Genomics最新文献_第10页

Genetic structural analysis of different breeds and geographical groups of Fenneropenaeus chinensis reveals population diversity 对不同品种和地理群组的五步蛇遗传结构分析揭示了种群多样性

IF 4.4 2区生物学

Genomics Pub Date : 2024-04-10 DOI: 10.1016/j.ygeno.2024.110843

Qiong Wang , Yuhan Jiang , Jian Li , Jitao Li , Yuying He

{"title":"Genetic structural analysis of different breeds and geographical groups of Fenneropenaeus chinensis reveals population diversity","authors":"Qiong Wang , Yuhan Jiang , Jian Li , Jitao Li , Yuying He","doi":"10.1016/j.ygeno.2024.110843","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110843","url":null,"abstract":"<div><p><em>Fenneropenaeus chinensis</em> is a commercially important shrimp species cultured in China. This study investigated eight <em>F. chinensis</em> populations in China, including four geographical populations, three commercial breeds, and one wild population captured from the Yellow Sea. Population stratification analysis revealed that the Hebei geographical population and commercial breeding “Huanghai No. 4” were relatively independent and stable, reflecting a relatively closed breeding environment, whereas gene introgression was present between other populations. Selective signature analysis detected artificial selection for vision, growth, and disease resistance in the Hebei population. Neuronal development-related genes were detected to be under selection in the Changyi and Rizhao populations. Fertility of the Rizhao population was also investigated. Additionally, genes in the glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate pathway were involved in the high pH tolerance of the “Huanghai No. 4” population. This study provided support for the genetic mechanism of parsing economic traits and the development of molecular breeding technologies.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000648/pdfft?md5=05d9a1bc563fd0134633784b08c6a787&pid=1-s2.0-S0888754324000648-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140547402","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}

引用次数: 0

Genome sequencing and assembly of Indian golden silkmoth, Antheraea assamensis Helfer (Saturniidae, Lepidoptera) 印度金丝夜蛾 Antheraea assamensis Helfer（鞘翅目，鳞翅目）的基因组测序与组装

IF 4.4 2区生物学

Genomics Pub Date : 2024-04-09 DOI: 10.1016/j.ygeno.2024.110841

Himanshu Dubey , A.R. Pradeep , Kartik Neog , Rajal Debnath , P.J. Aneesha , Suraj Kumar Shah , Indumathi Kamatchi , K.M. Ponnuvel , A. Ramesha , Kunjupillai Vijayan , Upendra Nongthomba , Utpal Bora , Sivaprasad Vankadara , K.M. VijayaKumari , Kallare P. Arunkumar

{"title":"Genome sequencing and assembly of Indian golden silkmoth, Antheraea assamensis Helfer (Saturniidae, Lepidoptera)","authors":"Himanshu Dubey , A.R. Pradeep , Kartik Neog , Rajal Debnath , P.J. Aneesha , Suraj Kumar Shah , Indumathi Kamatchi , K.M. Ponnuvel , A. Ramesha , Kunjupillai Vijayan , Upendra Nongthomba , Utpal Bora , Sivaprasad Vankadara , K.M. VijayaKumari , Kallare P. Arunkumar","doi":"10.1016/j.ygeno.2024.110841","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110841","url":null,"abstract":"<div><p>Muga silkworm (<em>Antheraea assamensis</em>), one of the economically important wild silkmoths, is unique among saturniid silkmoths. It is confined to the North-eastern part of India. Muga silk has the highest value among the other silks. Unlike other silkmoths, <em>A. assamensis</em> has a low chromosome number (<em>n</em> = 15), and ZZ/ZO sex chromosome system. Here, we report the first high-quality draft genome of <em>A. assamensis,</em> assembled by employing the Illumina and PacBio sequencing platforms. The assembled genome of <em>A. assamensis</em> is 501.18 Mb long, with 2697 scaffolds and an N50 of 683.23 Kb. The genome encompasses 18,385 protein-coding genes, 86.29% of which were functionally annotated. Phylogenetic analysis of <em>A. assamensis</em> revealed its divergence from other Antheraea species approximately 28.7 million years ago. Moreover, an investigation into detoxification-related gene families, CYP450, GST, and ABC-transporter, revealed a significant expansion in <em>A. assamensis</em> as compared to the <em>Bombyx mori</em>. This expansion is comparable to <em>Spodoptera litura</em>, suggesting adaptive responses linked to the polyphagous behavior observed in these insects. This study provides valuable insights into the molecular basis of evolutionary divergence and adaptations in muga silkmoth. The genome assembly reported in this study will significantly help in the functional genomics studies on <em>A. assamensis</em> and other <em>Antheraea</em> species along with comparative genomics analyses of Bombycoidea insects.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000624/pdfft?md5=af3f32a6d6e33c171f70c33f0d778d52&pid=1-s2.0-S0888754324000624-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140551365","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}

