The genome sequence of the flat clown beetle, Hololepta plana (Sulzer, 1776) (Coleoptera: Histeridae).

The genome sequence of the flat clown beetle, Hololepta plana (Sulzer, 1776) (Coleoptera: Histeridae) - PMC Skip to main content An official website of the United States government Here's how you know Here's how you know Search Log in Primary site navigation Search Log in Search PMC Full-Text Archive Search in PMC Journal List User Guide As a library, NLM provides access to scientific literature. Inclusion in an NLM database does not imply endorsement of, or agreement with, the contents by NLM or the National Institutes of Health. Learn more: PMC Disclaimer | PMC Copyright Notice Wellcome Open Res . 2026 May 18;11:289. [Version 1] doi: 10.12688/wellcomeopenres.26588.1 The genome sequence of the flat clown beetle, Hololepta plana (Sulzer, 1776) (Coleoptera: Histeridae) Michael F Geiser 1 , Jordan J Rainey 2 , Dmitry Telnov 1, 3, 4 , Maxwell V L Barclay 1 ; Natural History Museum 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 Consortium a Author information Article notes Copyright and License information 1 Natural History Museum, London, England, UK 2 Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic 3 Daugavpils University, Daugavpils, Latvia 4 Institute of Biology, University of Latvia, Rīga, Latvia a Email: mark.blaxter@sanger.ac.uk No competing interests were disclosed. Roles Michael F Geiser : Investigation, Resources Jordan J Rainey : Writing – Original Draft Preparation Dmitry Telnov : Writing – Original Draft Preparation Maxwell V L Barclay : Resources, Writing – Review & Editing Accepted 2026 May 1; Collection date 2026. Copyright: © 2026 Geiser MF et al. 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. PMC Copyright notice PMCID: PMC13237540  PMID: 42255359 Abstract We present a genome assembly from an individual female Hololepta plana (flat clown beetle; Arthropoda; Insecta; Coleoptera; Histeridae). The genome sequence has a total length of 139.51 megabases. Most of the assembly (97.93%) is scaffolded into 12 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled, with a length of 17.73 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces genomes for eukaryotic species found in Britain and Ireland. Keywords: Hololepta plana, flat clown beetle, genome sequence, chromosomal, Coleoptera Species taxonomy Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Altocrustacea; Allotriocarida; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Eumetabola; Endopterygota; Aparaglossata; Neuropteroidea; Coleoptera; Polyphaga; Staphyliniformia; Histeroidea; Histeridae; Histerinae; Hololeptini; Hololepta ; Hololepta plana (Sulzer, 1776) (NCBI:txid290657). Background Hololepta plana (Sulzer, 1776) is a member of the family Histeridae, commonly known as the clown beetles. This species is the only representative of the tribe Hololeptini Hope, 1840 in the UK. The combined characters of large adult size (approximately 8.5 mm), a flattened body, and a reduced prosternal projection leaving the ventral surface of the head exposed make H. plana one of the most recognisable of the 54 histerid species in Britain ( Lane, 2017 ). Hololepta plana is widely distributed across Europe and extends into Asia ( Lackner et al. , 2015 ). Sánchez-Ruiz et al. (2002) documented its range extending as far south as southern Spain. The northernmost known record is from Mäntsälä, Finland, reported by iNaturalist user “janijarvi” in 2022, with supporting images. The species is widespread in the boreal forest zone of Europe in the Baltic countries (D. Telnov, personal observations). The species was first recorded in Britain from Norfolk in 2009 ( Allen & Hance, 2009 ). Additional records have been added since then, mostly from south-western England. Lane (2021) summarises the British records and Barclay (2018) expanded on this. It has been recorded in vice-counties including West Norfolk ( Allen & Hance, 2009 ; Collier & Lane, 2015 ; Lane et al. , 2021 ), Middlesex ( Barclay, 2018 ; Lane et al. , 2021 ; Telfer, 2014 ), West Suffolk ( Lane, 2017 ; Lane et al. , 2021 ), Cambridgeshire ( Lane et al. , 2021 ), Buckinghamshire and Surrey ( Lane et al. , 2021 ). Lane’s species status review ( Lane, 2017 ) gives the IUCN status of H. plana as Data Deficient and the GB Rarity Status as Nationally Rare. It seems likely that it is a recent immigrant in Britain, particularly given the complete absence of old records for such a conspicuous species. Adults and larvae of H. plana prey on subcortical dipteran larvae ( Barclay, 2018 ; Trach, 2013 ). Their flattened bodies allow them to live beneath bark ( Kryzhanovsky & Reikhardt, 1976 ). In Britain, H. plana is most often found beneath the sappy, laminating bark of dead poplar trees ( Populus spp.) ( Lane, 2017 ). Barclay (2018) recorded the species from a dead tree of heaven ( Ailanthus altissima ), which also supported a large population of subcortical