Genomics最新文献

{"title":"Brain lncRNA-mRNA co-expression regulatory networks and alcohol use disorder","authors":"Ojong Tabi Ojong Besong ,&nbsp;Ji Sun Koo ,&nbsp;Huiping Zhang","doi":"10.1016/j.ygeno.2024.110928","DOIUrl":"10.1016/j.ygeno.2024.110928","url":null,"abstract":"<div><p>Prolonged alcohol consumption can disturb the expression of both coding and noncoding genes in the brain. These dysregulated genes may co-express in modules and interact within networks, consequently influencing the susceptibility to developing alcohol use disorder (AUD). In the present study, we performed an RNA-seq analysis of the expression of both long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in 192 postmortem tissue samples collected from eight brain regions (amygdala, caudate nucleus, cerebellum, hippocampus, nucleus accumbens, prefrontal cortex, putamen, and ventral tegmental area) of 12 AUD and 12 control subjects of European ancestry. Applying the limma-voom method, we detected a total of 57 lncRNAs and 51 mRNAs exhibiting significant differential expression (<em>P</em>_adj &lt; 0.05 and fold-change ≥2) across at least one of the eight brain regions investigated. Machine learning analysis further confirmed the potential of these top genes in predicting AUD. Through Weighted Gene Co-expression Network Analysis (WGCNA), we identified distinct lncRNA-mRNA co-expression modules associated with AUD in each of the eight brain regions. Additionally, lncRNA-mRNA co-expression networks were constructed for each brain region using Cytoscape to reveal gene regulatory interactions implicated in AUD. Hub genes within these networks were found to be enriched in several key KEGG pathways, including <em>Axon Guidance</em>, <em>MAPK Signaling</em>, <em>p53 Signaling</em>, <em>Adherens Junction</em>, and <em>Neurodegeneration</em>. Our results underscore the significance of networks involving AUD-associated lncRNAs and mRNAs in modulating neuroplasticity in response to alcohol exposure. Further elucidating these molecular mechanisms holds promise for the development of targeted therapeutic interventions for AUD.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001496/pdfft?md5=985fb9f6d87ace43e4fb38797a1213af&pid=1-s2.0-S0888754324001496-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142092720","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":"Whole transcriptome sequencing indicated the Anti-tumor immunity of NLRP3 in breast cancer","authors":"Da Qian ,&nbsp;Jie Qiu ,&nbsp;Yadan Xu ,&nbsp;Weimin Hong ,&nbsp;Chaoqi He ,&nbsp;Dandan Guan ,&nbsp;Qinghui Zheng ,&nbsp;Xiaozhen Liu ,&nbsp;Chaoshen Wu ,&nbsp;Xuli Meng ,&nbsp;Hongchao Tang","doi":"10.1016/j.ygeno.2024.110930","DOIUrl":"10.1016/j.ygeno.2024.110930","url":null,"abstract":"<div><p>Breast cancer (BC) is a prevalent cancer of the female reproductive system and a major contributor to cancer-related mortality. The activation of NLRP3, a key inflammasome, has been extensively associated with tumor-related molecular and cellular processes; however, the regulatory mechanisms and specific role of NLRP3 in breast cancer remain incompletely elucidated. This study aimed to evaluate the molecular mechanisms of NLRP3-related genes in BC. Utilizing bioinformatics methods, the present research analyzed the TCGA-BRCA dataset, which included four groups of transcriptome sequencing data as follows, normal (WT), NLRP3 knockout (KO), non-knockout-BRCA (BC-WT), and NLRP3-knockout-BRCA (BC-KO). Results indicated that NLRP3 was significantly down-regulated in TCGA-BRCA. Key module genes were mainly enriched in leukocyte cell-cell adhesion and cytokine-cytokine receptor interaction. Moreover, correlation analysis showed that NLRP3 was positively associated with cancer-associated fibroblasts and negatively associated with CD4⁺ Th1 T-cells. In addition, the DEGs1 and DEGs2 overlapping indicated 505 feature genes, with Chac1 (negative) and Ugt8a (positive) had the strongest correlation with differential immune cells (class-switched memory B cells). Pathway intersection revealed 13 co-KEGG pathways. The BC-KO group indicated markedly reduced levels of four genes (Ccl19, Ccl20, Ccl21a, and H2-Oa) and increased levels of two genes (Il2ra and H2-Ob). This study delved into the role of NLRP3 in BC, exploring its regulatory mechanisms and the impact gene knockout. Bioinformatics approaches identified NLRP3-associated genes, their enriched pathways, and interactions within the tumor microenvironment (TME), providing novel insights into NLRP3 function, TME dynamics, and potential targets for BC prevention and treatment.