Genomics最新文献

{"title":"TIMP1 promotes thyroid cancer cell progression through macrophage phenotypic polarization via the PI3K/AKT signaling pathway","authors":"Xu Lin ,&nbsp;Ruhua Zhao ,&nbsp;Yu Bin ,&nbsp;Ronghua Huo ,&nbsp;Gang Xue ,&nbsp;Jingfang Wu","doi":"10.1016/j.ygeno.2024.110914","DOIUrl":"10.1016/j.ygeno.2024.110914","url":null,"abstract":"<div><p>Increasing evidence suggests that tissue inhibitor of metalloproteinase 1 (TIMP1) played a pivotal role in immune regulation. Our study focused on examining the expression and function of TIMP1 in humans, particularly in its regulation of tumor-associated macrophages (TAMs) in papillary thyroid carcinoma (PTC). We observed an upregulation of TIMP1 in 16 different types of malignancies, including thyroid cancer. TIMP1 shaped the inflammatory TME in PTC. Inhibiting the expression of TIMP1 has been demonstrated to reduce the malignant biological traits of PTC cells. Furthermore, reducing TIMP1 expression impeded M2 macrophage polarization as well as facilitated M1 macrophage polarization in PTC. ELISA results demonstrated that downregulated TIMP1 expression correlated with decreased levels of IL10 and TGF-β in cell supernatants. Furthermore, the supernatant from polarized macrophages in the TIMP1-silenced group inhibited the motility of wild-type PTC cells. Therefore, TIMP1 may enhance the progression of PTC by stimulating the PI3K/AKT pathway via the secretion of IL10 and TGF-β, consequently influencing M2-type polarization in TAMs.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001356/pdfft?md5=5582fc7a09310a003596459f151017c6&pid=1-s2.0-S0888754324001356-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141916537","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":"Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance","authors":"Wei Yang ,&nbsp;Zhou Yang ,&nbsp;Lei Yang ,&nbsp;Zheng Li ,&nbsp;Zhaowu Zhang ,&nbsp;Tong Wei ,&nbsp;Renliang Huang ,&nbsp;Guotian Li","doi":"10.1016/j.ygeno.2024.110915","DOIUrl":"10.1016/j.ygeno.2024.110915","url":null,"abstract":"<div><p>The <em>indica</em> rice variety Huizhan shows elite traits of disease resistance and heat tolerance. However, the underlying genetic basis of these traits is not fully understood due to limited genomic resources. Here, we used Nanopore long-read and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan. Comparative genomics analysis uncovered a large chromosomal inversion and expanded gene families that are associated with plant growth, development and stress responses. Functional rice blast resistance genes, including <em>Pi2</em>, <em>Pib</em> and <em>Ptr</em>, and bacterial blight resistance gene <em>Xa27</em>, contribute to disease resistance of Huizhan. Furthermore, integrated genomics and transcriptomics analyses showed that <em>OsHIRP1</em>, <em>OsbZIP60</em>, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan. The high-quality genome assembly and comparative genomics results presented in this study facilitate the use of Huizhan as an elite parental line in developing rice varieties adapted to disease pressure and climate challenges.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001368/pdfft?md5=da8eb04e19267bc2298ea127b70265eb&pid=1-s2.0-S0888754324001368-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970945","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":"The expression spectrum of yak epididymal epithelial cells reveals the functional diversity of caput, corpus and cauda regions","authors":"Meilan Pan ,&nbsp;Xiaofeng Luo ,&nbsp;Zhenzhen Zhang ,&nbsp;Jingjing Li ,&nbsp;Khuram Shahzad ,&nbsp;Zhaxi Danba ,&nbsp;Gongbu Caiwang ,&nbsp;Wangmu Chilie ,&nbsp;Xiaoying Chen ,&nbsp;Wangsheng Zhao","doi":"10.1016/j.ygeno.2024.110912","DOIUrl":"10.1016/j.ygeno.2024.110912","url":null,"abstract":"<div><p>Sperm undergo a series of changes in the epididymis region before acquiring the ability to move and fertilize, and the identification of genes expressed in a region-specific manner in the epididymis provides a valuable insight into functional differences between regions. We collected epididymal tissue from three yaks and cultured epithelial cells from the caput, corpus and cauda regions of the yak epididymis using the tissue block method. RNA sequencing analysis (RNA-seq) technology was used to detect gene expression in yak epididymal caput, corpus and cauda epithelial cells. The results showed that the DEGs were highest in the caput <em>vs.