dipteran larvae. Other recorded hosts include oak and pine ( Quercus sp. and Pinus sylvestris ) and poplars including Populus tremula and P. alba ( Nagaraju et al. , 2022 ). In Latvia, the species has also been recorded beneath the bark of Norway maple ( Acer platanoides ), although it appears to prefer European aspen ( Populus tremula ) and other poplars (D. Telnov, unpublished data). Live specimens of H. plana were recently found from logs imported into India from Belgium ( Nagaraju et al. , 2022 ), suggesting that the species may have arrived in Britain via logs imported from mainland Europe. A chromosome-level genome sequence for H. plana is presented here. The assembly was produced using the Tree of Life pipeline from a specimen collected in Middlesex, England ( Figure 1 ). The genome sequence will support investigations into the origin of the British population of H. plana and uncover likely connections with subpopulations of the species in continental Europe. Figure 1. Photograph of the Hololepta plana (icHolPlan1) specimen used for genome sequencing. Open in a new tab Methods Sample acquisition and DNA barcoding The specimen used for genome sequencing was an adult female Hololepta plana (specimen ID NHMUK014436789, ToLID icHolPlan1; Figure 1 ), collected from Wormwood Scrubs Park, Hammersmith And Fulham, Middlesex, England, United Kingdom (latitude 51.52, longitude −0.25) on 2021-07-17. The specimen was collected and identified by Michael Geiser (Natural History Museum). The initial identification was verified by an additional DNA barcoding process according to the framework developed by Twyford et al. (2024) . A small sample was dissected from the specimen and stored in ethanol, while the remaining parts were shipped on dry ice to the Wellcome Sanger Institute (WSI) (see the protocol ). The tissue was lysed, the COI marker region was amplified by PCR, and amplicons were sequenced and compared to the BOLD database, confirming the species identification ( Crowley et al. , 2023 ). Following whole genome sequence generation, the relevant DNA barcode region was also used alongside the initial barcoding data for sample tracking at the WSI ( Twyford et al. , 2024 ). The standard operating procedures for Darwin Tree of Life barcoding are available on protocols.io . Nucleic acid extraction Detailed protocols for nucleic acid extraction developed at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory are available on protocols.io ( Howard et al. , 2025 ). The icHolPlan1 sample was weighed and triaged to determine the appropriate extraction protocol. Tissue from the head and thorax was homogenised by powermashing using a PowerMasher II tissue disruptor. High molecular weight (HMW) DNA was extracted using the Automated MagAttract v1 protocol. We used centrifuge-mediated fragmentation to produce DNA fragments in the 8–10 kb range, following the Covaris g-TUBE protocol for ultra-low input (ULI). Sheared DNA was purified by automated SPRI (solid-phase reversible immobilisation). The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system. For this sample, the final post-shearing DNA had a Qubit concentration of 0.856 ng/μL and a yield of 333.84 ng. PacBio HiFi library preparation and sequencing Library preparation and sequencing were performed at the WSI Scientific Operations core. Prior to library preparation, the DNA was fragmented to ~10 kb. Ultra-low-input (ULI) libraries were prepared using the PacBio SMRTbell® Express Template Prep Kit 2.0 and gDNA Sample Amplification Kit. Samples were normalised to 20 ng DNA. Single-strand overhang removal, DNA damage repair, and end-repair/A-tailing were performed according to the manufacturer’s instructions, followed by adapter ligation. A 0.85× pre-PCR clean-up was carried out with Promega ProNex beads. The DNA was evenly divided into two aliquots for dual PCR (reactions A and B), both following the manufacturer’s protocol. A 0.85× post-PCR clean-up was performed with ProNex beads. DNA concentration was measured using a Qubit Fluorometer v4.0 (Thermo Fisher Scientific) with the Qubit HS Assay Kit, and fragment size was assessed on an Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies) using the gDNA 55 kb BAC analysis kit. PCR reactions A and B were then pooled, ensuring a total mass of ≥500 ng in 47.4 μl. The pooled sample underwent another round of DNA damage repair, end-repair/A-tailing, and hairpin adapter ligation. A 1× clean-up was performed with ProNex beads, followed by DNA quantification using the Qubit and fragment size analysis using the Agilent Femto Pulse. Size selection was performed on the Sage Sciences PippinHT system, with target fragment size determined by Femto Pulse analysis (typically 4–9 kb). Size-selected libraries were cleaned with 1.0× ProNex beads and normalised to 2 nM before sequencing. The sample was sequenced using the Sequel IIe system (Pacific Biosciences, California, USA). The concentration of