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001514/pdfft?md5=1373f55937e1c0bd0daceafdddb4b0b3&pid=1-s2.0-S0888754324001514-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142096762","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":"Genetic structure analysis of yak breeds and their response to adaptive evolution","authors":"Qingbo Zheng ,&nbsp;Xiaoyun Wu ,&nbsp;Xiaoming Ma ,&nbsp;Xuelan Zhou ,&nbsp;Tong Wang ,&nbsp;Chaofan Ma ,&nbsp;Minghao Zhang ,&nbsp;Min Chu ,&nbsp;Xian Guo ,&nbsp;Chunnian Liang ,&nbsp;Pengjia Bao ,&nbsp;Ping Yan","doi":"10.1016/j.ygeno.2024.110933","DOIUrl":"10.1016/j.ygeno.2024.110933","url":null,"abstract":"<div><p>Yaks are crucial genetic resources in the Tibetan Plateau and surrounding regions. Throughout the long process of domestication, natural and artificial selection pressures have enabled yaks to demonstrate adaptive characteristics to the environment in terms of physiological structure and genetic molecules, but no systematic cell analysis has been carried out on this phenomenon of yaks. Here, the population structure and genetic diversity of yak were studied by WGRS, and the genes related to yak adaptability were excavated. Combined with scRNA-seq method, the transcription map of yak lung tissue and skin tissue was constructed, which provided a new comprehensive insight into yak adaptability. The analysis of yak population structure showed that there was obvious genetic differentiation between TZ _ yak and other seven yak populations, while there was significant genetic exchange between PL _ yak and SB _ yak at high altitude. WGRS and scRNA-seq analysis revealed that the gene <em>HIF1A</em> related to high altitude adaptation was expressed in various cell types, while <em>EPAS1</em> was predominantly expressed in epithelial and endothelial cells of yak lung tissue. Endothelial cells play a critical role in hypoxia-adapted VEGF signaling, which correlates closely with the high expression of <em>KDR</em> and <em>VEGFA</em> genes in endothelial cells and monocytes. Furthermore, in the selection signal of High _ yak vs Low _ yak, 19.8 % of the genes overlapped with the genes screened by skin scRNA-seq, including genes related to coat color such as <em>RORA</em>, <em>BNC2</em>, and <em>KIT</em>. Notably, <em>BNC2</em> is a gene associated with melanin deposition and shows high expression levels in HS cells. Additionally, <em>GRN</em> in melanocytes and <em>SORT1</em> in IRS play an important role in cell communication between melanocytes and IRS. These findings offer new insights into the natural polymorphism of yaks and provide a valuable reference for future research on high-altitude mammals, and potentially even human genetics.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S088875432400154X/pdfft?md5=48fe0a298ec245a427a516a4848cdc28&pid=1-s2.0-S088875432400154X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142106304","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":"Distinct transcriptional profiles in rat thyroid glands after developmental exposure to three in vitro thyroperoxidase inhibiting chemicals","authors":"Anna Kjerstine Rosenmai ,&nbsp;Terje Svingen ,&nbsp;Bertrand Evrard ,&nbsp;Khanh Hoang Nguyen ,&nbsp;Camilla Nielsen ,&nbsp;Marta Axelstad ,&nbsp;Frédéric Chalmel ,&nbsp;Louise Ramhøj","doi":"10.1016/j.ygeno.2024.110938","DOIUrl":"10.1016/j.ygeno.2024.110938","url":null,"abstract":"<div><div>Thyroperoxidase (TPO) is central in thyroid hormone (TH) synthesis and inhibition can lead to TH deficiency. Many chemicals can inhibit TPO activity <em>in vitro</em>, but how this may