Genomics, proteomics & bioinformatics最新文献_第5页

SPAE: Deciphering Cell Cycle Dynamics and Cell States in Single-cell RNA-seq Data. 在单细胞RNA-seq数据中解读细胞周期动力学和细胞状态。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-29 DOI: 10.1093/gpbjnl/qzag074

Jiahao Yi, Jiajia Liu, Peng Guo, Yuan-Nong Ye, Xiaobo Zhou

{"title":"SPAE: Deciphering Cell Cycle Dynamics and Cell States in Single-cell RNA-seq Data.","authors":"Jiahao Yi, Jiajia Liu, Peng Guo, Yuan-Nong Ye, Xiaobo Zhou","doi":"10.1093/gpbjnl/qzag074","DOIUrl":"10.1093/gpbjnl/qzag074","url":null,"abstract":"Rapid advances in single-cell RNA sequencing (scRNA-seq) technology have enabled the investigation of gene expression changes at the single-cell level, particularly for elucidating the heterogeneity among cells and complex biological processes. This technique reveals subtle molecular differences within individual cells, thereby offering a unique viewpoint for the investigation of cell cycle progression, cellular differentiation, and disease pathogenesis. However, accurately identifying and analyzing cell cycle dynamics in scRNA-seq data remains challenging due to the complexity of the data and the subtle differences between cell states. To address this challenge, we developed the integrated Sinusoidal and Piecewise AutoEncoder (SPAE), an autoencoder-based piecewise linear model, for characterizing the cell cycle dynamics and cell states in scRNA-seq data. Compared with existing methods, SPAE demonstrates substantially improved accuracy and robustness in cell cycle characterization. Additionally, SPAE can accurately predict cancer cell cycle transitions and effectively facilitate the removal of cell cycle effects from gene expression data. SPAE is available for non-commercial use at https://github.com/YaJahn/SPAE, and the code is also publicly accessible at https://ngdc.cncb.ac.cn/biocode/tool/8079.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148623238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrating Genomic Studies into Large Birth Cohorts. 将基因组研究整合到大规模出生队列中。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-29 DOI: 10.1093/gpbjnl/qzag067

Jian-Rong He, Dongmei Wei, Mingxi Huang, Jinhua Lu, Yashu Kuang, Zhenyu Luo, Shanshan Lin, Huimin Xia, Wenhao Zhou, Shujia Huang, Xiu Qiu

{"title":"Integrating Genomic Studies into Large Birth Cohorts.","authors":"Jian-Rong He, Dongmei Wei, Mingxi Huang, Jinhua Lu, Yashu Kuang, Zhenyu Luo, Shanshan Lin, Huimin Xia, Wenhao Zhou, Shujia Huang, Xiu Qiu","doi":"10.1093/gpbjnl/qzag067","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzag067","url":null,"abstract":"Adverse exposures during early life, including environmental and genetic factors, can have profound and long-lasting effects on health in later life. Birth cohorts provide invaluable platforms for studying these effects, as they enable the collection of longitudinal data across multiple life stages. This paper explores the integration of genomic research into large birth cohorts. By utilizing genome-wide association studies, multi-omics approaches, and advanced epidemiological techniques, birth cohorts can integrate genetic, environmental, and molecular data to enhance our understanding of the biological underpinnings of maternal and child health. However, several challenges persist. These include ethical concerns regarding data privacy and informed consent, the analytical complexity in multi-modal datasets, the slow translation of research findings into clinical practice, the inevitable attrition in long-term follow-up, and the scarcity of multi-generational enrollment. Despite these challenges, integrating genomic research into birth cohorts is a critical step toward personalized healthcare and effective disease prevention strategies, providing essential insights into the origins of maternal and child health outcomes.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148611451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

scReGAT: Leveraging Knowledge of Regulatory Interactions to Predict Long-range Gene Regulation at Single-cell Resolution. scReGAT：利用调控相互作用的知识来预测单细胞分辨率下的远程基因调控。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-28 DOI: 10.1093/gpbjnl/qzag072