the library loaded onto the Sequel IIe was in the range 40–135 pM. The SMRT link software, a PacBio web-based end-to-end workflow manager, was used to set-up and monitor the run, and to perform primary and secondary analysis of the data upon completion. Hi-C Sample preparation and crosslinking The Hi-C sample was prepared from 20–50 mg of frozen abdomen tissue of the icHolPlan1 sample using the Arima-HiC v2 kit (Arima Genomics). Following the manufacturer’s instructions, tissue was fixed and DNA crosslinked using TC buffer to a final formaldehyde concentration of 2%. The tissue was homogenised using the Diagnocine Power Masher-II. Crosslinked DNA was digested with a restriction enzyme master mix, biotinylated, and ligated. Clean-up was performed with SPRISelect beads before library preparation. DNA concentration was measured with the Qubit Fluorometer (Thermo Fisher Scientific) and Qubit HS Assay Kit. The biotinylation percentage was estimated using the Arima-HiC v2 QC beads. Hi-C library preparation and sequencing Biotinylated DNA constructs were fragmented using a Covaris E220 sonicator and size selected to 400–600 bp using SPRISelect beads. DNA was enriched with Arima-HiC v2 kit Enrichment beads. End repair, A-tailing, and adapter ligation were carried out with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs), following a modified protocol where library preparation occurs while DNA remains bound to the Enrichment beads. Library amplification was performed using KAPA HiFi HotStart mix and a custom Unique Dual Index (UDI) barcode set (Integrated DNA Technologies). Depending on sample concentration and biotinylation percentage determined at the crosslinking stage, libraries were amplified with 10–16 PCR cycles. Post-PCR clean-up was performed with SPRISelect beads. Libraries were quantified using the AccuClear Ultra High Sensitivity dsDNA Standards Assay Kit (Biotium) and a FLUOstar Omega plate reader (BMG Labtech). Prior to sequencing, libraries were normalised to 10 ng/μL. Normalised libraries were quantified again to create equimolar and/or weighted 2.8 nM pools. Pool concentrations were checked using the Agilent 4200 TapeStation (Agilent) with High Sensitivity D500 reagents before sequencing. Sequencing was performed using paired-end 150 bp reads on the Illumina NovaSeq 6000. Genome assembly Prior to assembly of the PacBio HiFi reads, a database of k -mer counts ( k = 31) was generated from the filtered reads using FastK . GenomeScope2 ( Ranallo-Benavidez et al. , 2020 ) was used to analyse the k -mer frequency distributions, providing estimates of genome size, heterozygosity, and repeat content. The HiFi reads were assembled using Hifiasm ( Cheng et al. , 2021 ) with the --primary option. Haplotypic duplications were identified and removed using purge_dups ( Guan et al. , 2020 ). The Hi-C reads ( Rao et al. , 2014 ) were mapped to the primary contigs using bwa-mem2 ( Vasimuddin et al. , 2019 ), and the contigs were scaffolded in YaHS ( Zhou et al. , 2023 ) with the --break option for handling potential misassemblies. The scaffolded assemblies were evaluated using Gfastats ( Formenti et al. , 2022 ), BUSCO ( Manni et al. , 2021 ) and MerquryFK ( Rhie et al. , 2020 ). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al. , 2023 ). Assembly curation The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants ( ASCC ) pipeline. TreeVal was used to generate the flat files and maps for use in curation. Manual curation was conducted primarily in PretextView and HiGlass ( Kerpedjiev et al. , 2018 ). Scaffolds were visually inspected and corrected as described by Howe et al . (2021) . Manual corrections included ten breaks, 35 joins, and removal of three haplotypic duplications. This reduced the scaffold count by 94.0%, increased the scaffold N50 by 41.5%, and reduced the total assembly length by 9.6%. The curation process is described at https://gitlab.com/wtsi-grit/rapid-curation . PretextSnapshot was used to generate a Hi-C contact map of the final assembly. Assembly quality assessment The MerquryFK tool ( Rhie et al. , 2020 ) was run in a Singularity container ( Kurtzer et al. , 2017 ) to evaluate k -mer completeness and assembly quality for the primary and alternate haplotypes using the k -mer database ( k = 31) computed prior to genome assembly. The analysis outputs included assembly QV scores and completeness statistics. The genome was analysed using the BlobToolKit pipeline , a Nextflow implementation of the earlier Snakemake version ( Challis et al. , 2020 ). The pipeline aligns PacBio reads using minimap2 ( Li, 2018 ) and SAMtools ( Danecek et al. , 2021 ) to generate coverage tracks. It runs BUSCO ( Manni et al. , 2021 ) using lineages identified from the NCBI Taxonomy ( Schoch et al. , 2020 ). For the three domain-level lineages, BUSCO genes are aligned to the UniProt Reference Proteomes database ( Bateman et al. , 2023 ) using DIAMOND blastp ( Buchfink et