Genome research最新文献_第3页

Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases 利用深度学习分类器和综合蛋白质数据库探测反刍动物真核微生物

IF 7 2区生物学

Genome research Pub Date : 2024-12-27 DOI: 10.1101/gr.279825.124

Ming Yan, Thea Os Andersen, Phil B. Pope, Zhongtang Yu

{"title":"Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases","authors":"Ming Yan, Thea Os Andersen, Phil B. Pope, Zhongtang Yu","doi":"10.1101/gr.279825.124","DOIUrl":"https://doi.org/10.1101/gr.279825.124","url":null,"abstract":"Metagenomics, particularly genome-resolved metagenomics, has significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations within various microbiomes, including those in the mammalian gastrointestinal (GI) tract, remain relatively underexplored in metagenomic studies due to the lack of comprehensive reference genome databases and robust bioinformatics tools. The GI tract of ruminants, particularly the rumen, contains a high eukaryotic biomass although a relatively low diversity of ciliates and fungi, which significantly impacts feed digestion, methane emissions, and rumen microbial ecology. In the present study, we developed GutEuk, a bioinformatics tool that improves upon the currently available Tiara and EukRep in accurately identifying eukaryotic sequences from metagenomes. GutEuk is optimized for high precision across different sequence lengths. It can also distinguish fungal and protozoal sequences, further elucidating their unique ecological, physiological, and nutritional impacts. GutEuk was shown to facilitate comprehensive analyses of protozoa and fungi within more than one thousand rumen metagenomes, revealing a greater genomic diversity among protozoa than previously documented. We further curated several ruminant eukaryotic protein databases, significantly enhancing our ability to distinguish the functional roles of ruminant fungi and protozoa from those of prokaryotes. Overall, the newly developed package GutEuk and its associated databases create new opportunities for in-depth study of GI tract eukaryotes.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"114 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887882","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}

引用次数: 0

Combining DNA and protein alignments to improve genome annotation with LiftOn 结合DNA和蛋白质比对改进LiftOn基因组注释

IF 7 2区生物学

Genome research Pub Date : 2024-12-27 DOI: 10.1101/gr.279620.124

Kuan-Hao Chao, Jakob M Heinz, Celine Hoh, Alan Mao, Alaina Shumate, Mihaela Pertea, Steven Salzberg

引用次数: 0

Inferring ancestry with the hierarchical soft clustering approach tangleGen. 用分层软聚类法 tangleGen 推断祖先。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.279399.124

Klara Elisabeth Burger, Solveig Klepper, Ulrike von Luxburg, Franz Baumdicker

{"title":"Inferring ancestry with the hierarchical soft clustering approach tangleGen.","authors":"Klara Elisabeth Burger, Solveig Klepper, Ulrike von Luxburg, Franz Baumdicker","doi":"10.1101/gr.279399.124","DOIUrl":"10.1101/gr.279399.124","url":null,"abstract":"Understanding the genetic ancestry of populations is central to numerous scientific and societal fields. It contributes to a better understanding of human evolutionary history, advances personalized medicine, aids in forensic identification, and allows individuals to connect to their genealogical roots. Existing methods, such as ADMIXTURE, have significantly improved our ability to infer ancestries. However, these methods typically work with a fixed number of independent ancestral populations. As a result, they provide insight into genetic admixture, but do not include a hierarchical interpretation. In particular, the intricate ancestral population structures remain difficult to unravel. Alternative methods with a consistent inheritance structure, such as hierarchical clustering, may offer benefits in terms of interpreting the inferred ancestries. Here, we present tangleGen, a soft clustering tool that transfers the hierarchical machine learning framework Tangles, which leverages graph theoretical concepts, to the field of population genetics. The hierarchical perspective of tangleGen on the composition and structure of populations improves the interpretability of the inferred ancestral relationships. Moreover, tangleGen adds a new layer of explainability, as it allows identifying the single-nucleotide polymorphisms that are responsible for the clustering structure. We demonstrate the capabilities and benefits of tangleGen for the inference of ancestral relationships, using both simulated data and data from the 1000 Genomes Project.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":" ","pages":"2244-2255"},"PeriodicalIF":6.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Reviewer Index, Volume 34, 2024. 审稿人索引，第34卷，2024年。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-23

引用次数: 0

Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR. 利用 MiXCR 从免疫谱系测序数据中进行超灵敏等位基因推断。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.278775.123

Artem Mikelov, George Nefediev, Alexander Tashkeev, Oscar L Rodriguez, Diego Aguilar Ortmans, Valeriia Skatova, Mark Izraelson, Alexey N Davydov, Stanislav Poslavsky, Souad Rahmouni, Corey T Watson, Dmitriy Chudakov, Scott D Boyd, Dmitry Bolotin