引用次数: 0

Variants in FOXC1 and FOXC2 identified in patients with conotruncal heart defects 在先天性心脏病患者中发现的 FOXC1 和 FOXC2 变异

IF 4.4 2区生物学

Genomics Pub Date : 2024-04-03 DOI: 10.1016/j.ygeno.2024.110840

Wei Wei , Bojian Li , Fen Li , Kun Sun , Xuechao Jiang , Rang Xu

引用次数: 0

De novo assembly and analysis of Sonneratia ovata genome and population analysis 从头组装和分析 Sonneratia ovata 基因组及种群分析。

IF 4.4 2区生物学

Genomics Pub Date : 2024-03-27 DOI: 10.1016/j.ygeno.2024.110837

Jeremy R. Shearman , Chaiwat Naktang , Chutima Sonthirod , Wasitthee Kongkachana , Sonicha U-Thoomporn , Nukoon Jomchai , Chatree Maknual , Suchart Yamprasai , Poonsri Wanthongchai , Wirulda Pootakham , Sithichoke Tangphatsornruang

{"title":"De novo assembly and analysis of Sonneratia ovata genome and population analysis","authors":"Jeremy R. Shearman , Chaiwat Naktang , Chutima Sonthirod , Wasitthee Kongkachana , Sonicha U-Thoomporn , Nukoon Jomchai , Chatree Maknual , Suchart Yamprasai , Poonsri Wanthongchai , Wirulda Pootakham , Sithichoke Tangphatsornruang","doi":"10.1016/j.ygeno.2024.110837","DOIUrl":"10.1016/j.ygeno.2024.110837","url":null,"abstract":"<div><p>Mangroves are an important part of coastal and estuarine ecosystems where they serve as nurseries for marine species and prevent coastal erosion. Here we report the genome of <em>Sonneratia ovata</em>, which is a true mangrove that grows in estuarine environments and can tolerate moderate salt exposure. We sequenced the <em>S. ovata</em> genome and assembled it into chromosome-level scaffolds through the use of Hi-C. The genome is 212.3 Mb and contains 12 chromosomes that range in size from 12.2 to 23.2 Mb. Annotation identified 29,829 genes with a BUSCO completeness of 95.9%. We identified salt genes and found copy number expansion of salt genes such as ADP-ribosylation factor 1, and elongation factor 1-alpha. Population analysis identified a low level of genetic variation and a lack of population structure within <em>S. ovata</em>.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000582/pdfft?md5=a3fdbd8480707c6ea6b48013c13f8d7e&pid=1-s2.0-S0888754324000582-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140318151","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}

引用次数: 0

Study on the interaction protein of transcription factor Smad3 based on TurboID proximity labeling technology 基于 TurboID 近距离标记技术的转录因子 Smad3 互作蛋白研究

IF 4.4 2区生物学

Genomics Pub Date : 2024-03-26 DOI: 10.1016/j.ygeno.2024.110839

Biao Yan , Ting Zeng , Xiaoshan Liu , Yuanyuan Guo , Hongguang Chen , Shuang Guo , Wu Liu

