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

{"title":"Exploring the gut microbiota and metabolome of Lateolabrax japonicus: A multi-omics approach","authors":"Gang Zhou ,&nbsp;Ying-si Wang ,&nbsp;Hui-juan Wang,&nbsp;Ting-li Sun,&nbsp;Ru-qun Peng,&nbsp;Su-juan Li,&nbsp;Hong Peng,&nbsp;Xia Wen,&nbsp;Xiao-xuan Zhu,&nbsp;Yun-qi Zhu,&nbsp;Zong-bin Cui,&nbsp;Qing-shan Shi,&nbsp;Xiao-bao Xie","doi":"10.1016/j.cbd.2024.101408","DOIUrl":"10.1016/j.cbd.2024.101408","url":null,"abstract":"<div><div>The intestinal microbiota plays a crucial role in the health and development of fish, engaging in intricate interactions with the host organism. As a significant species in aquaculture, <em>Lateolabrax japonicus</em> serves as an exemplary model for investigating these interactions and their subsequent effects on growth and health. This study utilized a multi-omics approach, incorporating metagenomic sequencing and non-targeted metabolomics, to delineate the gut microbiota and metabolome of <em>L. japonicus</em> throughout various developmental phases. Collected from a meticulously controlled aquaculture setting, the intestinal microbiota of L. <em>japonicus</em> underwent high-throughput sequencing to scrutinize microbial DNA and enumerate metabolites. The metagenomic analysis uncovered a heterogeneous gut microbiota in L. <em>japonicus</em>, predominantly composed of Proteobacteria and Firmicutes, with marked heterogeneity in microbial composition across developmental stages. A particularly noteworthy discovery was the prevalence of the genus <em>Acinetobacter</em>, which may significantly influence health and disease resistance. The metabolomic profiling discerned 4479 metabolites, each exhibiting pronounced stage-specific metabolic signatures, particularly within lipid, amino acid, and energy metabolism pathways. The correlation analysis between microbiota and metabolites highlighted the substantial impact of specific genera, such as <em>Acinetobacter</em> and <em>Gaeumannomyces</em>, on the metabolic milieu. This study provides a comprehensive overview of the dynamic shifts in the gut microbiota and metabolome of L. <em>japonicus</em>, highlighting stage-specific transitions that could be pivotal for refining aquaculture practices. The findings underscore the complex interdependence between microbiota composition and metabolic function, providing valuable insights into the modulation of fish health and growth.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101408"},"PeriodicalIF":2.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901223","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 proteomic analysis reveals the response mechanism of freshwater leech (Whitmania pigra) under heat-stress challenge","authors":"Shuaibing Wang ,&nbsp;Xiaochuan Zheng ,&nbsp;Quan Wang ,&nbsp;Aimin Wang ,&nbsp;Haihua Wang ,&nbsp;Huiyun Fu ,&nbsp;Mange Kaunda ,&nbsp;Liangwei Xiong ,&nbsp;Bo Liu","doi":"10.1016/j.cbd.2024.101406","DOIUrl":"10.1016/j.cbd.2024.101406","url":null,"abstract":"<div><div>Temperature is an environmental parameter that remarkably affects the survival and organism health of poikilothermal animal-<em>Whitmania pigra Whitman</em>. Heat stress destroys the physiological homeostasis of intestine tissue. However, no studies on the intestinal mucosa response of leech exposure to heat stress have been reported so far. To identify the biomarker proteins involved in heat stress response, we performed a Tandem mass tag (TMT)-based comparative proteomic analysis on leech's intestine after exposing to 27 °C and 35 °C. The cumulative mortality in the 35 °C heat stress group increased on the third day after stress compared with the control group. Mean-while, intestinal malondialdehyde (MDA) content was significantly up-regulated whereas total antioxidant capacity (T-AOC) was significantly down-regulated. A total of 3935 proteins were identified through proteomic analysis. Heat stress resulted in 144 differential proteins; 75 were up-regulated, and 69 were down-regulated. The differential expression proteins in response to heat stress are mainly involved in calcium-binding proteins, molecular chaperones, cytoskeleton integrity, immune function and inflammation response, DNA damage and repair, ribosomal protein synthesis, stress hormones and neuro-transmitters, tumorigenesis, and apoptosis. Protein-protein network interaction analysis showed that HSP, CD8A, C3, CD63, CD81, MRPL58, MRPL15, HNRNPA1, AMBP, IGHEP1, SERPINC1, CYP3A4, ATP12A, RPS13, CaM, HSP70 binding protein, HSPA6, C4A, ANXA7, ARG1, ARG2, ATP1B, CALCA, HTR1B, and GNGT1 are the critical proteins of leeches resistance to heat stress. Our results systematically provide substantial responsive candidate proteins combating heat stress and enhance our understanding of the intrinsic response mechanisms of thermal sensitivities animal <em>W. pigra</em> facing heat exposure.