Genome research最新文献

{"title":"Multisample motif discovery and visualization for tandem repeats","authors":"Yaran Zhang, Marc Hulsman, Alex Salazar, Niccoló Tesi, Lydian Knoop, Sven van der Lee, Sanduni Wijesekera, Jana Krizova, Erik-Jan Kamsteeg, Henne Holstege","doi":"10.1101/gr.279278.124","DOIUrl":"https://doi.org/10.1101/gr.279278.124","url":null,"abstract":"Tandem Repeats (TR) occupy a significant portion of the human genome and are the source of polymorphism due to variations in sizes and motif compositions. Some of these variations have been associated with various neuropathological disorders, highlighting the clinical importance of assessing the motif structure of TRs. Moreover, assessing the TR motif variation can offer valuable insights into evolutionary dynamics and population structure. Previously, characterizations of TRs have been limited by short-read sequencing technology, which lacks the ability to accurately capture the full TR sequences. As long-read sequencing becomes more accessible and can capture the full complexity of TRs, there is now also a need for tools to characterize and analyze TRs using long-read data across multiple samples. In this study, we present MotifScope, a novel algorithm for characterization and visualization of TRs based on a de novo <em>k</em>-mer approach for motif discovery. Comparative analysis against established tools reveals that MotifScope can identify a greater number of motifs and more accurately represent the underlying repeat sequence. Moreover, MotifScope has been specifically designed to enable motif composition comparisons across assemblies of different individuals, as well as across long-read sequencing reads within an individual, through combined motif discovery and sequence alignment. We showcase potential applications of MotifScope in diverse fields, including population genetics, clinical settings, and forensic analyses.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"98 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610478","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}

{"title":"Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding","authors":"Kai Li, Melissa L. Smith, J. Chris Blazier, Kelli J. Kochan, Jonathan M.D. Wood, Kerstin Howe, Anne E. Kwitek, Melinda R. Dwinell, Hao Chen, Julia L. Ciosek, Patrick Masterson, Terence D. Murphy, Theodore S. Kalbfleisch, Peter A. Doris","doi":"10.1101/gr.279292.124","DOIUrl":"https://doi.org/10.1101/gr.279292.124","url":null,"abstract":"We report the construction and analysis of a new reference genome assembly for <em>Rattus norvegicus</em>, the laboratory rat, a widely used experimental animal model organism. The assembly has been adopted as the rat reference assembly by the Genome Reference Consortium and is named GRCr8. The assembly has employed 40× Pacific Biosciences (PacBio) HiFi sequencing coverage and scaffolding using optical mapping and Hi-C. We used genomic DNA from a male BN/NHsdMcwi (BN) rat of the same strain and from the same colony as the prior reference assembly, mRatBN7.2. The assembly is at chromosome level with 98.7% of the sequence assigned to chromosomes. All chromosomes have increased in size compared with the prior assembly and <em>k</em>-mer analysis indicates that the subject animal is fully inbred and that the genome is represented as a single haploid assembly. Notable increases are observed in Chromosomes 3, 11, and 12 in the prospective rDNA regions. In addition, Chr Y has increased threefold in size and is more consistent with the rat karyotype than previous assemblies. Several other chromosomes have grown by the incorporation of sizable discrete new blocks. These contain highly repetitive sequences and encode numerous previously unannotated genes. In addition, centromeric sequences are incorporated in most chromosomes. Genome annotation has been performed by NCBI RefSeq, which confirms improvement in assembly quality and adds more than 1100 new protein coding genes. PacBio Iso-Seq data have been acquired from multiple tissues of the subject animal and are released concurrently with the new assembly to aid further analyses.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"70 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142597544","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}

