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Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
F1000 Research Limited London, UK

39184130
10.12688/wellcomeopenres.21262.1
Data Note
Articles
The genome sequence of the lesser stag beetle, Dorcus parallelipipedus (Linnaeus, 1758)
[version 1; peer review: 3 approved]

Crowley Liam M. Investigation Resources Writing – Review & Editing https://orcid.org/0000-0001-6380-0329
1
Phillips Dominic Writing – Original Draft Preparation https://orcid.org/0009-0000-6090-1984
2
University of Oxford and Wytham Woods Genome Acquisition Lab
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
Wellcome Sanger Institute Scientific Operations: Sequencing Operations
Wellcome Sanger Institute Tree of Life Core Informatics team
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 University of Oxford, Oxford, England, UK
2 Natural History Museum, London, England, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

17 4 2024
2024
9 20221 3 2024
Copyright: © 2024 Crowley LM et al.
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.

Dorcus parallelipipedus
lesser stag beetle
genome sequence
chromosomal
Coleoptera
Wellcome Trust218328 206194 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328 </a>]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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pmcSpecies taxonomy

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Scarabaeiformia; Scarabaeoidea; Lucanidae; Lucaninae; Dorcus; Dorcus parallelipipedus (Linnaeus, 1758) (NCBI:txid41107).

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, –1.34). 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%.

Figure 1. Photograph of the Dorcus parallelipipedus (icDorPara1) specimen used for genome sequencing.

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.

Table 1. Genome data for Dorcus parallelipipedus, icDorPara1.1.

Project accession data	
Assembly identifier	icDorPara1.1	
Species	Dorcus parallelipipedus	
Specimen	icDorPara1	
NCBI taxonomy ID	41107	
BioProject	PRJEB59788	
BioSample ID	SAMEA7701270	
Isolate information	icDorPara1, male: head (DNA sequencing), thorax (Hi-C
sequencing)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	61.7	≥ 50	
k-mer completeness	100.0%	≥ 95%	
BUSCO **	C:99.0%[S:96.9%,D:2.1%],
F:0.2%,M:0.8%,n:2,124	C ≥ 95%	
Percentage of assembly mapped to chromosomes	99.54%	≥ 95%	
Sex chromosomes	XY	localised homologous pairs	
Organelles	Mitochondrial genome: 18.19 kb	complete single alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR10879947	
Hi-C Illumina	ERR10890734	
Genome assembly	
Assembly accession	GCA_958336345.1	
Accession of alternate haplotype	GCA_958336325.1	
Span (Mb)	470.9	
Number of contigs	763	
Contig N50 length (Mb)	1.4	
Number of scaffolds	88	
Scaffold N50 length (Mb)	49.0	
Longest scaffold (Mb)	71.44	
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from Rhie et al. (2021).

** BUSCO scores based on the endopterygota_odb10 BUSCO set using version 5.3.2. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/icDorPara1_1/dataset/icDorPara1_1/busco.

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. 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. 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. 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.

Table 2. Chromosomal pseudomolecules in the genome assembly of Dorcus parallelipipedus, icDorPara1.

INSDC
accession	Chromosome	Length (Mb)	GC%	
OY284475.1	1	71.44	35.0	
OY284476.1	2	55.04	34.5	
OY284477.1	3	53.55	35.5	
OY284478.1	4	49.19	35.0	
OY284480.1	5	47.61	35.5	
OY284481.1	6	44.66	34.0	
OY284482.1	7	42.01	34.5	
OY284483.1	8	41.3	34.5	
OY284479.1	X	48.97	35.0	
OY284484.1	Y	14.91	35.5	
OY284485.1	MT	0.02	31.0	

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).

Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/41107.

Methods

Sample acquisition and nucleic acid extraction

A male Dorcus parallelipipedus (specimen ID Ox000491, ToLID icDorPara1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude –1.34) on 2020-06-20 by potting. The specimen was collected and identified by Liam Crowley (University of Oxford) and preserved on dry ice.

The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. In sample preparation, the icDorPara1 sample was weighed and dissected on dry ice ( Jay et al., 2023). Tissue from the head was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a). HMW DNA was extracted using the Automated MagAttract v1 protocol ( Sheerin et al., 2023). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 30 ( Todorovic et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA. 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.

Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023b).