</em> corpus comparison, and lowest in the corpus <em>vs.</em> cauda comparison. Six DEGs were verified by real-time fluorescence quantitative PCR (qRT-PCR), consistent with transcriptome sequencing results. The significantly enriched DNA replication pathway in the caput <em>vs.</em> corpus was coordinated with cell proliferation, while upregulated DEGs such as <em>POLD1</em> and <em>MCM4</em> were found in the DNA replication pathway. The AMPK signaling pathway was found significantly enriched in the caput <em>vs</em> cauda, suggesting its involvement in sperm maturation and capacitation. The TGF beta signaling pathway was screened in the corpus <em>vs</em> cauda and is crucial for mammalian reproductive regulation. Upregulated DEGs (<em>TGFB3</em>, <em>INHBA</em>, <em>INHBB</em>) are involved in the TGF beta signaling pathway. This study provides a reference for culturing yak epididymal epithelial cells <em>in vitro</em>, and elucidates the transcriptional profiles of epithelial cells in different segments of the epididymis, revealing the regulatory and functional differences between different segments, providing basic data for exploring the molecular mechanism of yak sperm maturation and improving the reproductive capacity of high-altitude mammals.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001332/pdfft?md5=d798ee86c9a0f2d044490f78d2c7beda&pid=1-s2.0-S0888754324001332-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141906386","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":"Unraveling the complexity of asymmetric DNA replication: Advancements in ribonucleotide mapping techniques and beyond","authors":"Alberto Bugallo ,&nbsp;Mónica Segurado","doi":"10.1016/j.ygeno.2024.110908","DOIUrl":"10.1016/j.ygeno.2024.110908","url":null,"abstract":"<div><p>DNA replication is a fundamental process for cell proliferation, governed by intricate mechanisms involving leading and lagging strand synthesis. In eukaryotes, canonical DNA replication occurs during the S phase of the cell cycle, facilitated by various components of the replicative machinery at sites known as replication origins. Leading and lagging strands exhibit distinct replication dynamics, with leading strand replication being relatively straightforward compared to the complex synthesis of lagging strands involving Okazaki fragment maturation. Central to DNA synthesis are DNA polymerases, with Polα, Polε, and Polδ playing pivotal roles, each specializing in specific tasks during replication. Notably, leading and lagging strands are replicated by different polymerases, contributing to the division of labor in DNA replication. Understanding the enzymology of asymmetric DNA replication has been challenging, with methods relying on ribonucleotide incorporation and next-generation sequencing techniques offering comprehensive insights. These methodologies, such as HydEn-seq, PU-seq, ribose-seq, and emRiboSeq, offer insights into polymerase activity and strand synthesis, aiding in understanding DNA replication dynamics. Recent advancements include novel conditional mutants for ribonucleotide excision repair, enzymatic cleavage alternatives, and unified pipelines for data analysis. Further developments in adapting techniques to different organisms, studying non-canonical polymerases, and exploring new sequencing platforms hold promise for expanding our understanding of DNA replication dynamics. Integrating strand-specific information into single-cell studies could offer novel insights into enzymology, opening avenues for future research and applications in repair and replication biology.