Genome Biology最新文献_第8页

Comparative benchmarking of single-cell clustering algorithms for transcriptomic and proteomic data 转录组学和蛋白质组学数据的单细胞聚类算法的比较基准

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-03 DOI: 10.1186/s13059-025-03719-y

Yu-Hang Yin, Fang Wang, Wei Li, Qiaoming Liu, Shengming Zhou, Murong Zhou, Zhongjun Jiang, Dong-Jun Yu, Guohua Wang

{"title":"Comparative benchmarking of single-cell clustering algorithms for transcriptomic and proteomic data","authors":"Yu-Hang Yin, Fang Wang, Wei Li, Qiaoming Liu, Shengming Zhou, Murong Zhou, Zhongjun Jiang, Dong-Jun Yu, Guohua Wang","doi":"10.1186/s13059-025-03719-y","DOIUrl":"https://doi.org/10.1186/s13059-025-03719-y","url":null,"abstract":"Differences in data distribution, feature dimensions, and quality between different single-cell modalities pose challenges for clustering. Although clustering algorithms have been developed for single-cell transcriptomic or proteomic data, their performance across different omics data types and integration scenarios remains poorly investigated, which limits the selection of methods and future method development. In this study, we conduct a systematic and comparative benchmark analysis of 28 computational algorithms on 10 paired transcriptomic and proteomic datasets, evaluating their performance across various metrics in terms of clustering, peak memory, and running time. We also discuss the impact of highly variable genes (HVGs) and cell type granularity on clustering performance. Additionally, the robustness of these clustering methods on two kinds of omics is evaluating by using 30 simulated datasets. Furthermore, to explore the benefits of integrating omics information for clustering tasks, we integrate single-cell transcriptomic and proteomic data using 7 state-of-the-art integration methods and assess the performance of existing single-omics clustering schemes on the integrated features. Our findings reveal modality-specific strengths and limitations, highlight the complementary nature of existing methods, and provide actionable insights to guide the selection of appropriate clustering approaches for specific scenarios. Overall, for top performance across two omics, consider scAIDE, scDCC, and FlowSOM, with FlowSOM also offering excellent robustness. For users prioritizing memory efficiency scDCC and scDeepCluster are recommended, while TSCAN, SHARP, and MarkovHC are recommended for users who prioritize time efficiency, and community detection-based methods offer a balance.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"28 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144930475","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

Ancient genomes provide evidence of demographic shift to Slavic-associated groups in Moravia 古代基因组提供了摩拉维亚人口向斯拉夫相关群体转移的证据

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-03 DOI: 10.1186/s13059-025-03700-9

Ilektra Schulz, Denisa Zlámalová, Carlos S Reyna-Blanco, Sam Morris, Guido Alberto Gnecchi-Ruscone, Raphael Eckel, Renáta Přichystalová, Pavlína Ingrová, Petr Dresler, Luca Traverso, Garrett Hellenthal, Jiří Macháček, Daniel Wegmann, Zuzana Hofmanová

{"title":"Ancient genomes provide evidence of demographic shift to Slavic-associated groups in Moravia","authors":"Ilektra Schulz, Denisa Zlámalová, Carlos S Reyna-Blanco, Sam Morris, Guido Alberto Gnecchi-Ruscone, Raphael Eckel, Renáta Přichystalová, Pavlína Ingrová, Petr Dresler, Luca Traverso, Garrett Hellenthal, Jiří Macháček, Daniel Wegmann, Zuzana Hofmanová","doi":"10.1186/s13059-025-03700-9","DOIUrl":"https://doi.org/10.1186/s13059-025-03700-9","url":null,"abstract":"The Slavs are a major ethnolinguistic group of Europe, yet the process that led to their formation remains disputed. As of the sixth century CE, people supposedly belonging to the Slavs populated the space between the Avar Khaganate in the Carpathian Basin, the Merovingian Frankish Empire to the West and the Balkan Peninsula to the South. Proposed theories to explain those events are, however, conceptually incompatible, as some invoke major population movements while others stress the continuity of local populations. We report high-quality genomic data of 18 individuals from two nearby burial sites in South Moravia that span from the fifth to the tenth century CE, during which the region became the core of the ninth century Slavic principality. In contrast to existing data, the individuals reported here can be directly connected to an Early-Slavic-associated culture and include the earliest known inhumation associated with any such culture. The data indicates a strong genetic shift incompatible with local continuity between the fifth and seventh century, supporting the notion that the Slavic expansion in South Moravia was driven by population movement.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"62 1","pages":"259"},"PeriodicalIF":12.3,"publicationDate":"2025-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144987691","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