Sequencing

Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II instrument. Hi-C data were also generated from 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 purge_dups ( Guan et al., 2020). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using YaHS ( Zhou et al., 2023). The assembly was checked for contamination and corrected using the TreeVal pipeline ( Pointon et al., 2023). Manual curation was performed using JBrowse2 ( Diesh et al., 2023), HiGlass ( Kerpedjiev et al., 2018) and PretextView ( Harry, 2022). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) or MITOS ( Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

A Hi-C map for the final assembly was produced using bwa-mem2 ( Vasimuddin et al., 2019) in the Cooler file format ( Abdennur & Mirny, 2020). To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury ( Rhie et al., 2020). This work was done using Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.

Table 3 contains a list of relevant software tool versions and sources.

Table 3. Software tools: versions and sources.

Software tool	Version	Source	
BlobToolKit	4.1.7	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.3.2	https://gitlab.com/ezlab/busco	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
Merqury	MerquryFK	https://github.com/thegenemyers/MERQURY.FK	
MitoHiFi	2	https://github.com/marcelauliano/MitoHiFi	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
purge_dups	1.2.3	https://github.com/dfguan/purge_dups	
sanger-tol/genomenote	v1.0	https://github.com/sanger-tol/genomenote	
sanger-tol/readmapping	1.1.0	https://github.com/sanger-tol/readmapping/tree/1.1.0	
TreeVal	-	https://github.com/sanger-tol/treeval	
YaHS	yahs-1.1.91eebc2	https://github.com/c-zhou/yahs	

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 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.

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

•   Legality of collection, transfer and use (national and international)

Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.

Data availability

European Nucleotide Archive: Dorcus parallelipipedus (lesser stag beetle). Accession number PRJEB59788; https://identifiers.org/ena.embl/PRJEB59788 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Dorcus parallelipipedus genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1.

Author information

Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7125292.

Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.

Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.

Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.

Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.

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.

10.21956/wellcomeopenres.23516.r91308
Reviewer response for version 1
Sylvester Terrence 1Referee https://orcid.org/0000-0001-6683-0793

1 The University of Memphis, Memphis, Tennessee, USA
17 9 2024 Copyright: © 2024 Sylvester T
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
The authors present the genome sequence of the lesser stag beetle. The authors have done an excellent job of generating the genome assembly and scaffolding it up to chromosome level. The present genome could further benefit from including an annotation. The authors follow a standard and widely accepted genome sequencing and assembly pipeline. Data are well presented and publicly available. I do not have other significant remarks on the work presented in this manuscript.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Genomics

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.

10.21956/wellcomeopenres.23516.r92713
Reviewer response for version 1
Angus Robert 1Referee
1 The Natural History Museum, London, UK
22 8 2024 Copyright: © 2024 Angus R
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
This is a clearly presented account of the genome of Dorcus parallelipipedus. The methods used are standard and the illustration of the beetle leaves no doubt of its identity.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

NA

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.

10.21956/wellcomeopenres.23516.r89041
Reviewer response for version 1
Giannoulis Themistoklis 1Referee https://orcid.org/0000-0002-1842-5432

1 University of Thessaly, Larissa, Greece
9 8 2024 Copyright: © 2024 Giannoulis T
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
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-of-the-art algorithms to analyze and present the data.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

