ArticleGigaScience2021
Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola).
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Type Genomics: A Framework for Integrating Genomic Data into Biodiversity and Taxonomic Research.Systematic biology · 2025Guideline
- De novo genome assembly of the endemic Italian springtail Orchesella dallaii (Collembola: Orchesellidae).G3 (Bethesda, Md.) · 2025Article
- StrataSeq: A Workflow for Rapid Development of Molecular Databases for Hard-To-Identify Species.Ecology and evolution · 2025Article
- FOGS: A SNPSTR Marker Database to Combat Wildlife Trafficking and a Cell Culture Bank for Ex-Situ Conservation.Molecular ecology resources · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- The First Cavernicolous Species ofInsects · 2025Article
- Fundamental questions in meiofauna research highlight how small but ubiquitous animals can improve our understanding of Nature.Communications biology · 2025Article
- Single specimen genome assembly of Culicoides stellifer shows evidence of a non-retroviral endogenous viral element.BMC genomics · 2025Article
- Long-read sequencing and genome assembly of natural history collection samples and challenging specimens.Genome biology · 2025Article
- 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
- Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.Nature communications · 2024Article
- Advances in single-cell long-read sequencing technologies.NAR genomics and bioinformatics · 2024Article
- The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils.The Journal of heredity · 2024Article
- The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution.Communications biology · 2023Article
- Ancient diversity in host-parasite interaction genes in a model parasitic nematode.Nature communications · 2023Article
- Mabs, a suite of tools for gene-informed genome assembly.BMC bioinformatics · 2023Article
- Draft genome assemblies of the avian louse Brueelia nebulosa and its associates using long-read sequencing from an individual specimen.G3 (Bethesda, Md.) · 2023Article
- Holotype sequencing ofZooKeys · 2023Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non-genetic model species. However, long-read sequencing today relies on sizable quantities of high-quality, high molecular weight DNA, which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present de novo genomes of 2 species of submillimeter Collembola. For each, we prepared the sequencing library from high molecular weight DNA extracted from a single specimen and using a novel ultra-low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole-genome amplification step.
resultsThe 2 assembled genomes have N50 values >5.5 and 8.5 Mb, respectively, and both contain ∼96% of BUSCO genes. Thus, they are highly contiguous and complete. The genomes are supported by an integrative taxonomy approach including placement in a genome-based phylogeny of Collembola and designation of a neotype for 1 of the species. Higher heterozygosity values are recorded in the more mobile species. Both species are devoid of the biosynthetic pathway for β-lactam antibiotics known in several Collembola, confirming the tight correlation of antibiotic synthesis with the species way of life.
conclusionsIt is now possible to generate high-quality genomes from single specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1 Mb) required by the Earth BioGenome Project.
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