al. , 2021 ). The genome is divided into chunks based on the density of BUSCO genes from the closest taxonomic lineage, and each chunk is aligned to the UniProt Reference Proteomes database with DIAMOND blastx. Sequences without hits are chunked using seqtk and aligned to the NT database with blastn ( Altschul et al. , 1990 ). The BlobToolKit suite consolidates all outputs into a blobdir for visualisation. The BlobToolKit pipeline was developed using nf-core tooling ( Ewels et al. , 2020 ) and MultiQC ( Ewels et al. , 2016 ), with containerisation through Docker ( Merkel, 2014 ) and Singularity ( Kurtzer et al. , 2017 ). Genome sequence report Sequence data PacBio sequencing of the Hololepta plana specimen generated 24.50 Gb (gigabases) from 2.46 million reads, which were used to assemble the genome. GenomeScope2.0 analysis estimated the haploid genome size at 143.25 Mb, with a heterozygosity of 0.29% and repeat content of 21.12% ( Figure 2 ). These estimates guided expectations for the assembly. Based on the estimated genome size, the sequencing data provided approximately 152× coverage. Hi-C sequencing produced 98.20 Gb from 325.17 million reads, which were used to scaffold the assembly. Table 1 summarises the specimen and sequencing details. Figure 2. Frequency distribution of k -mers generated using GenomeScope2. Open in a new tab The plot shows observed and modelled k -mer spectra, providing estimates of genome size, heterozygosity, and repeat content based on unassembled sequencing reads. Table 1. Specimen and sequencing data for hololepta plana (BioProject PRJEB64074). Platform PacBio HiFi Hi-C ToLID icHolPlan1 icHolPlan1 Specimen ID NHMUK014436789 NHMUK014436789 BioSample (source individual) SAMEA111458819 SAMEA111458819 BioSample (tissue) SAMEA111458840 SAMEA111458851 Tissue head and thorax abdomen Instrument Sequel IIe Illumina NovaSeq 6000 Run accessions ERR11673234 ERR11679387 Read count total 2.46 million 325.17 million Base count total 24.50 Gb 98.20 Gb Open in a new tab Assembly statistics The primary haplotype was assembled, and contigs corresponding to an alternate haplotype were also deposited in INSDC databases. The final assembly has a total length of 139.51 Mb in 45 scaffolds, with 100 gaps, and a scaffold N50 of 14.29 Mb ( Table 2 ). Table 2. Genome assembly data for hololepta plana. Genome assembly Primary assembly Assembly name icHolPlan1.2 Assembly accession GCA_963695495.2 Alternate haplotype accession GCA_963700325.2 Assembly level chromosome Span (Mb) 139.51 Number of chromosomes 12 Number of contigs 145 Contig N50 2.2 Mb Number of scaffolds 45 Scaffold N50 14.29 Mb Sex chromosomes X Organelles Mitochondrion: 17.73 kb Open in a new tab Most of the assembly sequence (97.93%) was assigned to 12 chromosomal-level scaffolds, representing 11 autosomes and the X sex chromosome. These chromosome-level scaffolds, confirmed by Hi-C data, are named according to size ( Figure 3 ; Table 3 ). X chromosome identified based on synteny with the genome of Leptodirus hochenwartii (GCA_947310635.1) ( Delić et al. , 2025 ). Figure 3. Hi-C contact map of the Hololepta plana genome assembly. Open in a new tab Assembled chromosomes are shown in order of size and labelled along the axes, with a megabase scale shown below. The plot was generated using PretextSnapshot. Table 3. Chromosomal pseudomolecules in the primary genome assembly of Hololepta plana icHolPlan1. INSDC accession Molecule Length (Mb) GC% OY968831.1 1 17.62 34.50 OY968832.1 2 16.83 35.50 OY968833.1 3 15.23 36 OY968834.1 4 14.46 35.50 OY968836.2 5 11.85 38 OY968837.1 6 11.63 36 OY968838.1 7 10.37 38 OY968839.1 8 6.98 39.50 OY968840.1 9 6.04 41 OY968841.1 10 5.74 41.50 OY968842.1 11 5.58 41.50 OY968835.1 X 14.29 35.50 Open in a new tab The mitochondrial genome was also assembled (length 17.73 kb, OY968843.1 ). This sequence is included as a contig in the multifasta file of the genome submission and as a standalone record. Assembly quality metrics The combined primary and alternate assemblies achieve an estimated QV of 55.1. The k -mer completeness is 93.62% for the primary assembly, 64.96% for the alternate haplotype, and 99.13% for the combined assemblies ( Figure 4 ). Figure 4. Evaluation of k -mer completeness using MerquryFK. Open in a new tab This plot illustrates the recovery of k -mers from the original read data in the final assemblies. The horizontal axis represents k -mer multiplicity, and the vertical axis shows the number of k -mers. The black curve represents k -mers that appear in the reads but are not assembled. The green curve corresponds to k -mers shared by both haplotypes, and the red and blue curves show k -mers found only in one of the haplotypes. BUSCO v.6.0.0 analysis using the endopterygota_odb10 reference set ( n = 2 124) identified 98.7% of the expected gene set (single = 97.9%, duplicated = 0.8%). The snail plot in Figure 5 summarises the scaffold length distribution and other assembly