manifest in the developing thyroid gland at the molecular level is unclear. Here, we characterized the thyroid gland transcriptome of male rats developmentally exposed to the <em>in vitro</em> TPO-inhibitors amitrole, 2-mercaptobenzimidazole (MBI), or cyanamide by use of Bulk-RNA-Barcoding (BRB) and sequencing. Amitrole exposure caused TH deficiency and 149 differentially expressed genes in the thyroid gland. The effects indicated an activated and growing thyroid gland. MBI caused intermittent changes to serum TH concentrations in a previous study and this was accompanied by 60 differentially expressed genes in the present study. More than half of these were also affected by amitrole, indicating that they could be early effect biomarkers of developmental TH system disruption due to TPO inhibition. Further work to validate the signature is needed, including assessment of substance independency and applicability domain.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001599/pdfft?md5=12f068f718b88b8fea3d77fbb761d282&pid=1-s2.0-S0888754324001599-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263596","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":"Impairment of oocyte quality caused by gut microbiota dysbiosis in obesity","authors":"Liying Shan ,&nbsp;Haitao Fan ,&nbsp;Jing Guo ,&nbsp;Heyang Zhou ,&nbsp;Fengguo Li ,&nbsp;Zhimin Jiang ,&nbsp;Duo Wu ,&nbsp;Xinlei Feng ,&nbsp;Ren Mo ,&nbsp;Yongbin Liu ,&nbsp;Teng Zhang ,&nbsp;Yang Zhou","doi":"10.1016/j.ygeno.2024.110941","DOIUrl":"10.1016/j.ygeno.2024.110941","url":null,"abstract":"<div><div>Obesity poses risks to oocyte maturation and embryonic development in mice and humans, linked to gut microbiota dysbiosis and altered host metabolomes. However, it is unclear whether symbiotic gut microbes have a pivotal role in oocyte quality. In mouse models of fecal microbiota transplantation, we demonstrated aberrant meiotic apparatus and impaired maternal mRNA in oocytes, which is coincident with the poor developmental competence of embryos. Using metabolomics profiling, we discovered that the cytosine and cytidine metabolism was disturbed, which could account for the fertility defects observed in the high-fat diet (HFD) recipient mice. Additionally, cytosine and cytidine are closely related with gut microbiota dysbiosis, which is accompanied by a notable reduction of abundance of <em>Christensenellaceae R-7 group</em> in the HFD mice. In summary, our findings provided evidence that modifying the gut microbiota may be of value in the treatment of infertile female individuals with obesity.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001629/pdfft?md5=8f2cb2a04be423f8074b7ebdca3ae05b&pid=1-s2.0-S0888754324001629-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142283609","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":"Role of circPAPD7 in regulating proliferation and differentiation of goat skeletal muscle satellite cells","authors":"Siyuan Zhan ,&nbsp;Wei Zhao ,&nbsp;Tao Zhong ,&nbsp;Linjie Wang ,&nbsp;Jiazhong Guo ,&nbsp;Jiaxue Cao ,&nbsp;Li Li ,&nbsp;Hongping Zhang","doi":"10.1016/j.ygeno.2024.110936","DOIUrl":"10.1016/j.ygeno.2024.110936","url":null,"abstract":"<div><p>The circular RNA (circRNA) plays a crucial role in various biological processes, particularly posttranscriptional regulation. However, the role of circRNA in the development of goat skeletal muscle has not been thoroughly explored. Here, we identified circPAPD7, which is a novel circular RNA that is preferentially expressed in the skeletal muscle. Functional assays demonstrated that circPAPD7 promoted proliferation and inhibited differentiation in goat skeletal muscle satellite cells (MuSCs). Mechanistically, it was discovered that circPAPD7 interacts with miR-26a-5p. Moreover, the rescue experiments indicated that the overexpression of circPAPD7 may reverse the inhibitory impact of miR-26a-5p on myoblast proliferation and the accelerated effects on differentiation. Furthermore, we provided evidence that circPAPD7 functions as a sponge for miR-26a-5p, thereby facilitating the upregulation of EZH2 expression in goat MuSCs. Together, the results revealed that circPAPD7 promote proliferation and inhibit differentiation of goat MuSCs via the miR-26a-5p/EZH2 pathway.