CLDN10-driven lineage decision in an amnion and primordial germ cell progenitor at the amnion-epiblast boundary in primates 灵长类动物羊膜-外胚层边界的羊膜和原始生殖细胞祖细胞cldn10驱动的谱系决定

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-02 DOI: 10.1186/s13059-025-03751-y

Nikola Sekulovski, Amber E. Carleton, Anusha Rengarajan, Chien-Wei Lin, Maliha Kabir, Lauren N. Juga, Allison E. Whorton, Lauren E. Elberfeld, Jenna C. Wettstein, Jenna K. Schmidt, Thaddeus G. Golos, Kenichiro Taniguchi

{"title":"CLDN10-driven lineage decision in an amnion and primordial germ cell progenitor at the amnion-epiblast boundary in primates","authors":"Nikola Sekulovski, Amber E. Carleton, Anusha Rengarajan, Chien-Wei Lin, Maliha Kabir, Lauren N. Juga, Allison E. Whorton, Lauren E. Elberfeld, Jenna C. Wettstein, Jenna K. Schmidt, Thaddeus G. Golos, Kenichiro Taniguchi","doi":"10.1186/s13059-025-03751-y","DOIUrl":"https://doi.org/10.1186/s13059-025-03751-y","url":null,"abstract":"A growing body of evidence from primate embryos as well as in vitro systems supports the notion that amnion and primordial germ cell (PGC) lineage progressing cells share a common precursor. To gain comprehensive transcriptomic insights into this critical but poorly understood precursor and its progeny, we examine the evolving transcriptome of a developing human pluripotent stem cell-derived model of amnion and PGC formation at the single cell level. This analysis reveals several continuous amniotic fate progressing states with state-specific markers. Additionally, a progenitor-like cell, that displays bi-potential characteristics for amnion and PGC-like cell lineages and is marked by CLDN10, is identified. Strikingly, we find that expression of CLDN10 is restricted to the amnion-epiblast boundary region in our human post-implantation amniotic sac model as well as in peri-gastrula cynomolgus macaque embryos; moreover, this boundary region presents amnion and PGC progenitor-like transcriptional characteristics. Furthermore, our loss of function analysis shows that CLDN10 promotes amniotic but suppresses PGC-like fate. Overall, based on the single cell transcriptomic resource in this study, we identify a CLDN10+ amnion and PGC progenitor-like population at the amnion-epiblast boundary of the primate peri-gastrula, and present additional molecular clues as to how amnion and PGC may be formed at the amnion-epiblast boundary in human peri-gastrula. ","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"16 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144928301","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

Imbalanced chromatin distribution in cellular senescence specifies paraspeckle dynamics 细胞衰老中染色质分布的不平衡指定了副斑动力学

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-02 DOI: 10.1186/s13059-025-03757-6

Joonwoo Lee, Jinmi Choi, Jeongeun Park, Seonduk Lee, Eun-Jung Cho, Youngdae Gwon

引用次数: 0

Mammalian conservation of endogenous G-quadruplex reveals their associations with complex traits 哺乳动物内源性g -四重体的保护揭示了它们与复杂性状的关联

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-01 DOI: 10.1186/s13059-025-03750-z

Ze-Hao Zhang, Zi-Yan Wang, Cong-Hui Li, Sheng Hu Qian, Wen Zhang, Zhen-Xia Chen

{"title":"Mammalian conservation of endogenous G-quadruplex reveals their associations with complex traits","authors":"Ze-Hao Zhang, Zi-Yan Wang, Cong-Hui Li, Sheng Hu Qian, Wen Zhang, Zhen-Xia Chen","doi":"10.1186/s13059-025-03750-z","DOIUrl":"https://doi.org/10.1186/s13059-025-03750-z","url":null,"abstract":"DNA G-quadruplexes (G4s) are four-stranded DNA structures. Endogenous G-quadruplexes (eG4s) have been identified as pivotal regulatory elements for gene expression in the human genome. The measurement of evolutionary conservation can be employed to ascertain the functional relevance of putative regulatory elements. However, the evolutionary profiles of human eG4s remain largely unknown. Here, we construct mammalian evolutionary profiles of human eG4s based on a comprehensive reference annotation of human eG4s from the integration of the eG4 database EndoQuad covering 41 human cell lines and our home-made G4 CUT&Tag data covering seven cell lines. We find that transposable elements contribute substantially to the evolutionary spread of primate-specific eG4s. A total of 92,910 highly conserved human eG4s were identified under mammalian constraint. By developing and utilizing the eG4 prediction tool eG4finder, which is based on a large language model, we verify the high structural conservation of highly conserved eG4s. The enrichment of highly conserved eG4s in developmental and aging pathways highlights their potential significance in key biological processes. Notably, highly conserved eG4s exhibit higher regulatory potential, regulatory activity and affinity for transcription factors. We demonstrate that highly conserved eG4s are the most powerful transcriptional activation elements in the total eG4 collection. Meanwhile, trait-associated variants and variants affecting the expression of high phenotypic severity genes are most enriched in highly conserved eG4s. Our study highlights the important regulatory functions and close association with complex human traits of human eG4s that are highly conserved in the mammalian lineage.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"30 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144923883","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