statistics for the primary assembly. The blob plot in Figure 6 shows the distribution of scaffolds by GC proportion and coverage. Figure 5. Assembly metrics for icHolPlan1.2. Open in a new tab The BlobToolKit snail plot provides an overview of assembly metrics and BUSCO gene completeness. The circumference represents the length of the whole genome sequence, and the main plot is divided into 1 000 bins around the circumference. The outermost blue tracks display the distribution of GC, AT, and N percentages across the bins. Scaffolds are arranged clockwise from longest to shortest and are depicted in dark grey. The longest scaffold is indicated by the red arc, and the deeper orange and pale orange arcs represent the N50 and N90 lengths. A light grey spiral at the centre shows the cumulative scaffold count on a logarithmic scale. A summary of complete, fragmented, duplicated, and missing BUSCO genes in the endopterygota_odb10 set is presented at the top right. An interactive version of this figure can be accessed on the BlobToolKit viewer . Figure 6. BlobToolKit blob plot for icHolPlan1.2. Open in a new tab The plot shows base coverage (vertical axis) and GC content (horizontal axis). The circles represent scaffolds, with the size proportional to scaffold length and the colour representing phylum membership. The histograms along the axes display the total length of sequences distributed across different levels of coverage and GC content. An interactive version of this figure is available on the BlobToolKit viewer . Table 4 lists the assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project Report on Assembly Standards January 2026 . The EBP metric, calculated for the primary assembly, is 6.C.Q54 , meeting the recommended reference standard. Table 4. Earth Biogenome Project summary metrics for the Hololepta plana assembly. Measure Value Benchmark EBP summary (primary) 6.C.Q54 6.C.Q40 Contig N50 length 2.20 Mb ≥ 1 Mb Scaffold N50 length 14.29 Mb = chromosome N50 Consensus quality (QV) Primary: 54.1; alternate: 55.9; combined: 55.1 ≥ 40 k -mer completeness Primary: 93.62%; alternate: 64.96%; combined: 99.13% ≥ 95% BUSCO C:98.7% [S:97.9%, D:0.8%], F:0.2%, M:1.1%, n:2 124 S > 90%; D < 5% Percentage of assembly assigned to chromosomes 97.93% ≥ 90% Open in a new tab Notes: The EBP summary uses log10(Contig N50); chromosome-level (C) or log10(Scaffold N50); Q (Merqury QV). BUSCO: C = complete; S = single-copy; D = duplicated; F = fragmented; M = missing; n = orthologues Funding Statement This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (220540) 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. [version 1; peer review: 2 approved] Data availability European Nucleotide Archive: Hololepta plana. Accession number PRJEB64074 . The genome sequence is released openly for reuse. The Hololepta plana genome sequencing initiative is part of the Darwin Tree of Life Project (PRJEB40665) and the Sanger Institute Tree of Life Programme (PRJEB43745). 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 Tables 1 and 2 . Production code used in genome assembly at the WSI Tree of Life is available at https://github.com/sanger-tol . Table 5 lists software versions used in this study. Table 5. Software versions and sources used for Hololepta plana. Software Version Source BLAST 2.14.0 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ BlobToolKit 4.4.6 https://github.com/blobtoolkit/blobtoolkit BUSCO 6.0.0 https://gitlab.com/ezlab/busco bwa-mem2 2.2.1 https://github.com/bwa-mem2/bwa-mem2 DIAMOND 2.1.8 https://github.com/bbuchfink/diamond fasta_windows 0.2.4 https://github.com/tolkit/fasta_windows FastK 1.1 https://github.com/thegenemyers/FASTK GenomeScope2.0 2.0.1 https://github.com/tbenavi1/genomescope2.0 Gfastats 1.3.6 https://github.com/vgl-hub/gfastats Hifiasm 0.19.5-r587 https://github.com/chhylp123/hifiasm HiGlass 1.13.4 https://github.com/higlass/higlass MerquryFK 1.1.2 https://github.com/thegenemyers/MERQURY.FK Minimap2 2.28-r1209 https://github.com/lh3/minimap2 MitoHiFi 3 https://github.com/marcelauliano/MitoHiFi MultiQC 1.14; 1.17 and 1.18 https://github.com/MultiQC/MultiQC Nextflow 24.10.4 https://github.com/nextflow-io/nextflow PretextSnapshot 0.0.5 https://github.com/sanger-tol/PretextSnapshot PretextView 1.0.3 https://github.com/sanger-tol/PretextView purge_dups 1.2.5 https://github.com/dfguan/purge_dups samtools 1.21 https://github.com/samtools/samtools sanger-tol/ascc 0.1.0 https://github.com/sanger-tol/ascc sanger-tol/blobtoolkit v0.9.0 https://github.com/sanger-tol/blobtoolkit sanger-tol/curationpretext 1.4.2 https://github.com/sanger-tol/curationpretext Seqtk 1.3 https://github.com/lh3/seqtk Singularity 3.9.0 https://github.com/sylabs/singularity TreeVal 1.4.0 https://github.com/sanger-tol/treeval YaHS 1.2a.2 https://github.com/c-zhou/yahs Open in a new tab Author information Contributors are listed at the following links: • Members of the Natural History Museum Genome Acquisition Lab • Members of the Darwin Tree of Life Barcoding collective • Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team • Members of Wellcome Sanger Institute Scientific Operations – Sequencing Operations • Members of the Wellcome Sanger Institute Tree of Life Core Informatics team • Members of the Tree of Life Core Informatics collective • Members of the Darwin Tree of Life Consortium 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 . 