{"title":"Study on the interaction protein of transcription factor Smad3 based on TurboID proximity labeling technology","authors":"Biao Yan , Ting Zeng , Xiaoshan Liu , Yuanyuan Guo , Hongguang Chen , Shuang Guo , Wu Liu","doi":"10.1016/j.ygeno.2024.110839","DOIUrl":"10.1016/j.ygeno.2024.110839","url":null,"abstract":"<div><p>TurboID is a highly efficient biotin-labelling enzyme, which can be used to explore a number of new intercalating proteins due to the very transient binding and catalytic functions of many proteins. TGF-β/Smad3 signaling pathway is involved in many diseases, especially in diabetic nephropathy and inflammation. In this paper, a stably cell line transfected with Smad3 were constructed by using lentiviral infection. To further investigate the function of TGF-β/Smad3, the protein labeling experiment was conducted to find the interacting protein with Smad3 gene. Label-free mass spectrometry analysis was performed to obtain 491 interacting proteins, and the interacting protein hnRNPM was selected for IP and immunofluorescence verification, and it was verified that the Smad3 gene had a certain promoting effect on the expression of hnRNPM gene, and then had an inhibitory effect on IL-6. It lays a foundation for further study of the function of Smad3 gene and its involved regulatory network.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000600/pdfft?md5=ffdf6bc7a2e0734f91561a8b8221768b&pid=1-s2.0-S0888754324000600-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305385","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}

引用次数: 0

Boosting edgeR (Robust) by dealing with missing observations and gene-specific outliers in RNA-Seq profiles and its application to explore biomarker genes for diagnosis and therapies of ovarian cancer 通过处理 RNA-Seq 图谱中的缺失观测值和基因特异性异常值来增强 edgeR（鲁棒性），并将其应用于探索卵巢癌诊断和治疗的生物标记基因。

IF 4.4 2区生物学

Genomics Pub Date : 2024-03-26 DOI: 10.1016/j.ygeno.2024.110834

Bandhan Sarker , Md. Matiur Rahaman , Muhammad Habibulla Alamin , Md. Ariful Islam , Md. Nurul Haque Mollah

{"title":"Boosting edgeR (Robust) by dealing with missing observations and gene-specific outliers in RNA-Seq profiles and its application to explore biomarker genes for diagnosis and therapies of ovarian cancer","authors":"Bandhan Sarker , Md. Matiur Rahaman , Muhammad Habibulla Alamin , Md. Ariful Islam , Md. Nurul Haque Mollah","doi":"10.1016/j.ygeno.2024.110834","DOIUrl":"10.1016/j.ygeno.2024.110834","url":null,"abstract":"<div><p>The edgeR (Robust) is a popular approach for identifying differentially expressed genes (DEGs) from RNA-Seq profiles. However, it shows weak performance against gene-specific outliers and is unable to handle missing observations. To address these issues, we proposed a pre-processing approach of RNA-Seq count data by combining the iLOO-based outlier detection and random forest-based missing imputation approach for boosting the performance of edgeR (Robust). Both simulation and real RNA-Seq count data analysis results showed that the proposed edgeR (Robust) outperformed than the conventional edgeR (Robust). To investigate the effectiveness of identified DEGs for diagnosis, and therapies of ovarian cancer (OC), we selected top-ranked 12 DEGs (<em>IL6, XCL1, CXCL8, C1QC, C1QB, SNAI2, TYROBP, COL1A2, SNAP25, NTS, CXCL2,</em> and <em>AGT</em>) and suggested hub-DEGs guided top-ranked 10 candidate drug-molecules for the treatment against OC. Hence, our proposed procedure might be an effective computational tool for exploring potential DEGs from RNA-Seq profiles for diagnosis and therapies of any disease.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000557/pdfft?md5=5947ffca20222991f38fad62d0e4ad43&pid=1-s2.0-S0888754324000557-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140287287","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}

引用次数: 0

Discovery and characterization of sgRNA-sequence-independent DNA cleavage from CRISPR/Cas9 in mouse embryos 小鼠胚胎中 CRISPR/Cas9 独立于 sgRNA 序列的 DNA 切割的发现与特征。

IF 4.4 2区生物学

Genomics Pub Date : 2024-03-25 DOI: 10.1016/j.ygeno.2024.110836

Liyun Yang , Lijiao Chen , Yang Zheng , Li Deng , Raoxian Bai , Ting Zhang , Zhengbo Wang , Shangang Li