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001290/pdfft?md5=b151a928ffaf0efcc9a705417da239dd&pid=1-s2.0-S0888754324001290-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141897248","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":"Enhancing schizophrenia phenotype prediction from genotype data through knowledge-driven deep neural network models","authors":"Daniel Martins ,&nbsp;Maryam Abbasi ,&nbsp;Conceição Egas ,&nbsp;Joel P. Arrais","doi":"10.1016/j.ygeno.2024.110910","DOIUrl":"10.1016/j.ygeno.2024.110910","url":null,"abstract":"<div><p>This article explores deep learning model design, drawing inspiration from the omnigenic model and genetic heterogeneity concepts, to improve schizophrenia prediction using genotype data. It introduces an innovative three-step approach leveraging neural networks' capabilities to efficiently handle genetic interactions. A locally connected network initially routes input data from variants to their corresponding genes. The second step employs an Encoder-Decoder to capture relationships among identified genes. The final model integrates knowledge from the first two and incorporates a parallel component to consider the effects of additional genes. This expansion enhances prediction scores by considering a larger number of genes. Trained models achieved an average AUC of 0.83, surpassing other genotype-trained models and matching gene expression dataset-based approaches. Additionally, tests on held-out sets reported an average sensitivity of 0.72 and an accuracy of 0.76, aligning with schizophrenia heritability predictions. Moreover, the study addresses genetic heterogeneity challenges by considering diverse population subsets.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001319/pdfft?md5=05dc9164810795ff25d26a05f27f02e0&pid=1-s2.0-S0888754324001319-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901499","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":"Screening of novel disease genes of sepsis-induced myocardial Disfunction by RNA sequencing and bioinformatics analysis","authors":"Hanyi Yao ,&nbsp;Zixi Xiao ,&nbsp;Shufang Liu ,&nbsp;Xingjian Gao ,&nbsp;Zehong Wu ,&nbsp;Dongping Li ,&nbsp;Zhangqing Yi ,&nbsp;Haojie Zhou ,&nbsp;Weizhi Zhang","doi":"10.1016/j.ygeno.2024.110911","DOIUrl":"10.1016/j.ygeno.2024.110911","url":null,"abstract":"<div><h3>Background</h3><p>There is still a lack of effective treatment for sepsis-induced myocardial dysfunction (SIMD), while the pathogenesis of SIMD still remains largely unexplained.</p></div><div><h3>Methods</h3><p>RNA sequencing results (GSE267388 and GSE79962) were used for cross-species integrative analysis. Bioinformatic analyses were used to delve into function, tissue- and cell- specificity, and interactions of genes. External datasets and qRT-PCR experiments were used for validation. L1000 FWD was used to predict targeted drugs, and 3D structure files were used for molecular docking.</p></div><div><h3>Results</h3><p>Based on bioinformatic analyses, ten differentially expressed genes were selected as genes of interest, seven of which were verified to be significantly differential expression. Bucladesine was considered as a potential targeted drug for SIMD, which banded to seven target proteins primarily by forming hydrogen bonds.</p></div><div><h3>Conclusion</h3><p>It was considered that <em>Cebpd</em>, <em>Timp1</em>, <em>Pnp</em>, <em>Osmr</em>, <em>Tgm2</em>, <em>Cp,</em> and <em>Asb2</em> were novel disease genes, while bucladesine was a potential therapeutic drug, of SIMD.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001320/pdfft?md5=cca2d967557214ef34591f2420bd9b5c&pid=1-s2.0-S0888754324001320-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901500","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":"Dissecting transposable elements and endogenous retroviruses upregulation by HDAC inhibitors in leiomyosarcoma cells: Implications for the interferon response","authors":"Nicolò Gualandi,&nbsp;Martina Minisini,&nbsp;Alessio Bertozzo,&nbsp;Claudio Brancolini","doi":"10.1016/j.ygeno.2024.110909","DOIUrl":"10.1016/j.ygeno.2024.110909","url":null,"abstract":"<div><p>Transposable elements (TEs) are of interest as immunomodulators for cancer