{"title":"Factors impacting target-enriched long-read sequencing of resistomes and mobilomes","authors":"Ilya B. Slizovskiy, Nathalie Bonin, Jonathan E. Bravo, Peter M. Ferm, Jacob Singer, Christina Boucher, Noelle R. Noyes","doi":"10.1101/gr.279226.124","DOIUrl":"https://doi.org/10.1101/gr.279226.124","url":null,"abstract":"We investigated the efficiency of target-enriched long-read sequencing (TELSeq) for detecting antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) within complex matrices. We aimed to overcome limitations associated with traditional antimicrobial resistance (AMR) detection methods, including short-read shotgun metagenomics, which can lack sensitivity, specificity, and the ability to provide detailed genomic context. By combining biotinylated probe-based enrichment with long-read sequencing, we facilitated the amplification and sequencing of ARGs, eliminating the need for bioinformatic reconstruction. Our experimental design included replicates of human fecal microbiota transplant material, bovine feces, pristine prairie soil, and a mock human gut microbial community, allowing us to examine variables including genomic DNA input and probe set composition. Our findings demonstrated that TELSeq markedly improves the detection rates of ARGs and MGEs compared to traditional sequencing methods, underlining its potential for accurate AMR monitoring. A key insight from our research is the importance of incorporating mobilome profiles to better predict the transferability of ARGs within microbial communities, prompting a recommendation for the use of combined ARG–MGE probe sets for future studies. We also reveal limitations for ARG detection from low-input workflows, and describe the next steps for ongoing protocol refinement to minimize technical variability and expand utility in clinical and public health settings. This effort is part of our broader commitment to advancing methodologies that address the global challenge of AMR.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"8 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580570","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}

{"title":"Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps","authors":"Kristine Bilgrav Saether, Jesper Eisfeldt, Jesse D. Bengtsson, Ming Yin Lun, Christopher M. Grochowski, Medhat Mahmoud, Hsiao-Tuan Chao, Jill A. Rosenfeld, Pengfei Liu, Marlene Ek, Jakob Schuy, Adam Ameur, Hongzheng Dai, Undiagnosed Diseases Network, James Paul Hwang, Fritz J. Sedlazeck, Weimin Bi, Ronit Marom, Josephine Wincent, Ann Nordgren, Claudia M.B. Carvalho, Anna Lindstrand","doi":"10.1101/gr.279346.124","DOIUrl":"https://doi.org/10.1101/gr.279346.124","url":null,"abstract":"Chromosomal inversions (INVs) are particularly challenging to detect due to their copy-number neutral state and association with repetitive regions. Inversions represent about 1/20 of all balanced structural chromosome aberrations and can lead to disease by gene disruption or altering regulatory regions of dosage-sensitive genes in <em>cis</em>. Short-read genome sequencing (srGS) can only resolve ∼70% of cytogenetically visible inversions referred to clinical diagnostic laboratories, likely due to breakpoints in repetitive regions. Here, we study 12 inversions by long-read genome sequencing (lrGS) (<em>n</em> = 9) or srGS (<em>n</em> = 3) and resolve nine of them. In four cases, the inversion breakpoint region was missing from at least one of the human reference genomes (GRCh37, GRCh38, T2T-CHM13) and a reference agnostic analysis was needed. One of these cases, an INV9 mappable only in de novo assembled lrGS data using T2T-CHM13 disrupts <em>EHMT1</em> consistent with a Mendelian diagnosis (Kleefstra syndrome 1; MIM#610253). Next, by pairwise comparison between T2T-CHM13, GRCh37, and GRCh38, as well as the chimpanzee and bonobo, we show that hundreds of megabases of sequence are missing from at least one human reference, highlighting that primate genomes contribute to genomic diversity. Aligning population genomic data to these regions indicated that these regions are variable between individuals. Our analysis emphasizes that T2T-CHM13 is necessary to maximize the value of lrGS for optimal inversion detection in clinical diagnostics. These results highlight the importance of leveraging diverse and comprehensive reference genomes to resolve unsolved molecular cases in rare diseases.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"16 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142563090","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}

{"title":"Geometric deep learning framework for de novo genome assembly","authors":"Lovro Vrček, Xavier Bresson, Thomas Laurent, Martin Schmitz, Kenji Kawaguchi, Mile Šikić","doi":"10.1101/gr.279307.124","DOIUrl":"https://doi.org/10.1101/gr.279307.124","url":null,"abstract":"The critical stage of every de novo genome assembler is identifying paths in assembly graphs that correspond to the reconstructed genomic sequences. The existing algorithmic methods struggle with this, primarily due to repetitive regions causing complex graph tangles, leading to fragmented assemblies. Here, we introduce GNNome, a framework for path identification based on geometric deep learning that enables training models on assembly graphs without relying on existing assembly strategies. By leveraging only the symmetries inherent to the problem, GNNome reconstructs assemblies from PacBio HiFi reads with contiguity and quality comparable to those of the state-of-the-art tools across several species. With every new genome assembled telomere-to-telomere, the amount of reliable training data at our disposal increases. Combining the straightforward generation of abundant simulated data for diverse genomic structures with the AI approach makes the proposed framework a plausible cornerstone for future work on reconstructing complex genomes with different ploidy and aneuploidy degrees. To facilitate such developments, we make the framework and the best-performing model publicly available, provided as a tool that can directly be used to assemble new haploid genomes.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"34 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541287","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}