U-FISH: a fluorescent spot detector for imaging-based spatial-omics analysis and AI-assisted FISH diagnosis U-FISH：用于基于成像的空间组学分析和人工智能辅助FISH诊断的荧光点检测器

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-09-01 DOI: 10.1186/s13059-025-03736-x

Weize Xu, Huaiyuan Cai, Qian Zhang, Zhengze Wang, Jiajun Yang, Xiaofeng Wu, Chengwen Li, Chenghua Cui, Changzhi Liu, Jin He, Florian Mueller, Jinxia Dai, Chen Hao, Wei Ouyang, Gang Cao

引用次数: 0

Chemoreceptor family in plant-associated bacteria responds preferentially to the plant signal molecule glycerol 3-phosphate 植物相关细菌中的化学受体家族优先响应植物信号分子甘油3-磷酸

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-29 DOI: 10.1186/s13059-025-03703-6

Félix Velando, Jiawei Xing, Roberta Genova, Jean Paul Cerna-Vargas, Raquel Vázquez-Santiago, Miguel A. Matilla, Igor B. Zhulin, Tino Krell

{"title":"Chemoreceptor family in plant-associated bacteria responds preferentially to the plant signal molecule glycerol 3-phosphate","authors":"Félix Velando, Jiawei Xing, Roberta Genova, Jean Paul Cerna-Vargas, Raquel Vázquez-Santiago, Miguel A. Matilla, Igor B. Zhulin, Tino Krell","doi":"10.1186/s13059-025-03703-6","DOIUrl":"https://doi.org/10.1186/s13059-025-03703-6","url":null,"abstract":"Chemotaxis to plant compounds is frequently the initial step for the colonization of plants by bacteria. Plant pathogens and plant-associated bacteria contain approximately twice as many chemoreceptors as the bacterial average does, indicating that chemotaxis is particularly important for bacteria–plant interactions. However, information on the corresponding chemoreceptors and their chemoeffectors is limited. We identify the chemoreceptor PacP from the phytopathogen Pectobacterium atrosepticum, which exclusively recognizes phosphorylated C3 compounds at its sCache ligand binding domain, mediating chemoattraction. Using a motif of PacP amino acid residues involved in ligand binding, we identify a chemoreceptor family, termed sCache_PC3, that is specific for phosphorylated C3 compounds. Isothermal titration calorimetry studies reveal that family members preferentially bind glycerol 3-phosphate, a key plant signaling molecule. Family members recognize glycerol 2-phosphate and glycolysis intermediates glyceraldehyde 3-phosphate, dihydroxyacetone phosphate, and 3-phosphoglycerate. This study presents the first evidence of chemoreceptors that bind phosphorylated compounds. We show that the sCache_PC3 family has evolved from an ancestral sCache domain that responds primarily to Krebs cycle intermediates. Members of the sCache_PC3 family are predominantly found in plant-associated bacteria, including many important phytopathogens belonging to the genera Brenneria, Dickeya, Musicola, Pectobacterium, and Herbaspirillum. Consistently, glycerol 3-phosphate is a signal molecule that is excreted by plants in response to stress and infection. Chemotaxis toward glycerol 3-phosphate may be a means for bacteria to localize stressed plants and move to infection sites. This study lays the groundwork for investigating the role of chemotaxis to phosphorylated C3 compounds in plant–bacteria interactions and virulence.\u0000","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"25 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144915577","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

Enhancing transcriptome expression quantification through accurate assignment of long RNA sequencing reads with TranSigner 通过使用TranSigner准确分配长RNA测序读数，增强转录组表达定量

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-28 DOI: 10.1186/s13059-025-03723-2

Hyun Joo Ji, Mihaela Pertea

引用次数: 0

Integrated phenomic and genomic analyses unveil modes of altered phenotypic plasticity during wheat improvement 综合表型和基因组分析揭示了小麦改良过程中表型可塑性改变的模式

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-28 DOI: 10.1186/s13059-025-03740-1

