Genomics最新文献

{"title":"Single-cell RNA sequencing reveals the heterogeneity of myofibroblasts in wound repair.","authors":"Miaonan Liu, Xiaoxuan Liu, Jingchi Zhang, Shaocong Liang, Yan Gong, Shengjun Shi, Xiaopeng Yuan","doi":"10.1016/j.ygeno.2024.110982","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110982","url":null,"abstract":"<p><p>Skin wound repair involves myofibroblasts crucial for tissue integrity. This study utilized single-cell RNA sequencing to explore myofibroblast diversity in various wound healing scenarios. Analysis of 89,148 cells from skin ulcers, keloids, and normal scars identified 14 cell clusters. Myofibroblast subcluster analysis unveiled 11 subsets, with subclusters 1 and 9 predominant in ulcers. Subcluster 1 exhibited heightened matrix metalloproteinase expression and involvement in bacterial response and angiogenesis, crucial in inflammation. Tissue validation confirmed subcluster 1 significance., while animal models supported upregulated CA12, TDO2, and IL-7R in chronic ulcers. These findings illuminate myofibroblast heterogeneity and their impact on wound healing, offering insights into potential therapeutic targets.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110982"},"PeriodicalIF":3.4,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871887","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":"Tissue-specific chromatin accessibility and transcriptional regulation in maize cold stress response.","authors":"Jinlei Han, Yan Dai, Jialiang Zhou, Jingjing Tian, Qi Chen, Xiaobing Kou, Ghulam Raza, Baohong Zhang, Kai Wang","doi":"10.1016/j.ygeno.2024.110981","DOIUrl":"10.1016/j.ygeno.2024.110981","url":null,"abstract":"<p><p>Maize, a vital crop globally, faces significant yield losses due to its sensitivity to cold stress, especially in temperate regions. Understanding the molecular mechanisms governing maize response to cold stress is crucial for developing strategies to enhance cold tolerance. However, the precise chromatin-level regulatory mechanisms involved remain largely unknown. In this study, we employed DNase-seq and RNA-seq techniques to investigate chromatin accessibility and gene expression changes in maize root, stem, and leaf tissues subjected to cold treatment. We discovered widespread changes in chromatin accessibility and gene expression across these tissues, with strong tissue specificity. Cold stress-induced DNase I hypersensitive sites (coiDHSs) were associated with differentially expressed genes, suggesting a direct link between chromatin accessibility and gene regulation under cold stress. Motif enrichment analysis identified ERF transcription factors (TFs) as central regulators conserved across tissues, with ERF5 emerging as pivotal in the cold response regulatory network. Additionally, TF co-localization analysis highlighted six TF pairs (ERF115-SHN3, ERF9-LEP, ERF7-SHN3, LEP-SHN3, LOB-SHN3, and AS2-LOB) conserved across tissues but showing tissue-specific binding preferences. These findings indicate intricate regulatory networks in maize cold response. Overall, our study provides insights into the chromatin-level regulatory mechanisms underpinning maize adaptive response to cold stress, offering potential targets for enhancing cold tolerance in agricultural contexts.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110981"},"PeriodicalIF":3.4,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863318","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":"Single-cell RNA sequencing unveils dynamic transcriptional profiles during the process of donkey spermatogenesis and maturation.","authors":"Yadan Jin, Fangdi Zhang, Ruixue Ma, Jingya Xing, Min Wang, Yujiang Sun, Guoliang Zhang","doi":"10.1016/j.ygeno.2024.110974","DOIUrl":"10.1016/j.ygeno.2024.110974","url":null,"abstract":"<p><strong>Introduction: </strong>With the increasing demand for donkey production, there has been a growing focus on the breeding of donkeys. However, our current understanding of the mechanisms underlying spermatogenesis and maturation in donkeys during reproduction remains limited.</p><p><strong>Objectives: </strong>This study is to provide a comprehensive single-cell landscape analysis of spermatogenesis and maturation in donkeys.</p><p><strong>Methods: </strong>In this study, we employed single-cell RNA sequencing to investigate cell composition, gene expression patterns, and regulatory roles during spermatogenesis and maturation in donkeys.</p><p><strong>Results: </strong>The expression patterns of CDK1, CETN3, and UBE2J1 were found to be indicative of specific germ cells during donkey spermatogenesis. Additionally, the DEFB121, ELSPBP1, and NPC2 genes were specifically identified in the principal cells of the donkey epididymis.