ArticleNucleic acids research2023
Single-worm long-read sequencing reveals genome diversity in free-living nematodes.
Article in Nucleic acids research, 2023. 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.
- The timescale of nematode evolution reveals late and convergent radiations of parasitism.Nature ecology & evolution · 2026Article
- Fragmentation of Long Reads Enables Reliable Mitogenome Assembly From Whole-Genome Amplification Data With Pervasive Palindromic Reads.Molecular ecology resources · 2026Article
- The genome of an enigmatic sea urchin parasite Echinomermella matsi Jones & Hagen, 1987 resolves its place among other invertebrate parasitic nematodes.G3 (Bethesda, Md.) · 2026Article
- From Rigid Order to Radical Variation: Mitogenome Evolution in the Main Lineages of a Lesser-Known Animal Phylum (Gastrotricha).Genome biology and evolution · 2026Article
- Pelodera: cosmopolitan phoretic saprotrophs and neglected models for origins of nematode parasitism.Parasites & vectors · 2025Review
- Ultraconserved Elements and Machine Learning Classifiers Enable Robust Phylogenetics and Taxonomy in Model and Non-Model Nematodes.Molecular ecology resources · 2025Article
- The Earth BioGenome Project Phase II: illuminating the eukaryotic tree of life.Frontiers in science · 2025Article
- Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations.Genome biology and evolution · 2025Article
- Insights from draft genomes of Heterodera species isolated from field soil samples.BMC genomics · 2025Article
- Long-read sequencing and genome assembly of natural history collection samples and challenging specimens.Genome biology · 2025Article
- Chromosomal genome assembly resolves drug resistance loci in the parasitic nematode Teladorsagia circumcincta.PLoS pathogens · 2025Article
- Article
- Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation.GigaScience · 2025Article
- Multiple Displacement Amplification Facilitates SMRT Sequencing of Microscopic Animals and the Genome of the Gastrotrich Lepidodermella squamata (Dujardin 1841).Genome biology and evolution · 2024Article
- Long-read sequencing and genome assembly of natural history collection samples and challenging specimens.bioRxiv : the preprint server for biology · 2024Article
- AssessingiScience · 2024Article
- Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection.BMC genomics · 2024Article
- A catalogue of chromosome counts for Phylum Nematoda.Wellcome open research · 2024Article
- Revisiting genomes of non-model species with long reads yields new insights into their biology and evolution.Frontiers in genetics · 2024Article
- DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution.Molecular biology and evolution · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Obtaining sufficient genetic material from a limited biological source is currently the primary operational bottleneck in studies investigating biodiversity and genome evolution. In this study, we employed multiple displacement amplification (MDA) and Smartseq2 to amplify nanograms of genomic DNA and mRNA, respectively, from individual Caenorhabditis elegans. Although reduced genome coverage was observed in repetitive regions, we produced assemblies covering 98% of the reference genome using long-read sequences generated with Oxford Nanopore Technologies (ONT). Annotation with the sequenced transcriptome coupled with the available assembly revealed that gene predictions were more accurate, complete and contained far fewer false positives than de novo transcriptome assembly approaches. We sampled and sequenced the genomes and transcriptomes of 13 nematodes from early-branching species in Chromadoria, Dorylaimia and Enoplia. The basal Chromadoria and Enoplia species had larger genome sizes, ranging from 136.6 to 738.8 Mb, compared with those in the other clades. Nine mitogenomes were fully assembled, and displayed a complete lack of synteny to other species. Phylogenomic analyses based on the new annotations revealed strong support for Enoplia as sister to the rest of Nematoda. Our result demonstrates the robustness of MDA in combination with ONT, paving the way for the study of genome diversity in the phylum Nematoda and beyond.
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