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001575/pdfft?md5=08b5f7ac9b2193423e46b6eb407608db&pid=1-s2.0-S0888754324001575-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142239555","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":"Differentially expressed circular RNA profiles and comprehensive analysis of circRNA-miRNA-mRNA regulatory network in microsatellite instability-high endometrial cancer","authors":"Weijia Wen ,&nbsp;Li Yuan ,&nbsp;Xueyuan Zhao ,&nbsp;Yan Jia ,&nbsp;Linna Chen ,&nbsp;Hongye Jiang ,&nbsp;Wei Wang ,&nbsp;Chunyu Zhang ,&nbsp;Shuzhong Yao","doi":"10.1016/j.ygeno.2024.110931","DOIUrl":"10.1016/j.ygeno.2024.110931","url":null,"abstract":"<div><p>The clinical benefit of anti-programmed cell death protein 1 (PD-1)-based immunotherapy among patients with microsatellite instable (MSI) endometrial cancer (EC) precedes that of microsatellite stable (MSS) EC, the mechanisms of which have not been fully understood. Circular RNAs (circRNAs) were reported to modulate immune evasion in several types of malignancies, while their roles in the immune regulation in EC remain largely unknown. Here, we conducted circRNA array analysis and mRNA-Sequencing of 10 MSI EC samples and 10 MSS EC samples and identified 1083 differentially expressed circRNAs (DE-circRNAs) and 864 differentially expressed mRNAs, based on which we constructed a circRNA-miRNA-mRNA comprehensive network consisting of 35 DE-circRNAs, 56 predicted miRNAs and 24 differentially expressed mRNAs. Finally, we confirmed hsa_circ_0058230 being positively correlated with CD8+ T cells infiltration, suggesting that it might take a part in anti-tumor immunity in EC.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001526/pdfft?md5=eada44f563206f78943efdc7bd21929b&pid=1-s2.0-S0888754324001526-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142096761","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":"Multi-omics analysis reveals a pericyte-associated gene expression signature for predicting prognosis and therapeutic responses in solid cancers","authors":"Xiangzhan Kong ,&nbsp;Xianhua Zhuo ,&nbsp;Xi Huang ,&nbsp;Lihuan Shang ,&nbsp;Tianjun Lan ,&nbsp;Hongquan Qin ,&nbsp;Xiaochun Chen ,&nbsp;Cui Lv ,&nbsp;Qiuping Xu ,&nbsp;Ping-Pui Wong","doi":"10.1016/j.ygeno.2024.110942","DOIUrl":"10.1016/j.ygeno.2024.110942","url":null,"abstract":"<div><div>The influence of the stroma on cancer progression has been underestimated, particularly the role of vascular pericytes in the tumor microenvironment. Herein, we identified 51 differentially expressed genes in tumor-derived pericytes (TPCs) by analyzing transcriptomic data from TCGA alongside our proteomic data. Using five key TPC-related genes, we constructed a prognostic risk model that accurately predicts prognosis and treatment responses in liver and lung cancers. Enrichment analyses linked these genes to blood vessel remodeling, function, and immune-related pathways. Single-cell RNA sequencing data from the GEO database validated these findings, showing significant upregulation of AKAP12 and RRAS in TPCs. Immunostaining confirmed increased expression of these genes in liver and lung tumors. Depletion of RRAS or AKAP12 in TPCs restored their blood vessel-supporting role. Overall, our findings suggest that TPC-related gene profiles can predict patient outcomes and therapeutic responses in solid cancers, and targeting these profiles could be an improved treatment strategy.