期刊
GIGASCIENCE
卷 10, 期 5, 页码 -出版社
OXFORD UNIV PRESS
DOI: 10.1093/gigascience/giab035
关键词
long-read genome sequencing; PacBio; soil invertebrates; eukaryote biodiversity; low-input DNA; integrative taxonomy
资金
- programme LOEWE-Landes-Offensive zur Entwicklung Wissenschaftlich-okonomischer Exzellenz of Hesse's Ministry of Higher Education, Research, and the Arts
- Max-Planck Society
- Pacific Biosciences
The novel ultra-low input protocol allows for high-quality genome sequencing from single specimens of minute, field-preserved metazoans, providing a new approach for biodiversity research. The genomes of two submillimeter Collembola species were successfully sequenced, demonstrating the feasibility and effectiveness of this method.
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 similar to 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 beta-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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