lu","doi":"10.1007/s10126-024-10380-2","DOIUrl":"10.1007/s10126-024-10380-2","url":null,"abstract":"<div><p>As an important aquaculture species and research model, Nile tilapia (<i>Oreochromis niloticus</i>) has not yet been systematically studied for the isolation, culture, and in vitro gene manipulation techniques of primary cells from various tissues. This study aimed to explore methods for isolating primary cells from various tissues, as well as developing in vitro gene manipulation techniques in Nile tilapia. Four different Nile tilapia tissues were enzymatically digested and separated using trypsin or collagenase. Collagenase (0.1%) was used for the digestion of the gonads, liver, and heart, while trypsin (0.25%) showed better adhesion efficiency for spleen tissue. Moreover, we assessed EGFP fluorescence intensity and cell survival rates following transfection with empty siRNA (siRNA-NC), lentivirus (LV-NC), and six adeno-associated virus (AAV-NC) serotypes (AAV2-NC, AAV5-NC, AAV6-NC, AAV8-NC, AAV9-NC, AAV-DJ-NC) in gonadal cells. The results demonstrated that cells transfected with siRNA-NC and LV-NC showed the highest levels of green fluorescent protein expression and survival rates in primary gonadal cells, compared to AAC-NC. Subsequently, we knocked down the <i>Kdm6bb</i> gene in Nile tilapia primary gonadal cells by transfecting them with LV-<i>Kdm6bb</i> and siRNA-<i>Kdm6bb</i>. qPCR and immunofluorescence analyses demonstrated a significant reduction in <i>Kdm6bb</i> mRNA levels following transfection with siRNA-<i>Kdm6bb</i> compared to siRNA-NC, and with LV-<i>Kdm6bb</i> compared to LV-NC. This study offers valuable tools for the validation of primary cell isolation and in vitro molecular regulatory mechanisms and functions in Nile tilapia.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758024","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}

{"title":"Effect of Selenium Nanoparticles on Alternative Splicing of Rainbow Trout Head Kidney under Heat Stress","authors":"Jiahui Zhang,&nbsp;Zhe Liu,&nbsp;Jinqiang Quan,&nbsp;Junhao Lu,&nbsp;Guiyan Zhao,&nbsp;Yucai Pan","doi":"10.1007/s10126-024-10382-0","DOIUrl":"10.1007/s10126-024-10382-0","url":null,"abstract":"<div><p>Alternative splicing (AS) is an important post-transcriptional regulation, which can expand the functional diversity of gene products and is a mechanism for eukaryotes to cope with abiotic stress. However, there are few studies on AS events in rainbow trout under heat stress. In this study, RNA-Seq data were used to clarify the effect of selenium nanoparticles (SeNPs) on the AS events of rainbow trout head kidney under heat stress. The results showed that a total of 45,398 AS events were identified from 9804 genes, of which Skipped Exon (SE) was the most common type of AS event. Through the analysis of the differentially expressed genes (DEGs) in each group, we learned that DEGs were enriched in the spliceosome, and the relevant genes were significantly changed, which promoted the occurrence of AS. We found that lysine degradation, ubiquitin mediated proteolysis, RNA degradation, protein processing in endoplasmic reticulum processing and other pathways were significantly enriched after addition of SeNPs. In addition, some immune related signaling pathways, such as the mTOR signaling pathway, interact with each other to enhance the resistance of rainbow trout to heat stress. These results indicated that AS in head kidney of rainbow trout changed under heat stress and SeNPs played a key role in alleviating heat stress for rainbow trout.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749519","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}

{"title":"Transcriptome Analysis Reveals the lncRNA-mRNA Co-expression Network Regulating the Aestivation of Sea Cucumber","authors":"Xiaomei Chen,&nbsp;Wentao Han,&nbsp;Rui Yang,&nbsp;Xuan Zhu,&nbsp;Shengwen Li,&nbsp;Yangfan Wang,&nbsp;Xue Sun,&nbsp;Yuli Li,&nbsp;Lisui Bao,&nbsp;Lingling Zhang,&nbsp;Shi Wang,&nbsp;Jing Wang","doi":"10.1007/s10126-024-10388-8","DOIUrl":"10.1007/s10126-024-10388-8","url":null,"abstract":"<div><p>LncRNAs are long non-coding RNAs that are widely recognized as crucial regulators of gene expression and metabolic control, involved in numerous dormancy-related processes. Aestivation is a common hypometabolism strategy of sea cucumber (<i>Apostichopus japonicus</i>) in response to high-temperature conditions and is typically characterized by the degradation of the intestine and respiratory tree. Although the aestivation process has been extensively studied in sea cucumbers, the role of lncRNAs in the context of aestivation states remains a conspicuous knowledge gap. Here, we identified and characterized 14,711 lncRNAs in <i>A. japonicus</i> and analyzed their differential expression patterns during the aestivation process in the intestine and respiratory tree. The results revealed the physiological differences, especially the metabolic processes, between the intestine and respiratory tree during the aestivation. The co-expression network of lncRNA-mRNA suggested the dominant role of lncRNA in regulating the differential response of the intestine and respiratory trees. Differentially co-expressed factors were significantly enriched in the deep-aestivation stage-specific modules. Conserved co-expressed factors included several transcription factors known to be involved in rhythm regulation, such as <i>Klf2</i> and <i>Egr1</i>. Furthermore, a specific trans-acting lncRNA (<i>lncrna.1393.1</i>) was identified as a potential regulator of <i>Klf2</i> and <i>Egr1</i>. Overall, the systematic identification, characterization, and expression analysis of lncRNAs in <i>A. japonicus</i> enhanced our knowledge of long non-coding regulation of aestivation in sea cucumber and provided new clues for understanding the common “toolkit” of dormancy regulatory mechanisms.</p></div>","PeriodicalId":690,"journal":{"name":"Marine Biotechnology","volume":"27 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142749524","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}