ArticleBMC biology2018
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads.
Article in BMC biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Comparative genomic and functional insights into life-cycle plasticity and host adaptation in a wild Nippostrongylus brasiliensis strain from Guangzhou.BMC genomics · 2026Article
- Single-worm long-read sequencing reveals genome diversity in free-living nematodes.Nucleic acids research · 2023Article
- A transcription factor DAF-5 functions in Haemonchus contortus development.Parasites & vectors · 2021Article
- Technology dictates algorithms: recent developments in read alignment.Genome biology · 2021Review
- Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoire.PLoS pathogens · 2021Article
- Consistent ultra-long DNA sequencing with automated slow pipetting.BMC genomics · 2021Article
- Increased Pathogenicity of the Nematophagous FungusFrontiers in fungal biology · 2021Article
- Speciation and adaptive evolution reshape antioxidant enzymatic system diversity across the phylum Nematoda.BMC biology · 2020Article
- Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (G3 (Bethesda, Md.) · 2020Article
- Article
- A de novo frameshift mutation in ZEB2 causes polledness, abnormal skull shape, small body stature and subfertility in Fleckvieh cattle.Scientific reports · 2020Article
- Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods.GigaScience · 2020Article
- Alternative splicing ofeLife · 2020Article
- Oxidative Stress Induction Is a Rational Strategy to Enhance the Productivity ofJournal of agricultural and food chemistry · 2020Article
- Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry.Frontiers in plant science · 2020Review
- De novo assembly of a chromosome-level reference genome of red-spotted grouper (Epinephelus akaara) using nanopore sequencing and Hi-C.Molecular ecology resources · 2019Article
- Recompleting theGenome research · 2019Article
- Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome.Scientific reports · 2019Article
- De novo clustering of long reads by gene from transcriptomics data.Nucleic acids research · 2019Article
- Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEukaryotic genome assembly remains a challenge in part due to the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing methods. At the same time, many nematodes are parasites and some represent a serious threat to human health. There is a pressing need for better molecular characterization of animal and plant parasitic nematodes. The advent of long-read DNA sequencing methods offers the promise of resolving complex genomes.
resultsUsing Nippostrongylus brasiliensis as a test case, applying improved base-calling algorithms and assembly methods, we demonstrate the feasibility of de novo genome assembly matching current community standards using only MinION long reads. In doing so, we uncovered an unexpected diversity of very long and complex DNA sequences repeated throughout the N. brasiliensis genome, including massive tandem repeats of tRNA genes.
conclusionBase-calling and assembly methods have improved sufficiently that de novo genome assembly of large complex genomes is possible using only long reads. The method has the added advantage of preserving haplotypic variants and so has the potential to be used in population analyses.
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