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101406"},"PeriodicalIF":2.2,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142901222","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 identified genes involved in ovarian development in Takifugu rubripes","authors":"Mingtao Hu ,&nbsp;Hongwei Yan ,&nbsp;Jinfeng Chen ,&nbsp;Rui Gao ,&nbsp;Weiyuan Li ,&nbsp;Huiting Zhou ,&nbsp;Jia Wang ,&nbsp;Qi Liu ,&nbsp;Xiuli Wang ,&nbsp;Pengfei Hu ,&nbsp;Chuang Fu","doi":"10.1016/j.cbd.2024.101407","DOIUrl":"10.1016/j.cbd.2024.101407","url":null,"abstract":"<div><div>Ovarian development is a complex process involving multiple genes, but the molecular mechanisms underlying this process in <em>Takifugu rubripes</em> remain poorly understood. This study aimed to identify genes associated with ovarian development in <em>T. rubripes</em> and to investigate the regulatory mechanisms of oocyte maturation. Transcriptome data were compared across four different developmental stages (stage II to V) to identify differentially expressed genes (DEGs) and perform GO and KEGG enrichment analysis. The expression patterns of randomly selected genes were then validated by qPCR. The results yielded a total of 1,289,401,820 raw data from all libraries, with 16,929 DEGs identified across all comparison groups. The DEGs were predominantly enriched in ovarian steroidogenesis, estrogen-mediated signaling, and TGF-beta signaling pathways. The qPCR analysis showed that <em>cyp17a1</em> was identified as being expressed at similar levels in stage II and III. Thereafter, <em>cyp17a1</em> was observed to undergo a continuous increase in expression from stage III to V. <em>cyp19a1</em>, <em>nanos1</em>, <em>foxl2</em> and <em>ar</em> were identified as being expressed at similar levels at stage II and III, then increase in expression from stage III to IV and subsequent downregulation from stage IV to V. <em>hsd17b1</em> was identified as being expressed at similar levels at stage II and IV. This study represents a transcriptomic study of ovarian development in female <em>T. rubripes</em>. Several essential ovarian-related genes and sex-related biological pathways were identified. The results will improve our understanding of the molecular mechanisms underlying ovarian development in this species.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101407"},"PeriodicalIF":2.2,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142908101","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":"Ocean warming and acidification alter calcification and innate immune system gene expression in juvenile American lobsters, Homarus americanus","authors":"Christine San Antonio ,&nbsp;Helen Poynton ,&nbsp;Keegan Krick ,&nbsp;Robyn Hannigan","doi":"10.1016/j.cbd.2024.101404","DOIUrl":"10.1016/j.cbd.2024.101404","url":null,"abstract":"<div><div>The Gulf of Maine, home to American lobster, <em>Homarus americanus,</em> is experiencing rapid ocean warming (OW) and acidification (OA) due to climate change. While some studies have investigated the effects of either ocean acidification (OA) or warming (OW) on lobsters, few explore the interaction of these stressors, particularly on gene expression. We evaluated the effects of OA and OW on early benthic juvenile lobster transcriptomics using RNA sequencing and RT-qPCR through two distinct aquarium experiments. Lobsters were reared under OW/OA conditions aligned with values predicted for 2100: decrease in pH by 0.3–0.4 units; mean sea surface warming of 2.89 °C. RNA was isolated from carapace hypodermal tissue in both experiments. The multi-stressor treatment in the RNAseq experiment had the greatest differential expression. Genes of interest pertaining to calcification and cuticle development were primarily downregulated under high temperature but upregulated under acidified and multi-stressor conditions. In the RT-qPCR experiment, crustin alone was significantly downregulated and only under the most extreme multi-stressor treatment. This gene along with the prophenoloxidase activating enzyme had expression that trended toward downregulation across all treatments, suggesting a possible correlation to immune suppression. Expression profiles for crustin and the calcification gene, carbonic anhydrase differed across treatments based on molt cycle timing, indicating that stressor impacts may vary depending on the molt cycle phase. Elevated temperature had a greater effect on the expression of calcification and cuticle development genes, though the direction of expression reversed with multiple stressors. These results indicate the impacts of OW and OA on early benthic juvenile lobsters are complex, possibly synergistic, vary with molt cycle, and potentially interfere with normal cuticle development, which may increase susceptibility to injury or disease.