The genome sequence of the devil’s coach horse, Ocypus olens (Müller, 1764)

We present a genome assembly from an individual female Ocypus olens (the devil’s coach horse; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence is 1,084 megabases in span. The majority (98.81%) of the assembly is scaffolded into 20 chromosomal pseudomolecules, with the X sex chromosome assembled.


Background
The devil's coach horse, Ocypus olens, is a large, all-black rove beetle. Reaching up to 32 mm, it is the largest beetle in the family Staphylinidae in the UK, and one of the largest worldwide. It's widespread and generally common across the Palaeartic and North Africa, including throughout mainland UK. It has been introduced to North America and Australasia. It can be found across a range of different habitats, especially damp woodland, grassland, brownfield sites and gardens. The devil's coach horse is largely nocturnal, sheltering under leaf litter, logs and stones during the day. It is a generalist predator as both a larva and adult, feeding on a wide range of invertebrate species and carrion (Bonacci et al., 2006). Adults can be found all year and overwintering occurs in this stage. Mating occurs in late summer/autumn and eggs are laid 2 to 3 weeks later (Nield, 1976). Adults can be relatively long-lived, living up to 2 years in this stage (Nield, 1976). When agitated, the abdomen is reared and the mandibles opened in a threat-posture. The devil's coach horse is capable of inflicting a painful bite to humans and readily produces defensive secretions from the mouth and tip of the abdomen. This species has been associated with evil and the devil in folklore since the Middle Ages.
A total of 40-fold coverage in Pacific Biosciences singlemolecule long reads and 41-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 541 missing/misjoins and removed 28 haplotypic duplications, reducing the assembly length by 0.45% and the scaffold number by 64.24%, and increasing the scaffold N50 by 188.60%.
The final assembly has a total length of 1,084 Mb in 187 sequence scaffolds with a scaffold N50 of 57.3 Mb ( Table 1). The majority, 98.81%, of the assembly sequence was assigned to 20 chromosomal-level scaffolds, representing 9 autosomes (numbered by sequence length), and the X sex chromosome (Figure 2- Figure 5; Table 2). The order and orientation of scaffolds in the centromeric regions is less certain than in the rest of the assembly. The assembly has a BUSCO v5.1.2 (Manni et al., 2021) completeness of 99.3% (single 98.2%, duplicated 1.1%) using the endopterygota_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and nucleic acid extraction
A single female O. olens was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.775, longitude -1.326) by Liam Crowley, University of Oxford, using a pooter. The sample was identified by the same individual, snap-frozen on dry ice and stored using a CoolRack.
DNA was extracted from the whole organism of icOcyOlen1 at the Wellcome Sanger Institute (WSI) Scientific Operations core from the whole organism using the Qiagen MagAttract  HMW DNA kit, according to the manufacturer's instructions. Following this, further DNA was extracted for a PacBio top-up. Tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse. High molecular weight (HMW) DNA was again extracted using the Qiagen MagAttract HMW DNA extraction kit. HMW DNA was sheared into an average fragment size between 12-20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
RNA was extracted from the whole organism in the Tree of Life Laboratory at the WSI using TRIzol (Invitrogen), according to the manufacturer's instructions. RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit. Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics Chromium read cloud sequencing libraries were   Table 3 contains a list of all software tool versions used, where appropriate.