</p><p><strong>Conclusions: </strong>We performed single-cell RNA sequencing to analyze the cellular composition and spatial distribution of donkey testis and epididymis, thereby generating comprehensive transcriptional atlases at the single-cell resolution.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110974"},"PeriodicalIF":3.4,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853480","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":"A chromosome-level genome of Lobelia seguinii provides insights into the evolution of Campanulaceae and the lobeline biosynthesis.","authors":"Na Zhang, Puguang Zhao, Wenda Zhang, Huiying Wang, Kaixuan Wang, Xiangyu Wang, Zhanjing Zhang, Ninghua Tan, Lingyun Chen","doi":"10.1016/j.ygeno.2024.110979","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110979","url":null,"abstract":"<p><p>Lobelia seguinii is a plant with great ecological and medicinal value and belongs to Campanulaceae. Lobelia contains lobeline, a well-known compound used to treat respiratory diseases. Nevertheless, lobeline biosynthesis needs further exploration. Moreover, whole-genome duplication (WGD) and karyotype evolution within Campanulaceae still need to be better understood. In this study, we obtained a chromosome-level genome of L. seguinii with a size of 1.4 Gb and 38,253 protein-coding genes. Analyses revealed two WGDs within Campanulaceae, one at the most recent common ancestor (MRCA) of Campanula and Adenophora, and another at the MRCA of Lobelioideae. Analyses further revealed that the karyotype of Platycodon grandiflorus represents the ancient type within Asterales. We proposed eight enzymes involved in the lobeline biosynthesis pathway of L. seguinii. Molecular cloning and heterologous expression of phenylalanine ammonia-lyase (PAL), a candidate enzyme involved in the first step of lobeline biosynthesis, verified its function to catalyze the deamination of phenylalanine to cinnamic acid. This study sheds light on the evolution of Campanulaceae and lobeline biosynthesis.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110979"},"PeriodicalIF":3.4,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142828056","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":"SlAN2 overexpression improves cold resistance in tomato (Solanum lycopersicum L.) by regulating glycolysis and ascorbic acid metabolism.","authors":"Minghui Ye, Deying Wang, Ruixin Li, Kunyang Zhuang, Hongjiao Wang, Xinyin Cao, Tengfei Qin, Hengjia Zhang, Shangjing Guo, Bingjie Wu","doi":"10.1016/j.ygeno.2024.110978","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110978","url":null,"abstract":"<p><p>Chilling stress seriously affects the growth and yield of tomato. Anthocyanin is a typical chilling-induced metabolite with strong antioxidant activity and photoprotective capacity. Here, we found that anthocyanin was also involved in ascorbic acid biosynthesis and glycolysis under chilling stress. SlAN2 is an important positive gene in anthocyanin biosynthesis. The results of physiological indicators showed that SlAN2 overexpression lines (A189) had a greater ability to tolerate cold stress than wild-type (WT) plants. Conjoint analysis of transcriptomics and metabonomics of A189 lines and WT plants was used to analyze the metabolic difference and the cold resistance mechanisms caused by anthocyanin under chilling stress. The anthocyanin accumulated more in A189 than that in WT under chilling stress at 4 °C for 24 h, which led to hexoses and ascorbic acid increased significantly. Results indicate that SlAN2 overexpression reduces the expression of key enzyme genes in glycolytic pathway such as phosphofructokinase (PFK) and pyruvate kinase (PK) genes, weakens glycolysis ability, and promotes accumulation of hexoses in A189 lines at 4 °C for 24 h compared with wild lines. Additionally, ascorbic acid content is increased by up-regulated the genes of ascorbate peroxidase (APX) and dehydroascorbate reductase (DHAR). The increased hexose content can reduce cell osmotic potential, freezing point and synthesize more ascorbic acid, while the increased ascorbic acid content can enhance the ability to scavenge reactive oxygen species, so improves the cold resistance of tomato. The glycolysis and ascorbic acid metabolism pathway mediated by SlAN2 provides a new insight for the molecular mechanism of anthocyanins in improving the cold resistance of tomato and provides a new theoretical basis for cultivating new cold-tolerant tomato varieties.