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101404"},"PeriodicalIF":2.2,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873655","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 reveals the cerebral sex-specific responses to chronic hypoxia in yellow catfish (Pelteobagrus fulvidraco)","authors":"Danqing Yin ,&nbsp;Cheng Zhao","doi":"10.1016/j.cbd.2024.101401","DOIUrl":"10.1016/j.cbd.2024.101401","url":null,"abstract":"<div><div>Hypoxia disrupts multiple physiological processes, including metabolism, immunity, and reproduction in teleosts. The brain plays a critical role in adapting to environmental changes, regulating the endocrine system, and controlling reproduction. The present study investigated the sex-specific cerebral responses to chronic hypoxia through an integrated analysis of the transcriptome, proteome, and metabolome of yellow catfish. Common cerebral responses in both females and males included activation of the HIF signaling pathway, angiogenesis, and improved oxygen delivery by red blood cells. Reproductive defects were indicated by the downregulation of <em>gh1</em>, <em>cga</em>, and <em>tshb</em> in both sexes. Thyroid hormone homeostasis was more severely disrupted by hypoxia in females than in males, accompanied by a significant decrease in the level of VTG in the female brain. Damaged brain function was evidenced by the highly enriched pathways of “cytokine-cytokine receptor interaction” and “ECM-receptor interaction,” and the blood-brain barrier (BBB) also appeared to be disrupted in female fish. In the male brain, reproductive-related genes or proteins, including <em>prl</em>, <em>lepr</em>, and AVP, were specifically decreased. Dysfunction in the male brain was also indicated by the enrichment of pathways such as “cytokine-cytokine receptor interaction” and “neuroactive ligand-receptor interaction,” based on differentially expressed genes (DEGs) and proteins (DEPs). Additionally, chronic hypoxia appeared to inhibit cerebral amino acid metabolism in males. In summary, our results offer insight into understanding the sex-specific cerebral responses induced by chronic hypoxia in teleosts.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101401"},"PeriodicalIF":2.2,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomic analysis of the response of Spodoptera frugiperda (Lepidoptera: Noctuidae) to short-term low-temperature stress","authors":"Huawei Ren,&nbsp;Junrui Zhi,&nbsp;Dingyin Li,&nbsp;Wenbo Yue,&nbsp;Li Liu","doi":"10.1016/j.cbd.2024.101394","DOIUrl":"10.1016/j.cbd.2024.101394","url":null,"abstract":"<div><div><em>Spodoptera frugiperda</em> is a major invasive pest that poses a serious threat to crops worldwide. Low temperature is a key factor limiting the survival and reproduction for this pest. To study the responses of <em>S. frugiperda</em> to low-temperature stress, high-throughput sequencing was used to perform transcriptomic analysis on the 6^th instar larvae under low-temperature stress at 5 °C and 10 °C, along with 25 °C as a control. As a result, 215 differentially expressed genes (DEGs) were identified under different low-temperature stresses. Upon functional annotation of the DEGs in KEGG and GO databases, the number of DEGs annotated in control vs. LT10 comparison was the largest (<em>n</em> = 150), whereas fewer DEGs (<em>n</em> = 89) were annotated in control vs. LT5 comparison. This discrepancy suggested that <em>S. frugiperda</em> might adopt different strategies to cope with low-temperature stress. The DEGs in the GO database were particularly associated with cell catalytic activity, cell anatomical entity process, cell apoptosis, and cell binding channel. KEGG annotation analysis of the different low-temperature stresses showed that most of the enriched pathways were related to carbon metabolism, oxidative phosphorylation, and lipid metabolism. The results will be the basis for mastering the cold tolerant mechanism of <em>S. frugiperda</em>, and is of great significance for its prevention.