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. References Allen AJ, Hance D: Hololepta plana (Sulzer, 1776) (Histeridae) in Norfolk – new to Britain. Coleopterist. 2009;18:153–154. [ Google Scholar ] Altschul SF, Gish W, Miller W, et al. : Basic Local Alignment Search Tool. J. Mol. Biol. 1990;215(3):403–410. 10.1016/S0022-2836(05)80360-2 [ DOI ] [ PubMed ] [ Google Scholar ] Barclay MVL: Hololepta plana (Sulzer) (Histeridae) from Margravine Cemetery, West London. Coleopterist. 2018;27:27–28. [ Google Scholar ] Bateman A, Martin M-J, Orchard S, et al. : UniProt: The Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2023;51(D1):D523–D531. 10.1093/nar/gkac1052 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Buchfink B, Reuter K, Drost H-G: Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods. 2021;18(4):366–368. 10.1038/s41592-021-01101-x [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Challis R, Richards E, Rajan J, et al. : BlobToolKit – interactive quality assessment of genome assemblies. G3: Genes, Genomes, Genetics. 2020;10(4):1361–1374. 10.1534/g3.119.400908 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Cheng H, Concepcion GT, Feng X, et al. : Haplotype-resolved de novo assembly using phased assembly graphs with Hifiasm. Nat. Methods. 2021;18(2):170–175. 10.1038/s41592-020-01056-5 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Collier MJ, Lane S: Recent Norfolk beetle records, including twelve additions to the county list. Coleopterist. 2015;24:46–52. [ Google Scholar ] Crowley L, Allen H, Barnes I, et al. : A sampling strategy for genome sequencing the British terrestrial Arthropod fauna. Wellcome Open Res. 2023;8:123. 10.12688/wellcomeopenres.18925.1 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Danecek P, Bonfield JK, Liddle J, et al. : Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2):giab008. 10.1093/gigascience/giab008 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Delić T, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team. Wellcome Sanger Institute Scientific Operations: Sequencing Operations et al. : The genome sequence of a cave beetle, Leptodirus hochenwartii F.J.Schmidt, 1832. Wellcome Open Res. 2025;10:159. 10.12688/wellcomeopenres.23959.1 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Ewels P, Magnusson M, Lundin S, et al. : MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048. 10.1093/bioinformatics/btw354 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Ewels PA, Peltzer A, Fillinger S, et al. : The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 2020;38(3):276–278. 10.1038/s41587-020-0439-x [ DOI ] [ PubMed ] [ Google Scholar ] Formenti G, Abueg L, Brajuka A, et al. : Gfastats: Conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics. 2022;38(17):4214–4216. 10.1093/bioinformatics/btac460 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Guan D, McCarthy SA, Wood J, et al. : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896–2898. 10.1093/bioinformatics/btaa025 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Howard C, Denton A, Jackson B, et al. : On the path to reference genomes for all biodiversity: Lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species. bioRxiv. 2025. 10.1101/2025.04.11.648334 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Howe K, Chow W, Collins J, et al. : Significantly improving the quality of genome assemblies through curation. GigaScience. 2021;10(1):giaa153. 10.1093/gigascience/giaa153 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Kerpedjiev P, Abdennur N, Lekschas F, et al. : HiGlass: Web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19(1):125. 10.1186/s13059-018-1486-1 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Kryzhanovsky OL, Reikhardt AN: Beetles of the Superfamily Histeroidea (Families Sphaeritidae, Histeridae, Synteliidae). Leningrad: Nauka Press;1976. [ Google Scholar ] Kurtzer GM, Sochat V, Bauer MW: Singularity: Scientific containers for mobility of compute. PLOS One. 2017;12(5):e0177459. 10.1371/journal.pone.0177459 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Lackner T, Mazur S, Newton AF: Family Histeridae Gyllenhal, 1808. Löbl I, Löbl D, editors. Catalogue of Palaearctic Coleoptera 2. Hydrophiloidea Staphylinoidea (Revised and Updated). Stenstrup: Apollo Books;2015;76–130. [ Google Scholar ] Lane SA:

A Review of the Status of the Beetles of Great Britain – the Clown Beetles and False Clown Beetles – Histeridae and Sphaeritidae.