therapies. TEs can fold into dsRNAs that trigger the interferon response. Here, we investigated the effect of different HDAC inhibitors (HDACIs) on the expression of TEs in leiomyosarcoma cells. Our data show that endogenous retroviruses (ERVs), especially ERV1 elements, are upregulated after treatment with HDAC1/2/3-specific inhibitors. Surprisingly, the interferon response was not activated. We observed an increase in A-to-I editing of upregulated ERV1. This could have an impact on the stability of dsRNAs and the activation of the interferon response. We also found that H3K27ac levels are increased in the LTR12 subfamilies, which could be regulatory elements controlling the expression of proapoptotic genes such as <em>TNFRSF10B</em>. In summary, we provide a detailed characterization of TEs modulation in response to HDACIs and suggest the use of HDACIs in combination with ADAR inhibitors to induce cell death and support immunotherapy in cancer.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001307/pdfft?md5=6f2801b75ee2c5d7fd35841f95f86b6b&pid=1-s2.0-S0888754324001307-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141893237","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":"Transcriptomic analysis of different intramuscular fat contents on the flavor of the longissimus dorsi tissues from Guangling donkey","authors":"Wufeng Li ,&nbsp;LiLi ,&nbsp;Xi Wang","doi":"10.1016/j.ygeno.2024.110905","DOIUrl":"10.1016/j.ygeno.2024.110905","url":null,"abstract":"<div><h3>Background</h3><p>In this study, researchers aimed to explore the impact of intramuscular fat (IMF) concentration on the flavor of donkey meat, specifically in the longissimus dorsi muscle of Guangling donkeys. The internal volatile organic compounds that cause the flavor differences between donkey muscles are not clear at present. Transcriptomic technologies were utilized to analyze gene expression and its relationship to donkey meat flavor.</p></div><div><h3>Method</h3><p>Thirty Guangling donkeys had their IMF content evaluated in the longissimus dorsi muscle. Based on IMF content, 16 donkeys of similar ages were divided into two groups: low-fat (L) and high-fat (H). Headspace solid-phase microextraction Gas chromatography-mass spectrometry (HS-SPME-GC–MS) and headspace solid phase microextraction mass spectrometry were used to identify potential flavor components that differed between the two groups.</p></div><div><h3>Results</h3><p>Five key volatile substances were identified, and WGCNA and KEGG analysis was conducted to analyze the genes associated with these substances. The results showed that pathways like PPAR signaling, nucleotide excision repair, glucagon signaling, arachidonic acid metabolism, and glycolysis/glycogenesis were involved in lipid deposition. Additionally, a gene-gene interaction network map was constructed, highlighting the importance of hub genes such as <em>EEF2, DDX49, GAP43, SNAP25, NDUFS8, MRPS11, RNASEH2A, POLR2E, POLR2C</em> and <em>ALB</em> in regulating key flavor substances.</p></div><div><h3>Conclusion</h3><p>This study provided valuable insights into the regulation of genes and protein expression related to flavor substances in donkey meat. It also deepened understanding of the influence of IMF on flavor and laid a foundation for future molecular breeding improvements in Guangling donkeys.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001265/pdfft?md5=bd806337e79ad9945333abd324d2c576&pid=1-s2.0-S0888754324001265-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859506","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":"W2V-repeated index: Prediction of enhancers and their strength based on repeated fragments","authors":"Weiming Xie ,&nbsp;Zhaomin Yao ,&nbsp;Yizhe Yuan ,&nbsp;Jingwei Too ,&nbsp;Fei Li ,&nbsp;Hongyu Wang ,&nbsp;Ying Zhan ,&nbsp;Xiaodan Wu ,&nbsp;Zhiguo Wang ,&nbsp;Guoxu Zhang","doi":"10.1016/j.ygeno.2024.110906","DOIUrl":"10.1016/j.ygeno.2024.110906","url":null,"abstract":"<div><p>Enhancers are crucial in gene expression regulation, dictating the specificity and timing of transcriptional activity, which