Genome Biology最新文献_第10页

LSGI: interpretable spatial gradient analysis for spatial transcriptomics data 空间转录组学数据的可解释空间梯度分析

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-08 DOI: 10.1186/s13059-025-03716-1

Qingnan Liang, Luisa Solis Soto, Cara Haymaker, Ken Chen

引用次数: 0

Oatk: a de novo assembly tool for complex plant organelle genomes 奥特克：复杂植物细胞器基因组的全新组装工具

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-07 DOI: 10.1186/s13059-025-03676-6

Chenxi Zhou, Max Brown, Mark Blaxter, Shane A. McCarthy, Richard Durbin

引用次数: 0

scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data 解释：使用线性模型来理解基于质谱的单细胞蛋白质组学数据

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-07 DOI: 10.1186/s13059-025-03713-4

Christophe Vanderaa, Laurent Gatto

引用次数: 0

scTail: precise polyadenylation site detection and its alternative usage analysis from reads 1 preserved 3′ scRNA-seq data scTail：从reads 1保存的3 ' scRNA-seq数据中精确检测聚腺苷化位点及其替代用途分析

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-07 DOI: 10.1186/s13059-025-03710-7

Ruiyan Hou, Yuanhua Huang

引用次数: 0

Identification of replicative aging and inflammatory aging signatures via whole-genome CRISPRi screens 通过全基因组CRISPRi筛选鉴定复制衰老和炎症衰老特征

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-06 DOI: 10.1186/s13059-025-03683-7

Lingling Wu, Xiang Zhu, Yanxia Liu, Dehua Zhao, Betty Chentzu Yu, Zheng Wei, Xueqiu Lin, Lei S. Qi

{"title":"Identification of replicative aging and inflammatory aging signatures via whole-genome CRISPRi screens","authors":"Lingling Wu, Xiang Zhu, Yanxia Liu, Dehua Zhao, Betty Chentzu Yu, Zheng Wei, Xueqiu Lin, Lei S. Qi","doi":"10.1186/s13059-025-03683-7","DOIUrl":"https://doi.org/10.1186/s13059-025-03683-7","url":null,"abstract":"Aging is a major risk factor for chronic diseases and cancer. Cellular aging, particularly in adult stem cells, offers a high-throughput framework for dissecting the molecular mechanisms of aging. We perform multiple genome-wide CRISPR interference (CRISPRi) screenings in human primary mesenchymal stem cells derived from adipose tissue during either replicative senescence or inflammation-induced senescence. These screens reveal distinct sets of potential novel regulators specific to each senescence pathway. Combining our perturbation-based functional genomic data with 405 genome-wide association study datasets, including 50 aging-related studies, we find that the inflammatory aging signatures identified from CRISPRi screenings are significantly associated with diverse aging processes, suggesting novel molecular signatures for analyzing and predicting aging status and aging-related disease. The signatures verified through comprehensive functional genomics and genetic analyses may provide new targets for modulating the aging process and enhancing the quality of cell therapy products.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"14 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144786793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromosome-level genome assembly of the autotetraploid yellow pitaya provides novel insights into evolution of trait patterning in pitaya species with different ploidy 同源四倍体黄色火龙果的染色体水平基因组组装为不同倍性火龙果物种的性状模式进化提供了新的见解

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-06 DOI: 10.1186/s13059-025-03695-3

Qamar U. Zaman, Ali Raza, Liu Hui, Mian Faisal Nazir, Vanika Garg, Muhammad Ikram, Guoqing Wang, Wei Lv, Darya Khan, Aamir Ali Khokhar, Zhang You, Annapurna Chitikineni, Babar Usman, Cui Jianpeng, Xulong Yang, Shiyou Zuo, Peifeng Liu, Sunjeet Kumar, Mengqi Guo, Zhi-Xin Zhu, Girish Dwivedi, Yong-Hua Qin, Rajeev K. Varshney, Hua-Feng Wang

