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Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.

التفاصيل البيبلوغرافية
العنوان: Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.
المؤلفون: Curry KD; Rice University, Department of Computer Science, Houston, TX 77005, United States.; Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France., Yu FB; Arc Institute, Palo Alto, CA 94304, United States., Vance SE; University of California, Berkeley, Department of Environmental Science, Policy, and Management, Berkeley, CA 94720, United States., Segarra S; Rice University, Department of Electrical and Computer Engineering, Houston, TX 77005, United States., Bhaya D; Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, United States., Chikhi R; Institut Pasteur, Université Paris Cité, Sequence Bioinformatics unit, 75015 Paris, France., Rocha EPC; Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France., Treangen TJ; Rice University, Department of Computer Science, Houston, TX 77005, United States.
المصدر: BioRxiv : the preprint server for biology [bioRxiv] 2024 Jan 30. Date of Electronic Publication: 2024 Jan 30.
نوع المنشور: Preprint
اللغة: English
بيانات الدورية: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE
مستخلص: Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.
Competing Interests: Competing interests No competing interest is declared.
التعليقات: Update in: Bioinformatics. 2024 Jun 28;40(Supplement_1):i58-i67. doi: 10.1093/bioinformatics/btae224. (PMID: 38940156)
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معلومات مُعتمدة: P01 AI152999 United States AI NIAID NIH HHS
فهرسة مساهمة: Keywords: gene transfer; long-read sequencing; metagenome; microbiome; structural variants
تواريخ الأحداث: Date Created: 20240214 Latest Revision: 20240708
رمز التحديث: 20240708
مُعرف محوري في PubMed: PMC10862772
DOI: 10.1101/2024.01.25.577285
PMID: 38352454
قاعدة البيانات: MEDLINE
الوصف
تدمد:2692-8205
DOI:10.1101/2024.01.25.577285