highlights the importance of their identification for unravelling the intricacies of genetic regulation. Therefore, it is critical to identify enhancers and their strengths. Repeated sequences in the genome are repeats of the same or symmetrical fragments. There has been a great deal of evidence that repetitive sequences contain enormous amounts of genetic information. Thus, We introduce the W2V-Repeated Index, designed to identify enhancer sequence fragments and evaluates their strength through the analysis of repeated K-mer sequences in enhancer regions. Utilizing the word2vector algorithm for numerical conversion and Manta Ray Foraging Optimization for feature selection, this method effectively captures the frequency and distribution of K-mer sequences. By concentrating on repeated K-mer sequences, it minimizes computational complexity and facilitates the analysis of larger K values. Experiments indicate that our method performs better than all other advanced methods on almost all indicators.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001277/pdfft?md5=0d0ea4c1427e7c0c571c9c7409b124e9&pid=1-s2.0-S0888754324001277-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859507","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":"Genome-wide association analysis reveals the genetic basis of thermal tolerance in dwarf surf clam Mulinia lateralis","authors":"Haoran Wang ,&nbsp;Zujing Yang ,&nbsp;Shenhai Wang ,&nbsp;Ang Zhao ,&nbsp;Hao Wang ,&nbsp;Zhi Liu ,&nbsp;Mingyi Sui ,&nbsp;Lijingjing Bao ,&nbsp;Qifan Zeng ,&nbsp;Jingjie Hu ,&nbsp;Zhenmin Bao ,&nbsp;Xiaoting Huang","doi":"10.1016/j.ygeno.2024.110904","DOIUrl":"10.1016/j.ygeno.2024.110904","url":null,"abstract":"<div><p>Recently, elevated seawater temperatures have resulted numerous adverse effects, including significant mortality among bivalves. The dwarf surf clam, <em>Mulinia lateralis</em>, is considered a valuable model species for bivalve research due to its rapid growth and short generation time. The successful cultivation in laboratory setting throughout its entire life cycle makes it an ideal candidate for exploring the potential mechanisms underlying bivalve responses to thermal stress. In this study, a total of 600 clams were subjected to a 17-day thermal stress experiment at a temperature of 30 °C which is the semi-lethal temperature for this species. Ninety individuals who perished initially were classified as heat-sensitive populations (HSP), while 89 individuals who survived the experiment were classified as heat-tolerant populations (HTP). Subsequently, 179 individuals were then sequenced, and 21,292 single nucleotide polymorphisms (SNPs) were genotyped for downstream analysis. The heritability estimate for survival status was found to be 0.375 ± 0.127 suggesting a genetic basis for thermal tolerance trait. Furthermore, a genome-wide association study (GWAS) identified three SNPs and 10 candidate genes associated with thermal tolerance trait in <em>M. lateralis</em>. These candidate genes were involved in the <em>ETHR</em>/<em>EHF</em> signaling pathway and played pivotal role in signal sensory, cell adhesion, oxidative stress, DNA damage repair, etc. Additionally, qPCR results indicated that, excluding <em>MGAT4A</em>, <em>ZAN</em>, and <em>RFC1</em> genes, all others exhibited significantly higher expression in the HTP (<em>p</em> &lt; 0.05), underscoring the critical involvement of the <em>ETHR</em>/<em>EHF</em> signaling pathway in <em>M. lateralis</em>' thermal tolerance. These results unveil the presence of standing genetic variations associated with thermal tolerance in <em>M. lateralis</em>, highlighting the regulatory role of the <em>ETHR</em>/<em>EHF</em> signaling pathway in the bivalve's response to thermal stress, which contribute to comprehension of the genetic basis of thermal tolerance in bivalves.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001253/pdfft?md5=da29085f952a8ca872e24d3ac5be6b91&pid=1-s2.0-S0888754324001253-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141859505","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}