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101394"},"PeriodicalIF":2.2,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142866673","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":"Responses of the mud snail Cipangopaludina cathayensis to thermal stress: Insights from metabolism, oxidative stress damage, and hepatopancreas transcriptional modulation","authors":"Jinyou Wei ,&nbsp;Yangyang Wu ,&nbsp;Chunxing Cheng ,&nbsp;Haizhen Tan ,&nbsp;Linli Li ,&nbsp;Jiaoyun Jiang","doi":"10.1016/j.cbd.2024.101398","DOIUrl":"10.1016/j.cbd.2024.101398","url":null,"abstract":"<div><div>Global warming linked to climate change poses a significant risk to aquatic animals. Invertebrates, such as <em>Cipangopaludina cathayensis</em> are especially susceptible to elevated temperature. Understanding how <em>C</em>. <em>cathayensis</em> responds to high-temperature stress is crucial for predicting the putative effects of climate change on its cultivation. In this study, we exposed <em>C. cathayensis</em> to various temperature conditions (26 °C, 28 °C, 30 °C, and 32 °C) for 3 h, revealing that both oxygen consumption and ammonia excretion rates increased gradually with increasing temperature, reaching maximum values of 77.711 ± 2.364 μg·(g·h)⁻¹ and 4.701 ± 0.036 μg·(g·h)⁻¹ at 30 °C and 28 °C, respectively. However, values of these parameters decreased when the culture temperature increased to 32 °C. High-temperature stress also resulted in a reduced O:N ratio and decreased energy metabolism rate. To investigate how high temperature impacts antioxidant activities, immune function, and transcriptional regulation in the hepatopancreas, <em>C. cathayensis</em> were exposed to temperatures of 26 °C or 32 °C for 3 and 7 days, respectively. Our results indicated that high temperature disrupted the antioxidant defense system and led to immunosuppression in the hepatopancreas. Comparative transcriptome analysis identified 6638 genes with significantly altered expression between these two temperature groups. Functional enrichment analysis of differentially expressed genes demonstrated that high temperature affected protein homeostasis, energy metabolism, and immune function of <em>C. cathayensis</em>. Together, these findings offer valuable information for evaluating the impacts of global warming on the culture of mud snail.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101398"},"PeriodicalIF":2.2,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824685","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":"Neuroendocrine regulatory network underlying physiological shifts between reproduction and aestivation of sea cucumber Apostichopus japonicus: Insights from transcriptome analysis","authors":"Lifei Ge ,&nbsp;Jixiu Wang ,&nbsp;Zhijing Jiang ,&nbsp;Zhiqing Ye ,&nbsp;Ying Wei ,&nbsp;Yibo Wang ,&nbsp;Yuting Liu ,&nbsp;Chenqian Wu ,&nbsp;Xiuwen Xu ,&nbsp;Jingwen Yang ,&nbsp;Lina Sun ,&nbsp;Tianming Wang","doi":"10.1016/j.cbd.2024.101393","DOIUrl":"10.1016/j.cbd.2024.101393","url":null,"abstract":"<div><div>The sea cucumber <em>Apostichopus japonicus</em> is an economically significant marine species in China, with numerous studies focusing on its diverse physiological processes, including seasonal reproduction and aestivation. The neuroendocrine system plays a critical role in regulating these physiological transitions. In this study, we utilized transcriptomic techniques and bioinformatics tools to identify key functional genes in the nerve ring of <em>A. japonicus</em> during four distinct physiological phases: pre-reproduction, post-reproduction, aestivation, and recovery from aestivation. Totally 33 neuropeptide precursors and 521 G protein-coupled receptors (GPCRs) were identified. Highlighted key genes, such as <em>AjCRZP</em>, <em>AjPDFP1b</em>, <em>AjSSP1</em>, <em>AjSSP2</em>, and <em>AjSSTR4</em>, were proposed to contribute to transitions of reproduction to aestivation. The temporal trends and functions of differentially expressed genes (DEGs) were validated through qRT-PCR assays. Additionally, we constructed a preliminary neuroendocrine regulatory network, with <em>AjGALR2</em> and <em>AjCHRM5</em> identified as central hub genes. These findings offer valuable insights into the neuroendocrine regulation of reproduction and aestivation in <em>A. japonicus</em>, providing a foundation for further mechanistic studies and enhancing our understanding of sea cucumber biology.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101393"},"PeriodicalIF":2.2,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142831249","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 analysis reveals the potential mechanism of plateau environment on muscle growth and development in yak","authors":"Dunzhu Luosang ,&nbsp;Yang Gao ,&nbsp;Liang Hong ,&nbsp;Nan Jiang ,&nbsp;Wangdui Basang","doi":"10.1016/j.cbd.2024.101395","DOIUrl":"10.1016/j.cbd.2024.101395","url":null,"abstract":"<div><div>Yak meat plays a significant economic role for yaks. The unique environment of the Qinghai-Tibet plateau profoundly impacts the meat production performance of yaks. Yet, the regulatory mechanisms influencing muscle growth and development in yaks within this plateau environment remain poorly understood. The study investigated the transcriptome gene expression in the buttock muscle tissue of yaks residing at varying altitudes. It revealed 516 