The genome sequence of the lesser stag beetle, Dorcus parallelipipedus (Linnaeus, 1758)

We present a genome assembly from an individual male Dorcus parallelipipedus (the lesser stag beetle; Arthropoda; Insecta; Coleoptera; Lucanidae). The genome sequence is 470.9 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 18.19 kilobases in length.


Background
Dorcus parallelipipedus (Linnaeus, 1758), also known as the Lesser Stag Beetle, is a species of beetle in the Lucanidae family, commonly referred to as the Stag Beetles.D. parallelipipedus is the only member of its genus in the UK and can be distinguished from members of the closely related genus Lucanus via the presence of a sharp medioexternal tooth on the hind and mid tibiae, black coloured upperside and striate fore tibial sculpture (Duff & Schmidt, 2020).This species may also be distinguished by an enlarged 7th antennomere, 3 segmented antennal club and a large mediointernal tooth on the mandible (Duff & Schmidt, 2020).Females possess a pair of median tubercles on the frons, the pronotum is as wide as the elytra and the entire body is shiny and punctured (Duff & Schmidt, 2020;UK Beetles, 2024).Among UK beetles, D. parallelipipedus is easily identified due to its large size, measuring between 20-32 mm (UK Beetles, 2024).
Adult Dorcus parallelipipedus can be found throughout the year.During winter months, they inhabit soft wood or piled vegetation.From April to September, particularly in spring and summer, they exhibit activity both during the day and at night (Duff & Schmidt, 2020).They are proficient fliers and are attracted to light sources.These beetles have a diverse array of host trees, including oak, lime, elder, willow, elm, beech, and various fruit trees (UK Beetles, 2024).The adult life stage can span several years and they may cohabit with larvae in wood.Females create small depressions or short tunnels in wood or bark before laying a single egg.The larval phase can last up to three years, with larvae occasionally congregating in heavily consumed wood pieces.Pupation typically occurs in summer or autumn within a chamber prepared by the larva, usually just beneath the bark.Adults emerge in late summer or autumn, when they feed primarily on sap, and they are known to be drawn to substances like syrup, treacle and ginger (UK Beetles, 2024).

Dorcus parallelipipedus is globally distributed throughout
Europe, from Portugal through to Russia, going as far north to southern Sweden.It has also been recorded through Anatolia and Israel (UK Beetles, 2024).Within the UK, D. parallelipipedus occurs throughout England, with few records more northwards than Nottinghamshire, being seemingly absent from Cornwall, West Wales and Scotland (NBN Atlas Partnership, 2024).Though it appears to be common throughout its range, it has suffered recent declines throughout its full range -much like other saproxylic beetles.
The whole mitochondrial genome of Dorcus parallelipipedus was sequenced by Linard et al. (2016) and later used in a phylogenetic analysis by Chen et al. (2018) to investigate the relationships between two new complete mitochondrial genomes of other Dorcus stag beetles.The full genome of D. parallelipipedus generated by the Darwin Tree of Life aims to complement this previous research on the mitochondrial genomes of this species and its relatives.Though registered as Least concern on the IUCN red list (Thomaes et al., 2015), the continued decline of other saproxylic beetles (Hagge et al., 2024;Sikora et al., 2023) highlights the importance of studying the full genome of these species and how we can use this information to assist in the conservation of such important species.
The genome of Dorcus parallelipipedus was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.Here we present a chromosomally complete genome sequence for Dorcus parallelipipedus, based on one specimen collected from Wytham Woods, Oxfordshire.

Genome sequence report
The genome was sequenced from one male Dorcus parallelipipedus (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 38-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 101 missing joins or mis-joins and removed 19 haplotypic duplications, reducing the assembly length by 0.57% and the scaffold number by 42.21%, and increasing the scaffold N50 by 3.36%. The final assembly has a total length of 470.9 Mb in 88 sequence scaffolds with a scaffold N50 of 49.0 Mb (Table 1).The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.54%) of the assembly sequence was assigned to 10 chromosomal-level scaffolds, representing 8 autosomes and the X and Y sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).Chromosomes X and Y were assigned based on read coverage statistics.While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.The estimated Quality Value (QV) of the final assembly is 61.7 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 99.0% (single = 96.9%,duplicated = 2.1%), using the endopterygota_odb10 reference set (n = 2,124).
Table 3 contains a list of relevant software tool versions and sources.

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The submission  thorax tissue of icDorPara1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.
The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Themistoklis Giannoulis
University of Thessaly, Larissa, Greece The article is very well written, it described the goal clearly and the methods are very well presented.It follows the format of other articles, which aim towards the same goal "One Species -One Genome".The authors have used cutting-edge technologies of DNA sequencing and state-ofthe-art algorithms to analyze and present the data.
Is the rationale for creating the dataset(s) clearly described?

Yes
Are the protocols appropriate and is the work technically sound?Yes Are sufficient details of methods and materials provided to allow replication by others?Yes Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Animal Genetics and Genomics, Phylogenetics, Evolution I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Dorcus parallelipipedus, icDorPara1.1:metrics.The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 470,898,720 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (71,441,279 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (48,965,044 and 41,300,529 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the endopterygota_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icDorPara1_1/dataset/icDorPara1_1/snail.

Figure 3 .
Figure 3. Genome assembly of Dorcus parallelipipedus, icDorPara1.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icDorPara1_1/dataset/icDorPara1_1/blob.

Figure 4 .
Figure 4. Genome assembly of Dorcus parallelipipedus, icDorPara1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icDorPara1_1/dataset/icDorPara1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Dorcus parallelipipedus, icDorPara1.1:Hi-C contact map of the icDorPara1.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=H-frUEYlQDGBaKkAm-ppPg.

:
Proposed standards and metrics for defining genome assembly quality" from Rhie et al. (2021).

Table 3 . Software tools: versions and sources. Software tool Version of
materials by a Darwin Tree of Life Partner is subject to the '

Darwin Tree of Life Project Sampling Code of Practice', which
can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.

the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.No competing interests were disclosed.

Is the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.