Baole Wen, Yanan Dang, Yu Zhang, Yi Long, Weidong Tian

{"title":"scReGAT: Leveraging Knowledge of Regulatory Interactions to Predict Long-range Gene Regulation at Single-cell Resolution.","authors":"Baole Wen, Yanan Dang, Yu Zhang, Yi Long, Weidong Tian","doi":"10.1093/gpbjnl/qzag072","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzag072","url":null,"abstract":"Understanding gene regulation at single-cell resolution is crucial for unraveling development, disease, and cellular identity. We introduce single-cell regulatory graph attention network (scReGAT), a deep learning framework that integrates prior knowledge of cis-regulatory element (cRE)-gene and transcription factor-gene interactions to reconstruct cell-specific regulatory networks. Central to scReGAT is a knowledge-guided regulatory graph (kRG), which combines experimentally validated regulatory interactions with cell-resolved chromatin accessibility profiles. These graphs serve as the foundation for training a Graph Attention Network (GAT) to predict gene expression and quantify the contribution of specific regulatory interactions using an interpretable regulatory score for each edge. In benchmarking across five single-cell multi-omics datasets, scReGAT successfully recapitulates known cell-type-specific cRE-gene interactions. In both neuroblastoma and osteogenic differentiation systems, it uncovers dynamic regulatory rewiring that predicts transcriptional transitions. Furthermore, by integrating genome-wide association studies loci from Alzheimer's disease, multiple sclerosis, and schizophrenia, scReGAT identifies disease-associated cell types and uncovers candidate regulatory mechanisms underlying complex trait associations. These results position scReGAT as a robust and generalizable framework for decoding long-range gene regulation at single-cell resolution. The source code of scReGAT can be accessed at https://github.com/TianLab-Bioinfo/scReGAT/ and https://ngdc.cncb.ac.cn/biocode/tool/BT008081.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148611509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DNA Methylation in Sex Chromosomes and Genes under Selection Underpins Sexual Size Dimorphism. 性染色体和选择下基因的DNA甲基化支持性别大小二态性。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-28 DOI: 10.1093/gpbjnl/qzag073

Qian Wang, Xiancai Hao, Dafni Anastasiadi, Kaiqiang Liu, Shuo Li, Bo Feng, Rui Wang, Michael G Ritchie, Yuyan Liu, Hong-Yan Wang, Lili Tang, Francesc Piferrer, Changwei Shao

{"title":"DNA Methylation in Sex Chromosomes and Genes under Selection Underpins Sexual Size Dimorphism.","authors":"Qian Wang, Xiancai Hao, Dafni Anastasiadi, Kaiqiang Liu, Shuo Li, Bo Feng, Rui Wang, Michael G Ritchie, Yuyan Liu, Hong-Yan Wang, Lili Tang, Francesc Piferrer, Changwei Shao","doi":"10.1093/gpbjnl/qzag073","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzag073","url":null,"abstract":"Sexual size dimorphism (SSD) refers to the differences in body size between males and females. Epigenetic mechanisms, such as DNA methylation, can shape phenotypes; however, their role in SSD remains unclear. Here, we used Cynoglossus semilaevis, a species with larger females (female-biased SSD), as a model to investigate the role of methylation in the emergence and regulation of SSD. Methylomes and transcriptomes were constructed in four tissues (brain, liver, muscle, and gonad) from three key life stages: juveniles (3 months post-fertilization), male mature stage (1 year post-fertilization; ypf), and female mature stage (3 ypf). In 1 ypf and 3 ypf females showed lower methylation levels, while the number of differentially methylated regions between sexes increased over the lifetime. Genes at the top of the growth hormone/insulin-like growth factor (GH/IGF) axis and hypothalamus-pituitary-gonadal axis (gh1, igf1, gnrh3, errγ, etc.) showed differential methylation between sexes, consistent with sex-related differences in growth. The female-specific W chromosome showed higher methylation than the autosomes or the Z chromosome. Genes of the IGF signaling network that negatively regulate growth and are located on the W chromosome were more highly methylated than their Z homologs. Furthermore, genes with a faster evolutionary rate in C. semilaevis exhibited lower methylation levels than the background genes, suggesting an important evolutionary role for DNA methylation in shaping SSD. Our results provide a comprehensive depiction of methylation regulation of SSD in vertebrates and improve our understanding of how methylation regulation can help organisms to respond to natural selection and allocate resources between the sexes.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148611496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