2017. Lane SA, Lucas CBH, Whiffin AL: The Histeridae, Sphaeritidae and Silphidae of Britain and Ireland. Field Studies Council;2021. [ Google Scholar ] Li H: Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–3100. 10.1093/bioinformatics/bty191 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Manni M, Berkeley MR, Seppey M, et al. : 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 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Merkel D: Docker: Lightweight Linux containers for consistent development and deployment. Linux J. 2014;2014(239):2. 10.5555/2600239.2600241 [ DOI ] [ Google Scholar ] Nagaraju DK, Kasturi N, Singh M, et al. : Interception of Hololepta plana (Sulzer) (Coleoptera, Histeridae) a rare beetle on poplar logs imported from Belgium. Insect Environ. 2022;25:18–20. [ Google Scholar ] Ranallo-Benavidez TR, Jaron KS, Schatz MC: GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. 2020;11(1):1432. 10.1038/s41467-020-14998-3 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Rao SSP, Huntley MH, Durand NC, et al. : 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 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Rhie A, McCarthy SA, Fedrigo O, et al. : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592(7856):737–746. 10.1038/s41586-021-03451-0 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Rhie A, Walenz BP, Koren S, et al. : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21(1):245. 10.1186/s13059-020-02134-9 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Sánchez-Ruiz A, Utrilla JA, Sánchez-Ruiz M, et al. : Ampliación de la distribución conocida de Hololepta (s. Str.) plana (Sulzer, 1776) en la península Ibérica (Coleoptera: Histeridae). Boletín de La SEA. 2002;31:202. [ Google Scholar ] Schoch CL, Ciufo S, Domrachev M, et al. : NCBI taxonomy: A comprehensive update on curation, resources and tools. Database. 2020;2020:baaa062. 10.1093/database/baaa062 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Telfer M: Tales of the unexpected. 2014. Reference Source Trach VA: On the morphology, biology, and distribution of Lobogynioides andreinii (Acari, Mesostigmata, Diplogyniidae). Entomol. Rev. 2013;93:105–112. 10.1134/S0013873813010144 [ DOI ] [ Google Scholar ] Twyford AD, Beasley J, Barnes I, et al. : A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project. Wellcome Open Res. 2024;9:339. 10.12688/wellcomeopenres.21143.1 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Uliano-Silva M, Ferreira JGRN, Krasheninnikova K, et al. : 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 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Vasimuddin M, Misra S, Li H, et al. : Efficient architecture-aware acceleration of BWA-MEM for multicore systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE,2019;314–24. 10.1109/IPDPS.2019.00041 [ DOI ] [ Google Scholar ] Zhou C, McCarthy SA, Durbin R: YaHS: Yet another Hi-C scaffolding tool. Bioinformatics. 2023;39(1):btac808. 10.1093/bioinformatics/btac808 [ DOI ] [ PMC free article ] [ PubMed ] [ Google Scholar ] Wellcome Open Res. 2026 Jun 4. doi: 10.21956/wellcomeopenres.29281.r156252 Reviewer response for version 1 Henrik Lantz 1 Author information Copyright and License information 1 SciLifeLab, Uppsala University, Uppsala, Sweden Competing interests: No competing interests were disclosed. Roles Henrik Lantz : Referee Copyright: © 2026 Lantz H 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. PMC Copyright notice This manuscript presents the genome sequence of the flat clown beetle, Hololepta plana, assembled as a part of the Darwin Tree of Life project. The species is rare in Britain, and was only first collected there in 2009, making experts think the species most likely is a recent immigrant. The species is large compared to closely related species and has specific morphological features which makes it a distinct species in the family Histeridae. The assembled genome is of high quality and can be used to determine the origin of the British population and how it is related to other populations in continental Europe. 97.93% of the assembly (a high number) is scaffolded into 12 chromosomal pseudomolecules, including the sex determination X chromosome. BUSCO score is also very high (98.7%) and the assembly easily meets all of the Earth Biogenome Project criteria except possibly the scaffold N50 value as not 100% of the scaffolds are assigned to chromosomes, but that difference is negligible. Methods follow a high international standard and are in general well-described, except for some few cases commented below. 1. Figure 1, and text: The specimen used has been documented by a picture which is good, and the text explains how tissues were dissected and used for DNA extraction and barcoding, but there is no information if any material has been saved in a museum and/or biobank. The morphology of the species seems distinctive enough that it should be possible to determine the identity of the specimen from the photo, but I would prefer that a high quality photo is preserved in a Natural History Museum and also any remaining tissue, if available. 