{"title":"Discovery and characterization of sgRNA-sequence-independent DNA cleavage from CRISPR/Cas9 in mouse embryos","authors":"Liyun Yang , Lijiao Chen , Yang Zheng , Li Deng , Raoxian Bai , Ting Zhang , Zhengbo Wang , Shangang Li","doi":"10.1016/j.ygeno.2024.110836","DOIUrl":"10.1016/j.ygeno.2024.110836","url":null,"abstract":"<div><p>The CRISPR/Cas9 system can induce off-target effects in programmed gene editing, but there have been few reports on cleavage detection and their affection in embryo development. To study these events, sgRNAs with different off-target rates were designed and compared after micro-injected into mouse zygotes, and γH2AX was used for DNA cleavage sites analysis by immunostaining and CUT&Tag. Although the low off-target sgRNA were usually selected for production gene editing animals, γH2AX immunofluorescence indicated that there was a relative DSB peak at 15 h after Cas9 system injection, and the number of γH2AX foci at the peak was significantly higher in the low off-target sgRNA-injected group than in the control group. Further, the result of CUT&Tag sequencing analysis showed more double-strand breaks (DSBs) related sequences were detected in low off-target sgRNA-injected group than control and the distribution of DSB related sequences had no chromosome specificity. Gene Ontology (GO) annotation analysis of the DSB related sequences showed that these sequences were mainly concentrated at genes associated with some important biological processes, molecular functions, and cell components. In a conclusion, there are many sgRNA-sequence-independent DSBs in early mouse embryos when the Cas9 system is used for gene editing and the DSB related sequence could be detected and characterized in the genome. These results and method should also be considered in using or optimizing the Cas9 system.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000570/pdfft?md5=5b68cbe9b26f1a40f409018c75132fae&pid=1-s2.0-S0888754324000570-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305383","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}

引用次数: 0

Hypoxic environment promotes angiogenesis and bone bridge formation by activating Notch/RBPJ signaling pathway in HUVECs 缺氧环境通过激活 HUVEC 的 Notch/RBPJ 信号通路促进血管生成和骨桥形成。

IF 4.4 2区生物学

Genomics Pub Date : 2024-03-25 DOI: 10.1016/j.ygeno.2024.110838

Wendong Liu , Mincheng Zou , Mimi Chen , Zheng Zhang , Yunpeng Mao , Yuhao Yang , Ya Liu , Qin Shi , Xiaodong Wang , Fuyong Zhang

{"title":"Hypoxic environment promotes angiogenesis and bone bridge formation by activating Notch/RBPJ signaling pathway in HUVECs","authors":"Wendong Liu , Mincheng Zou , Mimi Chen , Zheng Zhang , Yunpeng Mao , Yuhao Yang , Ya Liu , Qin Shi , Xiaodong Wang , Fuyong Zhang","doi":"10.1016/j.ygeno.2024.110838","DOIUrl":"10.1016/j.ygeno.2024.110838","url":null,"abstract":"<div><p>After epiphyseal fracture, the epiphyseal plate is prone to ischemia and hypoxia, leading to the formation of bone bridge and deformity. However, the exact mechanism controlling the bone bridge formation remains unclear. Notch/RBPJ signaling axis has been indicated to regulate angiogenesis and osteogenic differentiation. Our study aims to investigate the mechanism of bone bridge formation after epiphyseal plate injury, and to provide a theoretical basis for new therapeutic approaches to prevent the bone bridge formation. The expression of DLL4 and RBPJ was significantly up-regulated in HUVECs after ischemia and hypoxia treatment. Notch/RBPJ pathway positively regulated the osteogenic differentiation of BMSCs. HUVECs can induce osteogenic differentiation of BMSCs under ischemia and hypoxia. Notch/RBPJ pathway is involved in the regulation of the trans-epiphyseal bridge formation. Notch/RBPJ in HUVECs is associated with osteogenic differentiation of BMSCs and may participate in the regulation of the bone bridge formation across the epiphyseal plate.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000594/pdfft?md5=e014dca53727aeccb7f18e8e7cd9decf&pid=1-s2.0-S0888754324000594-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140305384","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}