{"title":"Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing","authors":"Jesper Eisfeldt, Edward J. Higginbotham, Felix Lenner, Jennifer Howe, Bridget A. Fernandez, Anna Lindstrand, Stephen W. Scherer, Lars Feuk","doi":"10.1101/gr.279263.124","DOIUrl":"https://doi.org/10.1101/gr.279263.124","url":null,"abstract":"Rare or de novo structural variation, primarily in the form of copy number variants, is detected in 5%–10% of autism spectrum disorder (ASD) families. While complex structural variants involving duplications can generally be detected using microarray or short-read genome sequencing (GS), these methods frequently fail to characterize breakpoints at nucleotide resolution, requiring additional molecular methods for validation and fine-mapping. Here, we use Oxford Nanopore Technologies PromethION long-read GS to characterize complex genomic rearrangements (CGRs) involving large duplications that segregate with ASD in five families. In total, we investigated 13 CGR carriers and were able to resolve all breakpoint junctions at nucleotide resolution. While all breakpoints were identified, the precise genomic architecture of one rearrangement remained unresolved with three different potential structures. The findings in two families include potential fusion genes formed through duplication rearrangements, involving <em>IL1RAPL1–DMD</em> and <em>SUPT16H–CHD8</em>. In two of the families originating from the same geographical region, an identical rearrangement involving <em>ANK2</em> was identified, which likely represents a founder variant. In addition, we analyze methylation status directly from the long-read data, allowing us to assess the activity of rearranged genes and regulatory regions. Investigation of methylation across the CGRs reveals aberrant methylation status in carriers across a rearrangement affecting the <em>CREBBP</em> locus. In aggregate, our results demonstrate the utility of nanopore sequencing to pinpoint CGRs associated with ASD in five unrelated families, and highlight the importance of a gene-centric description of disease-associated complex chromosomal rearrangements.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"86 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541288","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}

{"title":"A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities","authors":"Jesper Eisfeldt, Adam Ameur, Felix Lenner, Esmee Ten Berk de Boer, Marlene Ek, Josephine Wincent, Raquel Vaz, Jesper Ottosson, Tord Jonson, Sofie Ivarsson, Sofia Thunström, Alexandra Topa, Simon Stenberg, Anna Rohlin, Anna Sandestig, Margareta Nordling, Pia Palmebäck, Magnus Burstedt, Frida Nordin, Eva-Lena Stattin, Maria Sobol, Panagiotis Baliakas, Marie-Louise Bondeson, Ida Höijer, Kristine Bilgrav Saether, Lovisa Lovmar, Hans Ehrencrona, Malin Melin, Lars Feuk, Anna Lindstrand","doi":"10.1101/gr.279510.124","DOIUrl":"https://doi.org/10.1101/gr.279510.124","url":null,"abstract":"Clinical genetic laboratories often require a comprehensive analysis of chromosomal rearrangements/structural variants (SVs), from large events like translocations and inversions to supernumerary ring/marker chromosomes and small deletions or duplications. Understanding the complexity of these events and their clinical consequences requires pinpointing breakpoint junctions and resolving the derivative chromosome structure. This task often surpasses the capabilities of short-read sequencing technologies. In contrast, long-read sequencing techniques present a compelling alternative for clinical diagnostics. Here, Genomic Medicine Sweden—Rare Diseases has explored the utility of HiFi Revio long-read genome sequencing (lrGS) for digital karyotyping of SVs nationwide. The 16 samples from 13 families were collected from all Swedish healthcare regions. Prior investigations had identified 16 SVs, ranging from simple to complex rearrangements, including inversions, translocations, and copy number variants. We have established a national pipeline and a shared variant database for variant calling and filtering. Using lrGS, 14 of the 16 known SVs are detected. Of these, 13 are mapped at nucleotide resolution, and one complex rearrangement is only visible by read depth. Two Chromosome 21 rearrangements, one mosaic, remain undetected. Average read lengths are 8.3–18.8 kb with coverage exceeding 20× for all samples. De novo assembly results in a limited number of phased contigs per individual (N50 6–86 Mb), enabling direct characterization of the chromosomal rearrangements. In a national pilot study, we demonstrate the utility of HiFi Revio lrGS for analyzing chromosomal rearrangements. Based on our results, we propose a 5-year plan to expand lrGS use for rare disease diagnostics in Sweden.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"105 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541289","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}