differentially expressed genes in the buttock muscle tissue of yaks at high altitude (4500 m) and low altitude (3000 m). The Gene Ontology (GO) annotation indicated that these differentially expressed genes primarily function in RNA binding, identical protein binding, nucleotide binding, pre-mRNA branch point binding, unfolded protein binding, insulin receptor binding, fructose 1,6-bisphosphate 1-phosphatase activity, collagen binding, platelet-derived growth factor receptor binding, and sodium channel inhibitor activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the differentially expressed genes predominantly participated in pathways such as the spliceosome, aminoacyl tRNA biosynthesis, RNA polymerase, cutin, suberin, and wax biosynthesis, ribosome biogenesis in eukaryotes, plant hormone signal transduction, axon guidance, fructose and mannose metabolism, pentose phosphate pathway, and gastric acid secretion. This study unveiled the impact of the plateau environment on transcriptome gene expression in yak buttock muscle tissue, mapping out the gene expression profiles specific to yaks living at varying altitudes (3000 m and 4500 m). The findings offer crucial genomic insights into the mechanisms behind yak muscle adaptation to plateau environments.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101395"},"PeriodicalIF":2.2,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848715","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of gonadal transcriptome reveals core long non-coding RNA-mRNA regulatory network in sea cucumber Apostichopus japonicus","authors":"Ziming Li,&nbsp;Xinghai Liu,&nbsp;Xinyue Tang,&nbsp;Yujia Yang","doi":"10.1016/j.cbd.2024.101396","DOIUrl":"10.1016/j.cbd.2024.101396","url":null,"abstract":"<div><div><em>Apostichopus japonicus</em> is a representative temperate sea cucumber species, that mainly inhabits in coastal zone of the continental shelf. With high nutritional value and important medical value, <em>A. japonicus</em> become an important commercial aquaculture species and produce significant economic value in recent years. <em>A. japonicus</em> has no sexual dimorphism that can be used to distinguish female and male individuals by external appearance and morphology. The phenotype sex can be only detected by dissecting and observing gonad tissue, thus the breeding efficiency could be greatly reduced. This limitation has hindered the advancement of selective breeding programs and sea cucumber industry. To investigate the genetic basis of reproductive biology in <em>A. japonicus</em>, advanced sequencing techniques, such as next- and third-generation sequencing, have been employed to explore the roles of non-coding RNAs and other genetic factors, offering new insights into sex determination mechanisms. To further gain a deeper understanding of the knowledge underlying lncRNAs in gonadal differentiation, we conducted a comparative transcriptome sequencing analysis of gonadal tissues from both sexes. In our research, a total of 3990 novel lncRNAs and 1441 differentially expressed lncRNAs were identified between female and male gonads. Additionally, a molecular regulatory network indicating lncRNA-mRNA interactions was constructed based on transcriptional profiles, which provide insights into the potential cis- and trans- target genes of lncRNAs. The gonadal transcriptome analysis identified a number of novel long non-coding RNAs involved in female and male reproduction process. Both cis- and trans-acting regulatory networks indicating lncRNA-mRNA interaction were constructed based on transcriptional profiles. These findings provide new insights into the lncRNA-mediated regulation of reproductive biology in marine invertebrates, indicating the crucial roles of long non-coding sequences in regulating expression profiles. Further, the GO and KEGG enrichment analyses of cis- and trans- targeted mRNA for differentially expressed lncRNA indicated that sexual reproduction (GO:0019953), germ cell development (GO:0007281), and negative regulation of hormone secretion (GO:0046888) are potentially involved in gonadal differentiation through the regulation of long non-coding sequences. Notably, besides the classical reproduction related signaling pathway like Gonadotropin-releasing hormone (GnRH) secretion (ko04929), several regulatory pathways, such as Epidermal growth factor receptor (ErbB) signaling pathway (ko04012), TGF-beta signaling pathway (ko04350), and neurotrophin signaling pathway (ko04722) were also enriched and potentially involved in sex differentiation and gonadal development.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101396"},"PeriodicalIF":2.2,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820257","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}