Genome Biology最新文献_第2页

scExtract: leveraging large language models for fully automated single-cell RNA-seq data annotation and prior-informed multi-dataset integration scExtract：利用大型语言模型进行全自动单细胞RNA-seq数据注释和预先通知的多数据集集成

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-19 DOI: 10.1186/s13059-025-03639-x

Yuxuan Wu, Fuchou Tang

引用次数: 0

Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera) 蜂后工蜂等级决定中与极端表型可塑性相关的基因组内冲突

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-18 DOI: 10.1186/s13059-025-03628-0

Sean T. Bresnahan, Shaun Mahony, Kate Anton, Brock Harpur, Christina M. Grozinger

{"title":"Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)","authors":"Sean T. Bresnahan, Shaun Mahony, Kate Anton, Brock Harpur, Christina M. Grozinger","doi":"10.1186/s13059-025-03628-0","DOIUrl":"https://doi.org/10.1186/s13059-025-03628-0","url":null,"abstract":"Caste determination of honey bees (Apis mellifera) exemplifies developmental plasticity, where differences in larval diet result in identical genotypes yielding either long-lived, reproductive queens or short-lived, facultatively sterile workers. Beyond environmental factors, intragenomic conflict between genes inherited from the mother (matrigenes) versus the father (patrigenes) is hypothesized to influence the underlying traits. In honey bees, the Kinship Theory of Intragenomic Conflict predicts selection on patrigenes to favor traits enhancing individual fitness, such as accelerated growth or increased body size—traits more active in queen-destined larvae. Although parent-of-origin effects have been reported in honey bees, the associated gene regulatory mechanisms remain unknown. While DNA methylation underlies parent-biased transcription in eutherians, angiosperms, and some insects, it is not operating in honey bees or other social insects. Allele-specific transcriptome analyses on queen- and worker-destined larvae at 192 h post-fertilization (hpf) reveal hundreds of genes with parent-of-origin effects, with queen-destined larvae showing overrepresentation of patrigene-biased transcription relative to worker-destined larvae. Genes with parent-biased transcription resemble imprinted genes in other taxa regarding genomic clustering, recombination rate, intron length, and CpG density, with a subset showing parent-biased transcription in 24 hpf eggs. Allele-specific ChIP-seq analyses demonstrate that parent-of-origin effects on caste-specific profiles of H3K27me3, H3K4me3, and H3K27ac are associated with parent-of-origin transcription. These findings suggest that parent-of-origin intragenomic conflict may influence phenotypic plasticity and may be associated with histone post-translational modifications, suggesting a “noncanonical” genomic imprinting-like system in social insects.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"14 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144311662","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

k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance 基于k-mer的小麦GWAS揭示了新的和多样化的白粉病抗性来源

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-18 DOI: 10.1186/s13059-025-03645-z

Benjamin Jaegle, Yoav Voichek, Max Haupt, Alexandros G. Sotiropoulos, Kevin Gauthier, Matthias Heuberger, Esther Jung, Gerhard Herren, Victoria Widrig, Rebecca Leber, Yipu Li, Beate Schierscher, Sarah Serex, Maja Boczkowska, Marta-Puchta Jasińska, Paulina Bolc, Boulos Chalhoub, Nils Stein, Beat Keller, Javier Sánchez-Martín

引用次数: 0

Vispro improves imaging analysis for Visium spatial transcriptomics Vispro改进了Visium空间转录组学的成像分析

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-18 DOI: 10.1186/s13059-025-03648-w

Huifang Ma, Xingyuan Zhang, Yilong Qu, Anru R. Zhang, Zhicheng Ji

引用次数: 0

KPop: accurate and scalable comparative analysis of microbial genomes by sequence embeddings KPop：通过序列嵌入精确和可扩展的微生物基因组比较分析

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-18 DOI: 10.1186/s13059-025-03585-8

Xavier Didelot, Paolo Ribeca

引用次数: 0

Mumemto: efficient maximal matching across pangenomes Mumemto：跨泛基因组的高效最大匹配

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-17 DOI: 10.1186/s13059-025-03644-0

Vikram S. Shivakumar, Ben Langmead

引用次数: 0

Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean 丰富且代谢灵活的细菌谱系为深海中rubisco介导的碳固定提供了巨大的潜力

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-16 DOI: 10.1186/s13059-025-03625-3

Alexander L. Jaffe, Rebecca S. R. Salcedo, Anne E. Dekas

{"title":"Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean","authors":"Alexander L. Jaffe, Rebecca S. R. Salcedo, Anne E. Dekas","doi":"10.1186/s13059-025-03625-3","DOIUrl":"https://doi.org/10.1186/s13059-025-03625-3","url":null,"abstract":"Rubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of organisms that employ it for carbon fixation are still emerging, particularly in unlit ecosystems like the deep sea. We generate fifteen metagenomes along a spatially resolved transect off the California coast and combine them with globally distributed public data to examine the diversity, distribution, and metabolic features of rubisco-encoding organisms from the dark water column. Organisms with the form I and/or form II rubisco are detected in the vast majority of all samples and comprise up to around 20% of the binned microbial community. At 150 m and below, the potential for autotrophic carbon fixation via rubisco is dominated by just two orders of gammaproteobacteria and SAR324, encoding either the form I or II rubisco. Many of these organisms also possess genes for the oxidation of reduced sulfur compounds, which may energetically support carbon fixation. Transcriptomic profiling in the epi- and mesopelagic suggests that all major forms of rubisco (I, II, and III) can be highly expressed in the deep water column but are not done so constitutively, consistent with metabolic flexibility. Our results demonstrate that the genetic potential to fix carbon via rubisco is significant and spatially widespread in the dark ocean. We identify several rubisco-encoding species that are particularly abundant and cosmopolitan, highlighting the key role they may play in deep-sea chemoautotrophy and the global marine carbon cycle.","PeriodicalId":12611,"journal":{"name":"Genome Biology","volume":"22 1","pages":""},"PeriodicalIF":12.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144296293","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

A survey of computational approaches for characterizing microbial interactions in microbial mats 描述微生物垫中微生物相互作用的计算方法综述

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-16 DOI: 10.1186/s13059-025-03634-2

Vanesa L. Perillo, Michael Nute, Nicolae Sapoval, Kristen D. Curry, Logan Golia, Yongze Yin, Huw A. Ogilvie, Luay Nakhleh, Santiago Segarra, Devaki Bhaya, Diana G. Cuadrado, Todd J. Treangen

引用次数: 0

Cancer gene identification from RNA variant allelic frequencies using RVdriver 利用RVdriver从RNA变异等位基因频率中鉴定癌症基因

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-13 DOI: 10.1186/s13059-025-03557-y

James R. M. Black, Thomas P. Jones, Carlos Martínez-Ruiz, Maria Litovchenko, Clare Puttick, Charles Swanton, Nicholas McGranahan

引用次数: 0

cuteFC: regenotyping structural variants through an accurate and efficient force-calling method cuteFC：通过准确高效的力调用方法对结构变异进行基因分型

IF 12.3 1区生物学

Genome Biology Pub Date : 2025-06-13 DOI: 10.1186/s13059-025-03642-2

Tao Jiang, Shuqi Cao, Yadong Liu, Zhendong Zhang, Bo Liu, Ruibang Luo, Guohua Wang, Yadong Wang

引用次数: 0