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110978"},"PeriodicalIF":3.4,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823539","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":"Identification and expression analysis of lncRNAs in rice roots (Oryza sativa L.) under elevated CO₂ concentration and/or cadmium stress.","authors":"Ziyuan Feng, Xiaoyu Wang, Zihan Luo, Aihua Liu, Caixia Wen, Qi Ma, Wenyong Liu, Xuemei Li, Lianju Ma, Yueying Li, Bin Yang, Lanlan Wang","doi":"10.1016/j.ygeno.2024.110980","DOIUrl":"10.1016/j.ygeno.2024.110980","url":null,"abstract":"<p><p>The gradual rise of CO₂ is one of the global climate changes, Cd stress is also a major abiotic stress factor that affects rice (Oryza sativa L.). The rice seedlings were treated under two CO₂ concentrations and two CdCl₂ concentrations for 7 days (treatments names: 400 ± 20 μmol mol^-1 CO₂ and 0 μmol L^-1 CdCl₂ concentrations, AC; 400 ± 20 μmol mol^-1 CO₂ and 150 μmol L^-1 CdCl₂ concentrations, Cd; 800 ± 20 μmol mol^-1 CO₂ and 0 μmol L^-1 CdCl₂ concentrations, EC; 800 ± 20 μmol mol^-1 CO₂ and 150 μmol L^-1 CdCl₂ concentrations, EC + Cd). The lncRNAs informations were analyzed and excavated using high-throughput sequencing, target genes annotation, and qRT-PCR analysis techniques so as to reveal the regulatory mechanism of lncRNAs in rice roots under high CO₂ concentrations and/or Cd stress. The results show that: (1) 326 (AC vs Cd), 331 (AC vs EC), 343 (AC vs EC + Cd), 112 (Cd vs EC + Cd) DE-lncRNAs were identified. (2) MAPK signaling pathway-plant (relevant genes Os04g0534166, Os05g0399800 regulated by MSTRG.18576.11, MSTRG.20864.1) and diterpenoid biosynthesis (relevant genes Os12g0491800, Os02g0570400 regulated by MSTRG.8965.1, MSTRG.11509.1) were annotated in AC vs Cd; Under EC relative to AC, DE-lncRNAs were annotated significantly to the flavonoid biosynthesis (relevant genes Os10g0196100, Os10g0320100, Os11g0116300, Os03g0819600 regulated by MSTRG.4612.1, MSTRG.4668.1, MSTRG.6051.1, MSTRG.16669.1); Under composite treatments, relative to AC, DE-lncRNAs were mainly annotated in the plant hormone signal transduction pathway (relevant genes Os03g0180800, Os03g0180900, Os03g0181100 regulated by MSTRG.13776.1). Under combined treatment, elevated CO₂ alleviates Cd stress damage by regulating phenylpropanoid biosynthesis through DE-lncRNAs (relevant genes Os09g0419200 regulated by MSTRG. 29,573.1).</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110980"},"PeriodicalIF":3.4,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824168","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":"Genomic insights into Paspalum vaginatum: Mitochondrial and chloroplast genome mapping, evolutionary insights, and organelle-nucleus communication.","authors":"Ling Pan, Lirong Cai, Yang Lu, Junming Zhao, Xuebing Yan, Xiaoshan Wang","doi":"10.1016/j.ygeno.2024.110975","DOIUrl":"10.1016/j.ygeno.2024.110975","url":null,"abstract":"<p><p>Paspalum vaginatum, valued for its salt tolerance, is a vital species in the turfgrass and agricultural industries. Despite its significance, there are still gaps in its genetic composition, particularly in the mitochondrial (mtDNA) and chloroplast (cpDNA) genomes. Our study aimed to fill these knowledge gaps by investigating the evolutionary relationships within the paspalum family and examining the functions of organelle-encoded genes as well as the critical role of reactive oxygen species (ROS) in organelle-nucleus communication. By genome sequencing, assembly, and annotation, we determined 504,515 bp of P. vaginatum mtDNA and 140,483 bp of its cpDNA. Comparative analyses with other Paspalum species and major crops highlight the intricate evolutionary dynamics and varying levels of genetic relatedness observed across different organelle genomes. The complex response of organelle gene expression to salt stress in this study will aid in understanding the molecular mechanisms and evolutionary trajectories of P. vaginatum organelle genomes.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110975"},"PeriodicalIF":3.4,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822137","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":"Multiomics identification of programmed cell death-related characteristics for nonobstructive azoospermia based on a 675-combination machine learning computational framework.","authors":"Shuqiang Huang, Cuiyu Tan, Wanru Chen, Tongtong Zhang, Liying Xu, Zhihong Li, Miaoqi Chen, Xiaojun Yuan, Cairong Chen, Qiuxia Yan","doi":"10.1016/j.ygeno.2024.110977","DOIUrl":"https://doi.org/10.1016/j.ygeno.2024.110977","url":null,"abstract":"<p><strong>Background: </strong>Abnormal programmed cell death (PCD) plays a central role in spermatogenic dysfunction. However, the molecular mechanisms and biomarkers of PCD in patients with nonobstructive azoospermia (NOA) remain unclear.