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142320386","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":"Transcriptome analysis reveals that defects in cell cycle regulation contribute to preimplantation embryo arrest","authors":"Xin Li ,&nbsp;Yang Zou ,&nbsp;Baobao Geng ,&nbsp;Peipei Liu ,&nbsp;Liyun Cao ,&nbsp;Zhiqin Zhang ,&nbsp;Shaofeng Hu ,&nbsp;Changhua Wang ,&nbsp;Yan Zhao ,&nbsp;Qiongfang Wu ,&nbsp;Jun Tan","doi":"10.1016/j.ygeno.2024.110946","DOIUrl":"10.1016/j.ygeno.2024.110946","url":null,"abstract":"<div><div>Patients with preimplantation embryo arrest (PREMBA) often experience assisted reproductive failure primarily due to the lack of transferable embryos, and the molecular mechanisms underlying PREMBA remain unclear. In our study, the embryos from five women with recurrent preimplantation embryo arrest and three women with tubal factor infertility were used for single-embryo transcriptome sequencing. Meanwhile, the transcriptomes of normal human preimplantation embryos obtained from GSE36552 were utilized to perform a comparative analysis with the transcriptomes of PREMBA embryos. Our results showed dysregulation of the cell cycle phase transition might be a potential pathogenic factor contributing to PREMBA. Through integrated analysis of the differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA), we identified a number of hub genes using the protein-protein interaction network. The top 5 hub genes were as follows: <em>CCNB2</em>, <em>BUB1B</em>, <em>CDC25A</em>, <em>CCNB3</em>, and <em>PLK3</em>. The expression of hub genes was validated in PREMBA embryos and donated embryos using RT-qPCR. The knockdown of <em>Ccnb2</em> in mouse zygotes led to an increase in embryo fragmentation, a rise in apoptosis, and a reduction in blastocyst formation. Furthermore, silencing the expression of <em>CDC25A</em> in HEK293T cells resulted in a decrease in cell proliferation and an increase in apoptosis, providing further support for our findings. Our findings could predict the development outcomes of preimplantation embryos and be used as potential therapeutic targets to prevent recurrent failures of IVF/ICSI attempts.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142344809","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":"New insights into decoding the lifestyle of endophytic Fusarium lateritium Fl617 via comparing genomes","authors":"Yan Zhao ,&nbsp;Jiankang Wang ,&nbsp;Qing Xiao ,&nbsp;Guihua Liu ,&nbsp;Yongjie Li ,&nbsp;Xingping Zha ,&nbsp;Zhangjiang He ,&nbsp;Jichuan Kang","doi":"10.1016/j.ygeno.2024.110925","DOIUrl":"10.1016/j.ygeno.2024.110925","url":null,"abstract":"<div><p>Fungal-plant interactions have persisted for 460 million years, and almost all terrestrial plants on Earth have endophytic fungi. However, the mechanism of symbiosis between endophytic fungi and host plants has been inconclusive. In this dissertation, we used a strain of endophytic <em>Fusarium lateritium</em> (Fl617), which was found in the previous stage to promote disease resistance in tomato, and selected the pathogenic <em>Fusarium oxysporum</em> Fo4287 and endophytic <em>Fusarium oxysporum</em> Fo47, which are in the same host and the closest relatives of Fl617, to carry out a comparative genomics analysis of the three systems and to provide a new perspective for the elucidation of the special lifestyle of the fungal endophytes. We found that endophytic <em>F. lateritium</em> has a smaller genome, fewer clusters and genes associated with pathogenicity, and fewer plant cell wall degrading enzymes (PCWDEs). There were also relatively fewer secondary metabolisms and typical <em>Fusarium</em> spp. toxins, and a lack of the key <em>Fusarium</em> spp. pathogenicity factor, secreted in xylem (SIX), but the endophytic fungi may be more sophisticated in their regulation of the colonization process. It is hypothesized that the endophytic fungi may have maintained their symbiosis with plants due to the relatively homogeneous microenvironment in plants for a long period of time, considering only plant interactions and discarding the relevant pathogenicity factors, and that their endophytic evolutionary tendency may tend to be genome streamlining and to enhance the fineness of the regulation of plant interactions, thus maintaining their symbiotic status with plants.</p></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0888754324001460/pdfft?md5=b7dcd1db6399cc48cbbaf1f9c1c69986&pid=1-s2.0-S0888754324001460-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142046562","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}