WebCVTree4: Phylogenetic and Taxonomic Study Platform for Prokaryotes base on Whole Genomes. WebCVTree4：基于全基因组的原核生物系统发育与分类研究平台

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-27 DOI: 10.1093/gpbjnl/qzag070

Guanghong Zuo

{"title":"WebCVTree4: Phylogenetic and Taxonomic Study Platform for Prokaryotes base on Whole Genomes.","authors":"Guanghong Zuo","doi":"10.1093/gpbjnl/qzag070","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzag070","url":null,"abstract":"CVTree is an alignment-free methodology for inferring species phylogeny and taxonomy. This method allows for the efficient and accurate resolution of evolutionary relationships among large numbers of species based on whole-genome sequencing data. Since 2004, we have been continuously providing CVTree web services. Recently, the server has undergone a significant upgrade, culminating in the release of the WebCVTree4 platform. This upgrade involves a comprehensive update of the built-in genomic database. The core algorithm has been optimized to enable online phylogenetic reconstruction for tens of thousands of species, thereby facilitating the construction of whole-genome-based trees of life. Furthermore, we have developed a novel algorithm for comparing phylogenetic trees with established taxonomic systems, which supports rapid tree rooting, taxonomic annotation, and topology comparison. Additionally, the interactive front-end of the web interface has been enhanced to allow users to dynamically adjust tree layouts and export high-quality phylogenetic tree figures. These advancements enable WebCVTree4 to facilitate comprehensive comparative analyses that integrate whole-genome-based phylogenetic inference with taxonomy. As research in microbial evolution and taxonomy becomes increasingly dependent upon whole-genome data, WebCVTree4 will function as an efficient web-based platform to facilitate investigations in microbial phylogenetics and taxonomy. It is accessible at https://cvtree.online/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148610597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Global Structural Variation Map Reveals Novel Variants for Body Conformation and Racing Ability in Horses. 全球结构变异图揭示了马的身体形态和比赛能力的新变异。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-27 DOI: 10.1093/gpbjnl/qzag071

Ying Gong, Xuexue Liu, Zhuqing Zheng, Sha Zeng, Yanli Zhang, Yabin Pu, Jianfei Pan, Yuehui Ma, Lin Jiang

{"title":"A Global Structural Variation Map Reveals Novel Variants for Body Conformation and Racing Ability in Horses.","authors":"Ying Gong, Xuexue Liu, Zhuqing Zheng, Sha Zeng, Yanli Zhang, Yabin Pu, Jianfei Pan, Yuehui Ma, Lin Jiang","doi":"10.1093/gpbjnl/qzag071","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzag071","url":null,"abstract":"The selection of horses has been instrumental in shaping long-range mobility, advancing warfare strategies, and diversifying equine phenotypes. However, the structural variants (SVs) favored by this process remain largely unexplored. Utilizing high-fidelity Pacific Biosciences sequencing, we assembled three high-quality horse genomes, incorporating 237 Mb (9.48%) of novel sequences relative to the existing reference genome. These assemblies achieved an average Benchmarking Universal Single-Copy Orthologs completeness of 95.1%. By employing a graph-based approach, we genotyped 23,163 high-confidence, non-redundant SVs, which include 11,714 insertions and 11,449 deletions, across 390 horse genomes representing 61 breeds worldwide. Our findings provide evolutionary insights into the origins of diverse horse populations, through both SVs and single nucleotide polymorphisms. Notably, we identified a 273-bp deletion in the THSD7A gene and a 98-bp long terminal repeat insertion in the OPCML gene, both of which are significantly associated with racing ability and body index in horses (P = 3.87E-05 and 4.08E-05). These genes are linked to bone metabolism and racing ability, respectively. Luciferase assays demonstrated the regulatory potential of these sequences, showing they can significantly modulate the transcriptional activity of their associated genes. In summary, our findings highlight the potential of SVs as genetic markers and functional elements that shape equine phenotypes.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148611414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Role of the Gut-brain Axis in the Cancer-immunity Cycle. 肠脑轴在癌症免疫周期中的作用。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-24 DOI: 10.1093/gpbjnl/qzag069

