590 Tiere (Zoologie)
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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.
A new species of the genus Spinaethorax Papáč & Palacios-Vargas, 2016, recently erected for two cave species in Mexico, is described from a Vietnamese cave. It differs from the Mexican species most noticeably by the dorsal chaetotaxy of the head (number and morphology of chaetae), the shape of S-chaetae on the third antennomere, the dorsal chaetotaxy of the abdomen and the chaetotaxy of the dens. The pattern of special τ-chaetae is described for the first time in the genus. The affinities between Spinaethorax and the other genera of Neelipleona are discussed. Spinaethorax is propably closely related to Neelus Folsom, 1896. A table of the differential characters is provided for the three known species of Spinaethorax. Spinaethorax appears to be restricted to caves, but its presence in Vietnam indicates that this genus has a much larger distribution than previously recognized.