2. Figure 3. The HiC contact map shows some remaining contacts between different scaffolds, e.g., between OY968836.2 and OY968837.1 . This is most likely caused by repeats and not really something that needs to be corrected, but it would be good to have the results of the curation discussed more in detail in the text. 3. The BlobToolKit plot in Figure 6 shows some small blobs outside of the main cluster with no hits in the database, hinting at remaining contamination. While this is unlikely to cause any big problems in downstream analyses, I would prefer if the results of the de-contamination would be discussed in the text. 4. Simply stating that the mitochondrion was assembled using MitoHiFi is not enough to ensure reproducibility. Settings should be mentioned, or even better, scripts should be supplied in a GitHub repo. Are sufficient details of methods and materials provided to allow replication by others? Partly 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: Genome assembly, genome annotation, phylogenetics, taxonomy, systematics. 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. Wellcome Open Res. 2026 Jun 3. doi: 10.21956/wellcomeopenres.29281.r156249 Reviewer response for version 1 Rajib Deb 1 Author information Copyright and License information 1 ICAR-National Research Centre, Guwahat, Assam, India Competing interests: No competing interests were disclosed. Roles Rajib Deb : Referee Copyright: © 2026 Deb R 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. PMC Copyright notice The rationale for generating the genome dataset is clearly explained and biologically justified. The sequencing, assembly, and curation protocols are appropriate and technically sound, using current standard methodologies and software tools. Methods and materials are described in sufficient detail to enable reproducibility, including software versions, sequencing platforms, and accession numbers The genome assembly is of high quality, with strong BUSCO completeness and chromosome-level scaffolding statistics. The datasets are clearly presented and openly accessible through public repositories, making them usable for future research. However, following issues may be resolved: The manuscript could briefly clarify whether any residual unplaced scaffolds contain repetitive or low-complexity regions. A short statement on expected future genome annotation outcomes or comparative genomic applications would further enhance the utility of the note. Figure legends are generally clear, but adding a brief interpretation of the Hi-C contact map quality in the text would improve accessibility for non-specialist readers. Minor typographical and formatting consistency checks (e.g., spacing around percentages and symbols) may improve readability. 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. Associated Data This section collects any data citations, data availability statements, or supplementary materials included in this article. Data Availability Statement European Nucleotide Archive: Hololepta plana. Accession number PRJEB64074 . The genome sequence is released openly for reuse. The Hololepta plana genome sequencing initiative is part of the Darwin Tree of Life Project (PRJEB40665) and the Sanger Institute Tree of Life Programme (PRJEB43745). 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 Tables 1 and 2 . Production code used in genome assembly at the WSI Tree of Life is available at https://github.com/sanger-tol . Table 5 lists software versions used in this study. Table 5. Software versions and sources used for Hololepta plana. Software Version Source BLAST 2.14.0 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ BlobToolKit 4.4.6 https://github.com/blobtoolkit/blobtoolkit BUSCO 6.0.0 https://gitlab.com/ezlab/busco bwa-mem2 2.2.1 https://github.com/bwa-mem2/bwa-mem2 DIAMOND 2.1.8 https://github.com/bbuchfink/diamond fasta_windows 0.2.4 https://github.com/tolkit/fasta_windows FastK 1.1 https://github.com/thegenemyers/FASTK GenomeScope2.0 2.0.1 https://github.com/tbenavi1/genomescope2.0 Gfastats 1.3.6 https://github.com/vgl-hub/gfastats Hifiasm 0.19.5-r587 https://github.com/chhylp123/hifiasm HiGlass 1.13.4 https://github.com/higlass/higlass MerquryFK 1.1.2 https://github.com/thegenemyers/MERQURY.FK Minimap2 2.28-r1209 https://github.com/lh3/minimap2 MitoHiFi 3 https://github.com/marcelauliano/MitoHiFi MultiQC 1.14; 1.17 and 1.18 https://github.com/MultiQC/MultiQC Nextflow 24.10.4 https://github.com/nextflow-io/nextflow PretextSnapshot 0.0.5 https://github.com/sanger-tol/PretextSnapshot PretextView 1.0.3 https://github.com/sanger-tol/PretextView purge_dups 1.2.5 https://github.com/dfguan/purge_dups samtools 1.21 https://github.com/samtools/samtools sanger-tol/ascc 0.1.0 https://github.com/sanger-tol/ascc sanger-tol/blobtoolkit v0.9.0 https://github.com/sanger-tol/blobtoolkit sanger-tol/curationpretext 1.4.2 https://github.com/sanger-tol/curationpretext Seqtk 1.3 https://github.com/lh3/seqtk Singularity 3.9.0 https://github.com/sylabs/singularity TreeVal 1.4.0 https://github.com/sanger-tol/treeval YaHS 1.2a.2 https://github.com/c-zhou/yahs Open in a new tab Articles from Wellcome Open Research are provided here courtesy of The Wellcome Trust ACTIONS View on publisher site PDF (2.8 MB) Cite Collections Permalink RESOURCES Similar articles Cited by other articles Links to NCBI Databases Follow NCBI NCBI on X (formerly known as Twitter) NCBI on Facebook NCBI on LinkedIn NCBI on GitHub NCBI RSS feed Connect with NLM NLM on X (formerly known as Twitter) NLM on Facebook NLM on YouTube National Library of Medicine 8600 Rockville Pike Bethesda, MD 20894 Web Policies FOIA HHS Vulnerability Disclosure Help Accessibility Careers NLM NIH HHS USA.gov Back to Top

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