{"title":"Ultrasensitive allele inference from immune repertoire sequencing data with MiXCR.","authors":"Artem Mikelov, George Nefediev, Alexander Tashkeev, Oscar L Rodriguez, Diego Aguilar Ortmans, Valeriia Skatova, Mark Izraelson, Alexey N Davydov, Stanislav Poslavsky, Souad Rahmouni, Corey T Watson, Dmitriy Chudakov, Scott D Boyd, Dmitry Bolotin","doi":"10.1101/gr.278775.123","DOIUrl":"10.1101/gr.278775.123","url":null,"abstract":"Allelic variability in the adaptive immune receptor loci, which harbor the gene segments that encode B cell and T cell receptors (BCR/TCR), is of critical importance for immune responses to pathogens and vaccines. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread in immunology research making it the most readily available source of information about allelic diversity in immunoglobulin (IG) and T cell receptor (TR) loci. Here, we present a novel algorithm for extrasensitive and specific variable (V) and joining (J) gene allele inference, allowing the reconstruction of individual high-quality gene segment libraries. The approach can be applied for inferring allelic variants from peripheral blood lymphocyte BCR and TCR repertoire sequencing data, including hypermutated isotype-switched BCR sequences, thus allowing high-throughput novel allele discovery from a wide variety of existing data sets. The developed algorithm is a part of the MiXCR software. We demonstrate the accuracy of this approach using AIRR-seq paired with long-read genomic sequencing data, comparing it to a widely used algorithm, TIgGER. We applied the algorithm to a large set of IG heavy chain (IGH) AIRR-seq data from 450 donors of ancestrally diverse population groups, and to the largest reported full-length TCR alpha and beta chain (TRA and TRB) AIRR-seq data set, representing 134 individuals. This allowed us to assess the genetic diversity within the IGH, TRA, and TRB loci in different populations and to establish a database of alleles of V and J genes inferred from AIRR-seq data and their population frequencies with free public access through VDJ.online database.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":" ","pages":"2293-2303"},"PeriodicalIF":6.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463177","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models 在两种主要的CRX视网膜病变模型中，异常的同源结构域- dna合作二聚化是不同发育缺陷的基础

IF 7 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.279340.124

Yiqiao Zheng, Gary D. Stormo, Shiming Chen

{"title":"Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models","authors":"Yiqiao Zheng, Gary D. Stormo, Shiming Chen","doi":"10.1101/gr.279340.124","DOIUrl":"https://doi.org/10.1101/gr.279340.124","url":null,"abstract":"Paired-class homeodomain transcription factors (HD TFs) play essential roles in vertebrate development, and their mutations are linked to human diseases. One unique feature of paired-class HD is cooperative dimerization on specific palindrome DNA sequences. Yet, the functional significance of HD cooperative dimerization in animal development and its dysregulation in diseases remain elusive. Using the retinal TF Cone-rod Homeobox (CRX) as a model, we have studied how blindness-causing mutations in the paired HD, p.E80A and p.K88N, alter CRX’s cooperative dimerization, lead to gene misexpression and photoreceptor developmental deficits in dominant manners. CRXE80A maintains binding at monomeric WT CRX motifs but is deficient in cooperative binding at dimeric motifs. CRXE80A’s cooperativity defect impacts the exponential increase of photoreceptor gene expression in terminal differentiation and produces immature, non-functional photoreceptors in the CrxE80A retinas. CRXK88N is highly cooperative and localizes to ectopic genomic sites with strong enrichment of dimeric HD motifs. CRXK88N’s altered biochemical properties disrupt CRX’s ability to direct dynamic chromatin remodeling during development to activate photoreceptor differentiation programs and silence progenitor programs. Our study here provides in vitro and in vivo molecular evidence that paired-class HD cooperative dimerization regulates neuronal development and dysregulation of cooperative binding contributes to severe dominant blinding retinopathies.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"13 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879927","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}

引用次数: 0

Reviewer Index, Volume 34, 2024. 审稿人索引，第34卷，2024年。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-23

引用次数: 0

Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development. 分析超级增强子的时间动态可揭示骨骼肌发育过程中潜在的关键增强子及其基因调控网络。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.278344.123

Song Zhang, Chao Wang, Shenghua Qin, Choulin Chen, Yongzhou Bao, Yuanyuan Zhang, Lingna Xu, Qingyou Liu, Yunxiang Zhao, Kui Li, Zhonglin Tang, Yuwen Liu

