ArticleNucleic acids research2018
Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
60 citing papers in PubMed.
- The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements.Microbial genomics · 2026Article
- Benchmarking within-sample minority variant detection with short-read sequencing inbioRxiv : the preprint server for biology · 2026Article
- Review
- Advance in the assembly of the plant mitochondrial genomes using high-throughput DNA sequencing data of total cellular DNAs.Plant biotechnology journal · 2025Review
- A 69.9-kb long inverted repeat increases genome instability in a strain ofNAR genomics and bioinformatics · 2025Article
- Gene conversion and duplication contribute to genetic variation in an outbreak ofMicrobial genomics · 2025Article
- A method for in-depth analysis of circular DNA virus populations by unambiguously profiling the low abundant virus variants and partial genomic components.Nucleic acids research · 2025Article
- Characteristics of Corynespora cassiicola, the causal agent of tobacco Corynespora leaf spot, revealed by genomic and metabolic phenomic analysis.Scientific reports · 2024Article
- Genomic resources for the Yellowfin tuna Thunnus albacares.Molecular biology reports · 2024Article
- Comparative genomics of clinicalMicrobiology (Reading, England) · 2023Article
- Phenotypic and genomic characterization ofMicrobial genomics · 2023Article
- De novo genome assembly resolving repetitive structures enables genomic analysis of 35 European Mycoplasmopsis bovis strains.BMC genomics · 2023Article
- A Novel Robust Screening Assay IdentifiesMicroorganisms · 2023Article
- De Novo Structural Variations of Escherichia coli Detected by Nanopore Long-Read Sequencing.Genome biology and evolution · 2023Article
- Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference.BMC genomics · 2023Article
- Diversity of the type VI secretion systems in theMicrobial genomics · 2023Article
- Elucidation of the Bovine Intramammary Bacteriome and Resistome from healthy cows of Swiss dairy farms in the Canton Tessin.Frontiers in microbiology · 2023Article
- MEGAnnotator2: a pipeline for the assembly and annotation of microbial genomes.Microbiome research reports · 2023Article
- Whole-Genome Sequence of a Clinical Enterococcus gallinarum Strain in a Positive Hemoculture from Siriraj Hospital, Thailand.Microbiology resource announcements · 2022Article
- Hybrid assembly using long reads resolves repeats and completes the genome sequence of a laboratory strain ofHeliyon · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length, which contained several genes that may confer fitness advantages to the strain. Its complex genome, which also included a variable shufflon region, could not be de novo assembled with long reads produced by Pacific Biosciences' technology, but required very long reads from Oxford Nanopore Technologies. Importantly, a repeat analysis, whose results we release for over 9600 prokaryotes, indicated that very complex bacterial genomes represent a general phenomenon beyond Pseudomonas. Roughly 10% of 9331 complete bacterial and a handful of 293 complete archaeal genomes represented this 'dark matter' for de novo genome assembly of prokaryotes. Several of these 'dark matter' genome assemblies contained repeats far beyond the resolution of the sequencing technology employed and likely contain errors, other genomes were closed employing labor-intense steps like cosmid libraries, primer walking or optical mapping. Using very long sequencing reads in combination with assembly algorithms capable of resolving long, near identical repeats will bring most prokaryotic genomes within reach of fast and complete de novo genome assembly.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.