{"title":"Chromosome-level genome assembly of the autotetraploid yellow pitaya provides novel insights into evolution of trait patterning in pitaya species with different ploidy","authors":"Qamar U. Zaman, Ali Raza, Liu Hui, Mian Faisal Nazir, Vanika Garg, Muhammad Ikram, Guoqing Wang, Wei Lv, Darya Khan, Aamir Ali Khokhar, Zhang You, Annapurna Chitikineni, Babar Usman, Cui Jianpeng, Xulong Yang, Shiyou Zuo, Peifeng Liu, Sunjeet Kumar, Mengqi Guo, Zhi-Xin Zhu, Girish Dwivedi, Yong-Hua Qin, Rajeev K. Varshney, Hua-Feng Wang","doi":"10.1186/s13059-025-03695-3","DOIUrl":"https://doi.org/10.1186/s13059-025-03695-3","url":null,"abstract":"Yellow pitaya (Selenicereus megalanthus, 2n = 4x = 44) breeding remains severely hindered due to the lack of a reference genome. Here, we present a high-quality chromosome-level genome assembly of yellow pitaya using PacBio HiFi sequencing and Hi-C scaffolding technologies. We identify yellow pitaya as an autotetraploid with a genome size of 1.79 Gb, harboring 27,246 high-confidence genes probably from diploid ancestors, red pitaya (S. undatus). By comparative analysis of the 3D chromatin architecture, we identify varying number of compartment A/B, topologically associated domains (TADs), and structural variations in diploid (red pitaya) and polyploid (yellow pitaya) species. We find that TAD boundaries are enriched with transcription factor motifs in both species. We find significant alterations in expression of genes in the betalain biosynthesis pathway in both species. We detect differential expression of genes encoding key regulators of pericarp color within the TAD regions of polyploid pitaya and diploid pitaya. We also identify the expression differences in candidate genes that likely influence betacyanin and betaxanthin synthesis in both species. Our findings suggest that differential 3D genome organization, especially differences in TAD boundaries, may impact gene expression, which may further lead to different trait formation in different pitaya species. This provides theoretical implications for fast-forward breeding.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"16 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144786792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effects of chromosome number reduction on mitotic and meiotic stability in fission yeast 染色体数目减少对分裂酵母有丝分裂和减数分裂稳定性的影响

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-04 DOI: 10.1186/s13059-025-03704-5

Yueyue Jiang, Yanze Jian, Lingyun Nie, Xin Gu, Ziyi Lu, Yongkang Chu, Xing Liu, Xuebiao Yao, Jin-Qiu Zhou, Shengnan Zheng, Chuanhai Fu

{"title":"Effects of chromosome number reduction on mitotic and meiotic stability in fission yeast","authors":"Yueyue Jiang, Yanze Jian, Lingyun Nie, Xin Gu, Ziyi Lu, Yongkang Chu, Xing Liu, Xuebiao Yao, Jin-Qiu Zhou, Shengnan Zheng, Chuanhai Fu","doi":"10.1186/s13059-025-03704-5","DOIUrl":"https://doi.org/10.1186/s13059-025-03704-5","url":null,"abstract":"Genetic information is stored on multiple chromosomes in eukaryotic organisms and is passed on to offspring through cell division. How chromosome number influences cell division and chromosome segregation is not yet understood. In this study, we use artificial chromosome-fusion fission yeast cells, which contain one or two chromosomes, as models to investigate the effects of a reduced chromosome number on mitosis and meiosis. In mitosis, chromosome number reduction, particularly full fusion into one chromosome, prolongs mitotic duration in a manner dependent on the spindle assembly checkpoint and improves chromosome segregation accuracy in spindle assembly checkpoint-deficient cells. By contrast, in meiosis, chromosome number reduction impairs prophase oscillatory nuclear movement, prolongs meiosis I duration but shortens meiosis II duration, and severely compromises meiosis I chromosome segregation. Our work uncovers different effects of reduced chromosome number on mitotic and meiotic stability and offers insights into how organisms may select the appropriate number of chromosomes in evolution.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"32 1","pages":"232"},"PeriodicalIF":12.3,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144778302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals 低甲基化拟南芥个体体细胞转座因子动员的长读检测

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-07-30 DOI: 10.1186/s13059-025-03691-7

Andrea Movilli, Svitlana Sushko, Fernando A. Rabanal, Detlef Weigel

{"title":"Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals","authors":"Andrea Movilli, Svitlana Sushko, Fernando A. Rabanal, Detlef Weigel","doi":"10.1186/s13059-025-03691-7","DOIUrl":"https://doi.org/10.1186/s13059-025-03691-7","url":null,"abstract":"Because transposable elements (TEs) can cause heritable genetic changes, past work on TE mobility in Arabidopsis thaliana has mostly focused on new TE insertions in the germline of hypomethylated plants. It is, however, well-known that TEs can also be active in the soma, although the high-confidence detection of somatic events has been challenging. Here, we leverage the high accuracy of PacBio HiFi long reads to evaluate the somatic mobility of TEs in individuals of an A. thaliana non-reference strain lacking activity of METHYLTRANSFERASE1 (MET1), a major component of the DNA methylation maintenance machinery. Most somatically mobile families coincide with those found in germline studies of hypomethylated genotypes, although the exact TE copies differ. We also discover mobile elements that had been missed by standard TE annotation methods. Somatic TE activity is variable among individual plants, but also within TE families. Finally, our approach points to the possible involvement of alternative transposition as a cause for somatic hypermutability in a region that contains two closely spaced VANDAL21 elements. Long-read sequencing reveals widespread TE transposition in the soma of A. thaliana hypomethylated mutants. Assessing somatic instead of germline mobilization is a fast and reliable method to investigate different aspects of TE mobility at the single plant level.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"27 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144747319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Artificial chromosome reorganization reveals high plasticity of the budding and fission yeast genomes 人工染色体重组揭示了芽殖酵母和裂变酵母基因组的高度可塑性

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-07-29 DOI: 10.1186/s13059-025-03689-1