{"title":"Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development.","authors":"Song Zhang, Chao Wang, Shenghua Qin, Choulin Chen, Yongzhou Bao, Yuanyuan Zhang, Lingna Xu, Qingyou Liu, Yunxiang Zhao, Kui Li, Zhonglin Tang, Yuwen Liu","doi":"10.1101/gr.278344.123","DOIUrl":"10.1101/gr.278344.123","url":null,"abstract":"Super-enhancers (SEs) govern the expression of genes defining cell identity. However, the dynamic landscape of SEs and their critical constituent enhancers involved in skeletal muscle development remains unclear. In this study, using pig as a model, we employed cleavage under targets and tagmentation (CUT&Tag) to profile the enhancer-associated histone modification marker H3K27ac in skeletal muscle across two prenatal and three postnatal stages, and investigated how SEs influence skeletal muscle development. We identify three SE families with distinct temporal dynamics: continuous (Con, 397), transient (TS, 434), and de novo (DN, 756). These SE families are associated with different temporal gene expression trajectories, biological functions, and DNA methylation levels. Notably, several lines of evidence suggest a potential prominent role of Con SEs in regulating porcine muscle development and meat traits. To pinpoint key cis-regulatory units in Con SEs, we developed an integrative approach that leverages information from eRNA annotation, genome-wide association study (GWAS) signals, and high-throughput capture self-transcribing active regulatory region sequencing (STARR-seq) experiments. Within Con SEs, we identify 20 candidate critical enhancers with meat and carcass-associated DNA variations that affect enhancer activity, and infer their upstream transcription factors and downstream target genes. As a proof of concept, we experimentally validate the role of one such enhancer and its potential target gene during myogenesis. Our findings reveal the dynamic regulatory features of SEs in skeletal muscle development and provide a general integrative framework for identifying critical enhancers underlying the formation of complex traits.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":" ","pages":"2190-2202"},"PeriodicalIF":6.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11694746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142463175","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq 利用长读RNA-seq评估证据驱动的基因组注释策略

IF 7 2区生物学

Genome research Pub Date : 2024-12-23 DOI: 10.1101/gr.279864.124

Alejandro Paniagua, Cristina Agustin-García, Francisco J Pardo-Palacios, Thomas Brown, Maite De Maria, Nancy D Denslow, Camila Mazzoni, Ana Conesa

{"title":"Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq","authors":"Alejandro Paniagua, Cristina Agustin-García, Francisco J Pardo-Palacios, Thomas Brown, Maite De Maria, Nancy D Denslow, Camila Mazzoni, Ana Conesa","doi":"10.1101/gr.279864.124","DOIUrl":"https://doi.org/10.1101/gr.279864.124","url":null,"abstract":"While the production of a draft genome has become more accessible due to long-read sequencing, the annotation of these new genomes has not been developed at the same pace. Long-read RNA sequencing (lrRNA-seq) offers a promising solution for enhancing gene annotation. In this study, we explore how sequencing platforms, Oxford Nanopore R9.4.1 chemistry or PacBio Sequel II CCS, and data processing methods influence evidence-driven genome annotation using long reads. Incorporating PacBio transcripts into our annotation pipeline significantly outperformed traditional methods, such as ab initio predictions and short-read-based annotations. We applied this strategy to a nonmodel species, the Florida manatee, and compared our results to existing short-read-based annotation. At the loci level, both annotations were highly concordant, with 90% agreement. However, at the transcript level, the agreement was only 35%. We identified 4,906 novel loci, represented by 5,707 isoforms, with 64% of these isoforms matching known sequences in other mammalian species. Overall, our findings underscore the importance of using high-quality curated transcript models in combination with ab initio methods for effective genome annotation.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"32 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879924","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}

引用次数: 0

Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle. 牛磺酸泛基因组揭示了与白头牛色素沉着相关的KIT上游片段重复。

IF 6.2 2区生物学

Genome research Pub Date : 2024-12-18 DOI: 10.1101/gr.279064.124

Sotiria Milia, Alexander Leonard, Xena Marie Mapel, Sandra Milena Bernal Ulloa, Cord Drögemüller, Hubert Pausch

{"title":"Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle.","authors":"Sotiria Milia, Alexander Leonard, Xena Marie Mapel, Sandra Milena Bernal Ulloa, Cord Drögemüller, Hubert Pausch","doi":"10.1101/gr.279064.124","DOIUrl":"10.1101/gr.279064.124","url":null,"abstract":"Cattle have been selectively bred for coat color, spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream the KIT gene has been proposed. Here, we construct a graph pangenome from 24 haplotype assemblies representing seven taurine cattle breeds to identify and characterize the white head-associated locus for the first time based on long-read sequencing data and pangenome analyses. We introduce a pangenome-wide association mapping approach which examines assembly path similarities within the graph to reveal an association between two most likely serial alleles of a complex structural variant 66 kb upstream KIT and facial depigmentation. The complex structural variant contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs, and other repetitive elements, leading to misleading alignments of short and long reads when using a linear reference. We align 250 short-read sequencing samples spanning 15 cattle breeds to the pangenome graph, further validating that the alleles of the structural variant segregate with head depigmentation. We estimate an increased count of repeats in Hereford relative to Simmental and other white-headed cattle breeds from the graph alignment coverage, suggesting a large under-assembly in the current Hereford-based cattle reference genome which had fewer copies. Our work shows that exploiting assembly path similarities within graph pangenomes can reveal trait-associated complex structural variants.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":" ","pages":""},"PeriodicalIF":6.2,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853891","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}

引用次数: 0