Yulun Wu, Tao Jiang, Bo Zhu, Hui Zhou

引用次数: 0

Integrated Single-cell Proteomic and Transcriptomic Landscape of Mouse Folliculogenesis. 小鼠卵泡发生的综合单细胞蛋白质组学和转录组学研究。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-23 DOI: 10.1093/gpbjnl/qzag068

Hongchao Li, Xinshuai Zhang, Huimin Kang, Yun Yang, Xinyu Xiao, Yan Wang, Bin Fu, Jie Chen, Xinwen Dong, Yuanjun Zhai, Jing Yang, Jianming Ying, Fuchu He, Yang Li, Xiaowen Wang

{"title":"Integrated Single-cell Proteomic and Transcriptomic Landscape of Mouse Folliculogenesis.","authors":"Hongchao Li, Xinshuai Zhang, Huimin Kang, Yun Yang, Xinyu Xiao, Yan Wang, Bin Fu, Jie Chen, Xinwen Dong, Yuanjun Zhai, Jing Yang, Jianming Ying, Fuchu He, Yang Li, Xiaowen Wang","doi":"10.1093/gpbjnl/qzag068","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzag068","url":null,"abstract":"Folliculogenesis is a complex process essential to female fertility, characterized by multifaceted communication between oocytes and granulosa cells (GCs). While transcriptional regulation during folliculogenesis has been extensively studied, the proteomic landscape remains largely unexplored. Here, we profiled both the proteomic and transcriptomic landscapes of single oocytes and their surrounding mini-bulk GCs across four consecutive stages, from secondary to preovulatory follicles. Integrated dual-omics analysis provided a high-resolution characterization of cell type-specific transcriptional and proteomic changes. Proteomic profiling revealed coordinated metabolic programs, in which oocytes shift toward lipid storage while GCs enhance energy production and steroidogenic metabolism to support oocyte maturation. These metabolic changes in oocytes were accompanied by dynamic remodeling of mitochondrial organization. In addition, we identified novel transcription factors involved in regulating folliculogenesis, as well as a SATB1-centered regulatory network that may reflect preparatory chromatin remodeling preceding zygotic genome activation. Furthermore, GDF9-BMPR2 signaling progressively increased from the secondary stage to the preovulatory stage, indicating strengthened intercellular communication between oocytes and GCs. Together, these findings provide mechanistic insights into oocyte development and follicle growth, with potential implications for novel fertility treatments and diagnostic strategies.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148564207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MicroWorldOmics: All-in-one Desktop Solution for Microbiome Profiling, Virome Analysis, and Unexplored "Dark Matter" Discovery. MicroWorldOmics：用于微生物组分析、病毒组分析和未探索的“暗物质”发现的一体化桌面解决方案。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-20 DOI: 10.1093/gpbjnl/qzag059

Runze Li, Wei Dong, Zhuang Yang, Mingjie Wang, Jinbo Xiong, Yu Ma, Xiaoqing Hu, Yufan Yang, Jiao Wan, Renwei Wu, Ranfeng Ye, Bin Liu, Hung Nguyen-Viet, Zhong Peng, Shan Wang, Jinquan Li