Xueting Zhu, Shaochun Liu, Tiantian Ye, Xin Gu, Feiyu Pu, Zhen Zhou, Zhi-Jing Wu, Jin-Qiu Zhou

{"title":"Artificial chromosome reorganization reveals high plasticity of the budding and fission yeast genomes","authors":"Xueting Zhu, Shaochun Liu, Tiantian Ye, Xin Gu, Feiyu Pu, Zhen Zhou, Zhi-Jing Wu, Jin-Qiu Zhou","doi":"10.1186/s13059-025-03689-1","DOIUrl":"https://doi.org/10.1186/s13059-025-03689-1","url":null,"abstract":"The genome of a eukaryotic cell is usually organized on a set of chromosomes. Recently, karyotype engineering has been applied to various organisms, but whether and to what extent a naturally evolved genome can resist or tolerate massive artificial manipulations remains unexplored. Using unicellular yeast models of both Saccharomyces cerevisiae and Schizosaccharomyces pombe, we deliberately construct dozens of single-chromosome strains with different chromosome architectures. Three S. cerevisiae strains have the individual chromosomes fused into a single chromosome, but with the individual chromosomes in different orders. Eighteen S. cerevisiae strains have a single chromosome but with different centromeric sequences. Fifteen S. cerevisiae strains have a single chromosome with the centromere at different distances relative to the telomeres. Two S. pombe strains have a single, circular chromosome, and three strains have a single, linear chromosome with the centromere at different distances relative to the telomeres. All of these single-chromosome strains are viable, but the strains with an acrocentric or a telocentric chromosome have abnormal cell morphologies, and grow more slowly than those with a metacentric or sub-metacentric chromosome, and show increased genome instability with chromosome segregation abnormalities or genome diploidization. The functional genomes of both the evolutionarily distant yeasts S. cerevisiae and S. pombe are highly tolerant of diversified genome organizations. The phenotypic abnormalities and increased genome instability of the acrocentric/telocentric single-chromosome yeasts suggest that yeasts with metacentric chromosomes have an evolutionary advantage.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"24 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Empowering bioinformatics communities with Nextflow and nf-core 通过Nextflow和nf-core增强生物信息学社区的能力

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-07-29 DOI: 10.1186/s13059-025-03673-9

Björn E. Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Krishna Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip A. Ewels, Sonia Eynard, James A. Fellows Yates, Daniel Fischer, Evan W. Floden, Sylvain Foissac, Gisela Gabernet, Maxime U. Garcia, Gareth Gillard, Manu Kumar Gundappa, Cervin Guyomar, Christopher Hakkaart, Friederike Hanssen, Peter W. Harrison, Matthias Hörtenhuber, Cyril Kurylo, Christa Kühn, Sandrine Lagarrigue, Delphine Lallias, Daniel J. Macqueen, Edmund Miller, Júlia Mir-Pedrol, Gabriel Costa Monteiro Moreira, Sven Nahnsen, Harshil Patel, Alexander Peltzer, Frederique Pitel, Yuliaxis Ramayo-Caldas, Marcel da Câmara Ribeiro-Dantas, Dominique Rocha, Mazdak Salavati, Alexey Sokolov, Jose Espinosa-Carrasco, Cedric Notredame, the nf-core community

{"title":"Empowering bioinformatics communities with Nextflow and nf-core","authors":"Björn E. Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Krishna Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip A. Ewels, Sonia Eynard, James A. Fellows Yates, Daniel Fischer, Evan W. Floden, Sylvain Foissac, Gisela Gabernet, Maxime U. Garcia, Gareth Gillard, Manu Kumar Gundappa, Cervin Guyomar, Christopher Hakkaart, Friederike Hanssen, Peter W. Harrison, Matthias Hörtenhuber, Cyril Kurylo, Christa Kühn, Sandrine Lagarrigue, Delphine Lallias, Daniel J. Macqueen, Edmund Miller, Júlia Mir-Pedrol, Gabriel Costa Monteiro Moreira, Sven Nahnsen, Harshil Patel, Alexander Peltzer, Frederique Pitel, Yuliaxis Ramayo-Caldas, Marcel da Câmara Ribeiro-Dantas, Dominique Rocha, Mazdak Salavati, Alexey Sokolov, Jose Espinosa-Carrasco, Cedric Notredame, the nf-core community","doi":"10.1186/s13059-025-03673-9","DOIUrl":"https://doi.org/10.1186/s13059-025-03673-9","url":null,"abstract":"Standardized analysis pipelines contribute to making data bioinformatics research compliant with the paradigm of Findability, Accessibility, Interoperability, and Reusability (FAIR), and facilitate collaboration. Nextflow and Snakemake, two popular command-line solutions, are increasingly adopted by users, complementing GUI-based platforms such as Galaxy. We report recent developments of the nf-core framework with the new Nextflow Domain-Specific Language (DSL2). An extensive library of modules and subworkflows enables research communities to adopt common standards progressively, as resources and needs allow. We present an overview of some of the research communities built around nf-core and showcase its adoption by six EuroFAANG farmed animal research consortia.\u0000","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"27 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0