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.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
==== Refs
Abdennur N Mirny LA : Cooler: Scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36 (1 ):311–316. 10.1093/bioinformatics/btz540 31290943
Allio R Schomaker‐Bastos A Romiguier J : MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20 (4 ):892–905. 10.1111/1755-0998.13160 32243090
Bernt M Donath A Jühling F : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69 (2 ):313–319. 10.1016/j.ympev.2012.08.023 22982435
Challis R Richards E Rajan J : BlobToolKit - interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10 (4 ):1361–1374. 10.1534/g3.119.400908 32071071
Chen Y Liu J Cao Y : Two new complete mitochondrial genomes of Dorcus stag beetles (Coleoptera, Lucanidae). Genes Genomics. 2018;40 (8 ):873–880. 10.1007/s13258-018-0699-8 30047116
Cheng H Concepcion GT Feng X : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18 (2 ):170–175. 10.1038/s41592-020-01056-5 33526886
Denton A Oatley G Cornwell C : Sanger Tree of Life Sample Homogenisation: PowerMash. protocols.io. 2023a. 10.17504/protocols.io.5qpvo3r19v4o/v1
Denton A Yatsenko H Jay J : Sanger Tree of Life Wet Laboratory Protocol Collection V.1. protocols.io. 2023b. 10.17504/protocols.io.8epv5xxy6g1b/v1
Di Tommaso P Chatzou M Floden EW : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35 (4 ):316–319. 10.1038/nbt.3820 28398311
Diesh C Stevens GJ Xie P : JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biol. 2023;24 (1 ): 74. 10.1186/s13059-023-02914-z 37069644
Duff A Schmidt U : Beetles of Britain and Ireland. Geotrupidae to Scraptiidae.West Runton, Norfolk: AG Duff Publishing,2020;3 .
Guan D McCarthy SA Wood J : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36 (9 ):2896–2898. 10.1093/bioinformatics/btaa025 31971576
Hagge J Müller J Bässler C : Change in saproxylic beetle, fungi and bacteria assemblages along horizontal and vertical gradients of sun-exposure in forest. Biol Conserv. 2024;291 : 110493. 10.1016/j.biocon.2024.110493
Harry E : PretextView (Paired REad TEXTure Viewer): A desktop application for viewing pretext contact maps. 2022; [Accessed 19 October 2022]. Reference Source
Jay J Yatsenko H Narváez-Gómez JP : Sanger Tree of Life Sample Preparation: Triage and Dissection. protocols.io. 2023. 10.17504/protocols.io.x54v9prmqg3e/v1
Kerpedjiev P Abdennur N Lekschas F : HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19 (1 ): 125. 10.1186/s13059-018-1486-1 30143029
Linard B Arribas P Andújar C : Lessons from genome skimming of arthropod‐preserving ethanol. Mol Ecol Resour. 2016;16 (6 ):1365–1377. 10.1111/1755-0998.12539 27235167
Manni M Berkeley MR Seppey M : BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38 (10 ):4647–4654. 10.1093/molbev/msab199 34320186
NBN Atlas Partnership: Dorcus parallelipipedus (Linnaeus, 1758).NBN Atlas,2024; [Accessed 16 February 2024]. Reference Source
Pointon DL Eagles W Sims Y : sanger-tol/treeval v1.0.0 – Ancient Atlantis. 2023. 10.5281/zenodo.10047653
Rao SSP Huntley MH Durand NC : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159 (7 ):1665–1680. 10.1016/j.cell.2014.11.021 25497547
Rhie A McCarthy SA Fedrigo O : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592 (7856 ):737–746. 10.1038/s41586-021-03451-0 33911273
Rhie A Walenz BP Koren S : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21 (1 ): 245. 10.1186/s13059-020-02134-9 32928274
Sheerin E Sampaio F Oatley G : Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.1. protocols.io. 2023. 10.17504/protocols.io.x54v9p2z1g3e/v1
Sikora K Zając K Bieniek A : Phylogeography and distribution modelling reveal the history and future of a saproxylic beetle of European conservation concern. J Biogeogr. 2023;50 (7 ):1299–1314. 10.1111/jbi.14626
Simão FA Waterhouse RM Ioannidis P : BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31 (19 ):3210–3212. 10.1093/bioinformatics/btv351 26059717
Strickland M Cornwell C Howard C : Sanger Tree of Life Fragmented DNA clean up: Manual SPRI. protocols.io. 2023. 10.17504/protocols.io.kxygx3y1dg8j/v1
Surana P Muffato M Qi G : sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0). Zenodo. 2023a. 10.5281/zenodo.7755669
Surana P Muffato M Sadasivan Baby C : sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b. 10.5281/zenodo.6785935
Thomaes A Drumont A Crevecoeur L : Red List of the saproxylic scarab beetles (Coleoptera: Lucanidae, Cetoniidae and Dynastidae) for Flanders. Bulletin de La Société Royale Belge d’Entomologie. 2015;151 (3 ):210–219. Reference Source
Todorovic M Sampaio F Howard C : Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor ®3 for PacBio HiFi. protocols.io. 2023. 10.17504/protocols.io.8epv5x2zjg1b/v1
UK Beetles: Dorcus parallelipipedus (Linnaeus, 1758).UK Beetles,2024; [Accessed 16 February 2024]. Reference Source
Uliano-Silva M Ferreira JGRN Krasheninnikova K : MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics. 2023;24 (1 ): 288. 10.1186/s12859-023-05385-y 37464285
Vasimuddin M Misra S Li H : Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems.In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).IEEE,2019;314–324. 10.1109/IPDPS.2019.00041
Wellcome Sanger Institute: The genome sequence of the lesser stag beetle, Dorcus parallelipipedus (Linnaeus, 1758). European Nucleotide Archive,[dataset], accession number PRJEB59788,2023
Zhou C McCarthy SA Durbin R : YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39 (1 ): btac808. 10.1093/bioinformatics/btac808 36525368