{"title":"The chromatin tapestry as a framework for neurodevelopment.","authors":"Ben Nolan, Timothy E Reznicek, Christopher T Cummings, M Jordan Rowley","doi":"10.1101/gr.278408.123","DOIUrl":"10.1101/gr.278408.123","url":null,"abstract":"<p><p>The neuronal nucleus houses a meticulously organized genome. Within this structure, genetic material is not simply compacted but arranged into a precise and functional 3D chromatin landscape essential for cellular regulation. This mini-review highlights the importance of this chromatin landscape in healthy neurodevelopment, as well as the diseases that occur with aberrant chromatin architecture. We discuss insights into the fundamental mechanistic relationship between histone modifications, DNA methylation, and genome organization. We then discuss findings that reveal how these epigenetic features change throughout normal neurodevelopment. Finally, we highlight single-gene neurodevelopmental disorders that illustrate the interdependence of epigenetic features, showing how disruptions in DNA methylation or genome architecture can ripple across the entire epigenome. As such, we emphasize the importance of measuring multiple chromatin architectural aspects, as the disruption of one mechanism can likely impact others in the intricate epigenetic network. This mini-review underscores the vast gaps in our understanding of chromatin structure in neurodevelopmental diseases and the substantial research needed to understand the interplay between chromatin features and neurodevelopment.</p>","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"34 10","pages":"1477-1486"},"PeriodicalIF":6.2,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11529992/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142545051","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}

{"title":"Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications","authors":"Dayea Park, Can Cenik","doi":"10.1101/gr.279270.124","DOIUrl":"https://doi.org/10.1101/gr.279270.124","url":null,"abstract":"Long-read sequencing technology enables highly accurate detection of allele-specific RNA expression, providing insights into the effects of genetic variation on splicing and RNA abundance. Furthermore, the ability to directly sequence RNA using the Oxford Nanopore technology promises the detection of RNA modifications in tandem with ascertaining the allelic origin of each molecule. Here, we leverage these advantages to determine allele-biased patterns of N6-methyladenosine (m6A) modifications in native mRNA. We utilized human and mouse cells with known genetic variants to assign allelic origin of each mRNA molecule combined with a supervised machine learning model to detect read-level m6A modification ratios. Our analyses revealed the importance of sequences adjacent to the DRACH-motif in determining m6A deposition, in addition to allelic differences that directly alter the motif. Moreover, we discovered allele-specific m6A modification (ASM) events with no genetic variants in close proximity to the differentially modified nucleotide, demonstrating the unique advantage of using long reads and surpassing the capabilities of antibody-based short-read approaches. This technological advancement promises to advance our understanding of the role of genetics in determining mRNA modifications.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"5 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142541354","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}

{"title":"Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors","authors":"Mara Lohde, Gabriel E. Wagner, Johanna Dabernig-Heinz, Adrian Viehweger, Sascha D. Braun, Stefan Monecke, Celia Diezel, Claudia Stein, Mike Marquet, Ralf Ehricht, Mathias W. Pletz, Christian Brandt","doi":"10.1101/gr.278848.123","DOIUrl":"https://doi.org/10.1101/gr.278848.123","url":null,"abstract":"Our study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long <em>Klebsiella pneumoniae</em> outbreak with Illumina short-read sequencing data as the point of reference. We detect considerable base errors through cgMLST and phylogenetic analysis of genomes sequenced with Oxford Nanopore Technologies, leading to the false exclusion of some outbreak-related strains from the outbreak cluster. Nearby methylation sites cause these errors and can also be found in other species besides <em>K. pneumoniae</em>. Based on these data, we explore PCR-based sequencing and a masking strategy, which both successfully address these inaccuracies and ensure accurate outbreak tracing. We offer our masking strategy as a bioinformatic workflow (MPOA) to identify and mask problematic genome positions in a reference-free manner. Our research highlights limitations in using Oxford Nanopore Technologies for sequencing prokaryotic organisms, especially for investigating outbreaks. For time-critical projects that cannot wait for further technological developments by Oxford Nanopore Technologies, our study recommends either using PCR-based sequencing or using our provided bioinformatic workflow. We advise that read mapping–based quality control of genomes should be provided when publishing results.","PeriodicalId":12678,"journal":{"name":"Genome research","volume":"235 1","pages":""},"PeriodicalIF":7.0,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489048","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}