ArticleGenome research2019
Plasmid detection and assembly in genomic and metagenomic data sets.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
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Who cites it
90 citing papers in PubMed.
- High-risk antimicrobial resistance genomic traits in multidrug-resistant Salmonella across China's food chain: projections to 2050.Nature communications · 2026Article
- Two coinfecting archaeal viruses provide insights into virus-virus interactions.Communications biology · 2026Article
- National genomic surveillance reveals global plasmid and chromosomal dissemination routes of blanpj antimicrobials and resistance · 2026Article
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.Nature biotechnology · 2026Article
- Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.Microbiome · 2026Article
- Bridging ecological processes to elevated antibiotic resistance risk in tomato microbiome under fungicide stress.The ISME journal · 2026Article
- ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.Microbiome · 2025Article
- Analysis of Clinical Gram-Negative Carbapenem Resistant Acinetobacter baumannii and Klebsiella pneumoniae Isolates from Wounds of Patients at a Hospital Reveals Complex Resistome and the First Report of blaCurrent microbiology · 2025Article
- Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species.Briefings in bioinformatics · 2025Article
- Taxonomy, function and plasmids of microbial soil communities of Polish salt graduation towers.Scientific data · 2025Article
- Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis.Environmental microbiome · 2025Article
- First identification and whole-genome characterization of human-associated Enterobacter roggenkampii and Enterobacter sichuanensis carrying blaJournal of global antimicrobial resistance · 2025Article
- Comprehensive genome data analysis ofData in brief · 2025Article
- Non-cyanobacterial diazotrophs support the survival of marine microalgae in nitrogen-depleted environment.Genome biology · 2025Article
- Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements.Nature microbiology · 2025Article
- Potential effect ofFrontiers in microbiology · 2025Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.ACS synthetic biology · 2024Article
- Whole genome sequencing data ofData in brief · 2024Article
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
30 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.
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