Linqian Han, Xiaoming Wang, Ryan Benke, Laura E. Tibbs-Cortes, Peng Zhao, Karen A. Sanguinet, Zhiwu Zhang, Shengbao Xu, Jianming Yu, Xianran Li

{"title":"Integrated phenomic and genomic analyses unveil modes of altered phenotypic plasticity during wheat improvement","authors":"Linqian Han, Xiaoming Wang, Ryan Benke, Laura E. Tibbs-Cortes, Peng Zhao, Karen A. Sanguinet, Zhiwu Zhang, Shengbao Xu, Jianming Yu, Xianran Li","doi":"10.1186/s13059-025-03740-1","DOIUrl":"https://doi.org/10.1186/s13059-025-03740-1","url":null,"abstract":"Wheat has a critical role in global food security. During the improvement of wheat from landraces to cultivars, a suite of traits has been modified for higher yields. However, changing patterns of wheat in response to different environmental conditions, or phenotypic plasticity, during this improvement remain to be elucidated. We measure 17 agronomic traits for 406 wheat accessions consisting of landraces and cultivars in 10 environments. Analyses reveal varied contributions from genotype and environment to phenotypic variation across the evaluated traits. Using environmental indices identified by Critical Environmental Regressor through Informed Search (CERIS), we model the phenotypic values across environments of each accession with two reaction-norm parameters (intercept and slope). Genome Wide Association Studies (GWAS) identify loci significantly associated with variation in the two parameters, including Ppd-D1 and two Green Revolution genes (Rht-D1 and Rht-B1). Compared with the corresponding wild-type allele, Rht-D1b alters intercept and slope of more traits than Rht-B1b. Among nine possible modes of phenotypic plasticity change from landraces to cultivars, three predominant modes account for 88% of evaluated traits. Generally, two reaction-norm parameters decrease simultaneously for plant architecture traits but increase simultaneously for yield component traits. We systematically evaluate phenome-wide wheat phenotypic plasticity. Two reaction-norm parameters based on specific environmental indices capture varied degrees of phenotypic plasticity for each trait across wheat accessions. Two Green Revolution genes have different effect spectra in altering phenome-wide phenotypic plasticity. By incorporating the evolutionary dimension, we reveal dominant modes of phenotypic plasticity change during wheat improvement.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"13 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144910968","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

Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks 杨树茎在单核水平上的深层组织分析揭示了未表征的细胞类型和细胞特异性基因调控网络

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-08-28 DOI: 10.1186/s13059-025-03728-x

Henry W. Schmidt, Daniel Conde, Wendell J. Pereira, Paolo M. Triozzi, Kelly M. Balmant, Christopher Dervinis, Matias Kirst

{"title":"Deep tissue profiling of Populus stem at single nucleus level reveals uncharacterized cell types and cell-specific gene regulatory networks","authors":"Henry W. Schmidt, Daniel Conde, Wendell J. Pereira, Paolo M. Triozzi, Kelly M. Balmant, Christopher Dervinis, Matias Kirst","doi":"10.1186/s13059-025-03728-x","DOIUrl":"https://doi.org/10.1186/s13059-025-03728-x","url":null,"abstract":"Single-cell genomics is revolutionizing plant developmental biology, enabling the transcriptome profiling of individual cells and their lineage relationships. However, plant cell walls polymers hamper the dissociation and analysis of intact cells. This rigid structure can conceal cell types embedded in complex, lignified, multi-cell layered tissues such as those undergoing secondary growth. Their absence leads to incomplete single-cell genomic atlases and lineage inferences. We isolate nuclei to capture transcripts representing the diversity of cells throughout the stem of the woody perennial Populus trichocarpa generating a high-resolution transcriptome atlas of cell types and lineage trajectories. RNA sequencing of 11,673 nuclei identifies 26 clusters representing cell types in the cambium, xylem, phloem, and periderm. Comparative analysis with protoplast-derived transcriptome data reveals significant biases, with nuclei-based sequencing providing a higher representation of cells in lignified inner xylem tissues. Among previously underrepresented types, we uncover vessel-associated cells (VAC), a largely uncharacterized parenchyma subtype and the terminus of a xylem cell lineage. Gene regulatory analysis identifies a VAC-specific network and the Populus MYB48 as its primary regulator. Functional validation of MYB48 knockout mutants show an increase in vessel number and size, pointing to a role of VACs in vessel development. Our study demonstrates the capture and transcriptome characterization of cell types embedded in plant secondary growth, identifying novel regulators of xylem development and stress adaptation. The discovery of MYB48 as a key regulator of VAC function highlights a previously uncharacterized mechanism influencing vessel development, with applications to improving wood formation and stress resilience.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"5 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144910966","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