</p><p><strong>Methods: </strong>The genetic conditions of NOA patients were analysed using bulk transcriptomic, single-cell transcriptomic, single nucleotide polymorphism (SNP), and clinical data from multiple centres. A total of 675 machine learning methods were applied to construct models from 12 different PCDs and to screen for distinctive genes. A new PCDscore system was created to measure the degree of PCD in patients. Using the NOA mouse model, TUNEL, qRT-PCR, Western blotting, and immunohistochemistry (IHC) were utilized to validate the PCD status in NOA testes and the expression levels of hub PCD-related genes (PCDRGs). Mouse testicular samples were used for sequencing of the whole transcriptome. The sequencing results were used to evaluate the correlation between PCD scores and expression of hub genes.</p><p><strong>Results: </strong>A PCDscore system was built using 12 characteristic PCDRGs chosen by machine learning. PCD scores correlated with gene interaction and immune activity changes. Leydig, Sertoli, and T cells were prominent in cell interactions with PCDscore changes. PCDscore in the NOA mouse testis was increased. Among the 12 PCDRGs, BCL2L14, GGA1, GPX4, PHKG2, and SLC39A8 were strongly linked to spermatogenesis. BCL2L14, GGA1, GPX4, and PHKG2 strongly correlated with PCD statuses. The changes in the expression of these genes may be due to the effects of SNPs, which may lead to the male reproductive system disorders.</p><p><strong>Conclusions: </strong>Our study provides new insights into PCD-related mechanisms in NOA patients via multiomics and proposes reliable models for the diagnosis of NOA via the use of PCD biomarkers. A deeper understanding of these mechanisms may aid in the clinical diagnosis and treatment of NOA.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110977"},"PeriodicalIF":3.4,"publicationDate":"2024-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142812830","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":"Expansion of peripheral cytotoxic CD4+ T cells in Alzheimer's disease: New insights from multi-omics evidence.","authors":"Jiongxue Chen, Jiatian Xie, Fuyin Deng, Jinhua Cai, Sitai Chen, Xingrong Song, Shangzhou Xia, Qingyu Shen, Xinying Guo, Yamei Tang","doi":"10.1016/j.ygeno.2024.110976","DOIUrl":"10.1016/j.ygeno.2024.110976","url":null,"abstract":"<p><p>The significance of the adaptive immune response in Alzheimer's disease (AD) is increasingly recognized. We analyzed scRNA-Seq data from AD patients, revealing a notable rise in CD4 cytotoxic T cells (CD4-CTLs) in peripheral blood mononuclear cells (PBMCs), validated in vivo and in vitro. This rise correlates with cognitive decline in AD patients. We also identified transcription factors TBX21 and MYBL1 as key drivers of CD4-CTL expansion. Further analyses indicate these cells are terminally differentiated, showing clonal expansion, metabolic changes, and unique communication patterns. Mendelian randomization identified risk genes SRGN and ITGB1, suggesting their genetic regulation in CD4-CTLs may contribute to AD. To summarize, our findings characterize the expansion of CD4-CTLs in the PBMCs of AD patients, providing valuable understanding into the possible mechanisms involved in the expansion of CD4-CTLs in AD.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110976"},"PeriodicalIF":3.4,"publicationDate":"2024-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806497","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":"Evolutionary dynamics of repetitive elements and their relationship with genome size in Acrididae.","authors":"Lina Zhao, Hao Yuan, Xuanzeng Liu, Huihui Chang, Xuan Jing, Yimeng Nie, Yuan Huang","doi":"10.1016/j.ygeno.2024.110971","DOIUrl":"10.1016/j.ygeno.2024.110971","url":null,"abstract":"<p><p>It is widely accepted that repetitive elements (REs) represent the primary mechanism driving genome size variation across eukaryotes. The observed genome sizes and REs of 59 species within the Acrididae were obtained and characterized. The genome sizes observed ranged from 6.60 pg to 19.35 pg, while the proportion of REs varied from 57.92 % to 83.58 %. The primary contributors were identified as LTR (2.34 % ∼ 20.98 %) and LINEs (6.70 % ∼ 16.33 %). The results of ancestral reconstruction indicated that the proportion of REs in ancestral nodes was 69.53 %, which suggests that they have undergone extensive genome expansion or contraction. A significant positive correlation was identified between the proportion of REs and genome size. Transposable elements were found to account for approximately 41 % of the observed variation in genome size. Moreover, the LTR was identified as the most significant RE type in relation to genome size expansion within the Acrididae.</p>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":" ","pages":"110971"},"PeriodicalIF":3.4,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791568","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}