{"title":"MicroWorldOmics: All-in-one Desktop Solution for Microbiome Profiling, Virome Analysis, and Unexplored \"Dark Matter\" Discovery.","authors":"Runze Li, Wei Dong, Zhuang Yang, Mingjie Wang, Jinbo Xiong, Yu Ma, Xiaoqing Hu, Yufan Yang, Jiao Wan, Renwei Wu, Ranfeng Ye, Bin Liu, Hung Nguyen-Viet, Zhong Peng, Shan Wang, Jinquan Li","doi":"10.1093/gpbjnl/qzag059","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzag059","url":null,"abstract":"The large amount of high-throughput sequencing data generated in ecology, medicine, and pharmacology has increased the complexity of data analysis and interpretation. However, the microbiome and virome fields still lack a user-friendly and programming-free desktop application for comprehensive analysis of microbiome and virome data, with a particular gap in virome analysis and \"dark matter\" exploration. To address this gap, we introduce MicroWorldOmics, a plugin-based desktop application designed to offer a streamlined one-stop solution for life sciences and biomedical research. Its plugin-based architecture allows users to analyze data interactively and in parallel, simplifying tasks that typically require advanced bioinformatics skills. MicroWorldOmics is a comprehensive software suite tailored for microbiome and virome research, featuring 92 sub-applications across four main modules: epidemiology analysis, in-depth metagenomic/amplicon and virome profiling, and \"dark matter\" exploration. MicroWorldOmics leverages over 80 Python modules and 600 R packages for diverse bioinformatics, statistics, deep learning, and visualization tasks, accommodating multiple input and output formats including GFF3, FASTA, CSV, PNG, JPG, JSON, and TXT. To enhance user productivity, the software is compatible with Windows, Linux, and macOS systems, and includes demo data for easy benchmarking. In summary, MicroWorldOmics is intended to facilitate microbiome and virome data analysis for life sciences and biomedicine researchers without a programming background. It is available at https://hzaurzli.github.io/.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148537941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pangenome Graph Reveals the Structural Variation Landscape in 2929 Cattle Samples and Its Impact on Gene Regulation. 全基因组图谱揭示了2929个牛样本的结构变异格局及其对基因调控的影响。

IF 7.9

Genomics, proteomics & bioinformatics Pub Date : 2026-07-16 DOI: 10.1093/gpbjnl/qzag065

Pengju Zhao, Chen Peng, Yahui Gao, Shoulu Dai, Liu Yang, Jiayi He, Dongyou Yu, Zhengguang Wang, Xiao Wang, Yang Zhou, Lingzhao Fang, George E Liu

{"title":"Pangenome Graph Reveals the Structural Variation Landscape in 2929 Cattle Samples and Its Impact on Gene Regulation.","authors":"Pengju Zhao, Chen Peng, Yahui Gao, Shoulu Dai, Liu Yang, Jiayi He, Dongyou Yu, Zhengguang Wang, Xiao Wang, Yang Zhou, Lingzhao Fang, George E Liu","doi":"10.1093/gpbjnl/qzag065","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzag065","url":null,"abstract":"Structural variations (SVs) represent a significant source of genomic diversity, with demonstrated roles in livestock gene expression and traits. However, a comprehensive understanding of the SV landscape across large sample sets and its impact on gene regulation in cattle remains incomplete. This study aimed to construct high-fidelity pangenome graphs by integrating both assembly-based and whole-genome sequencing (WGS) derived SV catalogs. We evaluated the efficacy of pangenome graphs for SV genotyping and identified 80,328 high-quality SVs from a cohort of 2929 samples. We systematically characterized these SVs, including their linkage disequilibrium with single nucleotide polymorphisms (SNPs), functional annotations, formation mechanisms, and genomic distributions. Furthermore, we generated paired WGS (24.4 ×) and blood RNA-seq data in 170 Simmental cattle. Utilizing our pangenome graphs, we identified 637 SV-expression quantitative trait loci (SV-eQTL), which accounted for 10.81% of expression heritability of target genes, with 38.09% of the effects linked to promoter/enhancer regions. Forty-six of these SV-eQTL were replicated using CattleGTEx results through SV imputation using a joint SNP-SV reference panel. Notably, insertions in the GHSR gene were significantly associated with its expression levels, likely linked to Bos indicus cattle adaptation to heat tolerance. Our findings provide novel insights into the SV landscape and its contribution to gene regulation, underscoring its importance in cattle genetics and genomics.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":7.9,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148474883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0