引用次数: 0

Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq 通过 QTL-seq 和 RNA-seq 联合分析鉴定与花生荚果长度相关的候选基因。

IF 4.4 2区生物学

Genomics Pub Date : 2024-03-22 DOI: 10.1016/j.ygeno.2024.110835

Zhenghao Lv , Guohu Lan , Baiyi Bai , Penghao Yu , Chuantang Wang , He Zhang , Chao Zhong , Xinhua Zhao , Haiqiu Yu

{"title":"Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq","authors":"Zhenghao Lv , Guohu Lan , Baiyi Bai , Penghao Yu , Chuantang Wang , He Zhang , Chao Zhong , Xinhua Zhao , Haiqiu Yu","doi":"10.1016/j.ygeno.2024.110835","DOIUrl":"10.1016/j.ygeno.2024.110835","url":null,"abstract":"<div><p>Pod length (PL) is one of the major traits determining pod size and yield of peanut. Discovering the quantitative trait loci (QTL) and identifying candidate genes associated with PL are essential for breeding high-yield peanut. In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F<sub>2</sub> population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265.93 kb region by traditional QTL approach. RNA-seq analysis showed that there were four differentially expressed genes (DEGs) in the candidate region, among which <em>Arahy.PF2L6F</em> (<em>AhCDC48</em>) and <em>Arahy.P4LK2T</em> (<em>AhTAA1</em>) were speculated to be PL-related candidate genes. These results were informative for the elucidation of the underlying regulatory mechanism in peanut pod length and would facilitate further identification of valuable target genes.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000569/pdfft?md5=6e4de44c178144cdc0471b9e49f2abcd&pid=1-s2.0-S0888754324000569-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140193560","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}

引用次数: 0

GCN2-eIF2α signaling pathway negatively regulates the growth of triploid crucian carp GCN2-eIF2α信号通路对三倍体鲫鱼的生长有负向调节作用。

IF 4.4 2区生物学

Genomics Pub Date : 2024-03-20 DOI: 10.1016/j.ygeno.2024.110832

Xuejing Wang , Fangyuan Peng , Shuli Yuan , Zhen Huang , Lingwei Tang , Song Chen , Jinhui Liu , Wen Fu , Liangyue Peng , Wenbin Liu , Yamei Xiao

{"title":"GCN2-eIF2α signaling pathway negatively regulates the growth of triploid crucian carp","authors":"Xuejing Wang , Fangyuan Peng , Shuli Yuan , Zhen Huang , Lingwei Tang , Song Chen , Jinhui Liu , Wen Fu , Liangyue Peng , Wenbin Liu , Yamei Xiao","doi":"10.1016/j.ygeno.2024.110832","DOIUrl":"10.1016/j.ygeno.2024.110832","url":null,"abstract":"<div><p>GCN2-eIF2α signaling pathway plays crucial roles in cell growth,development, and protein synthesis. However, in polyploid fish, the function of this pathway is rarely understood. In this study, genes associated with the GCN2-eIF2α pathway (<em>pkr, pek, gcn2, eif2α</em>) are founded lower expression levels in the triploid crucian carp (3nCC) muscle compared to that of the red crucian carp (RCC). In muscle effect stage embryos of the 3nCC, the mRNA levels of this pathway genes are generally lower than those of RCC, excluding <em>hri</em> and <em>fgf21.</em> Inhibiting <em>gcn2</em> in 3nCC embryos downregulates downstream gene expression (<em>eif2α, atf4, fgf21</em>), accelerating embryonic development. In contrast, overexpressing of <em>eif2α</em> can alter the expression levels of downstream genes (<em>atf4</em> and <em>fgf21</em>), and decelerates the embryonic development. These results demonstrate the GCN2-eIF2α pathway's regulatory impact on 3nCC growth, advancing understanding of fish rapid growth genetics and offering useful molecular markers for breeding of excellent strains.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":4.4,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324000533/pdfft?md5=4a195c211f288171419c13fca25a5579&pid=1-s2.0-S0888754324000533-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140189635","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}

引用次数: 0