Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola) - Archive ouverte HAL Access content directly
Journal Articles GigaScience Year : 2021

Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)

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Carola Greve
Cyrille d'Haese
Magnus Wolf
Michael Hiller
Axel Janke
Miklós Bálint

Abstract

Abstract Background Genome 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. Results The 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. Conclusions It 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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mnhn-03365231 , version 1 (05-10-2021)

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Clément Schneider, Christian Woehle, Carola Greve, Cyrille d'Haese, Magnus Wolf, et al.. Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola). GigaScience, 2021, 10 (5), ⟨10.1093/gigascience/giab035⟩. ⟨mnhn-03365231⟩

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