Abstract
We present a genome assembly from an individual male specimen of Rhagonycha lutea (soldier beetle; Arthropoda; Insecta; Coleoptera; Cantharidae). The genome sequence has a total length of 479.80 megabases. Most of the assembly (90.1%) is scaffolded into 7 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 20.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 24,745 protein-coding genes.
Keywords: Rhagonycha lutea, soldier beetle, genome sequence, chromosomal, Coleoptera
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Elateriformia; Elateroidea; Cantharidae; Cantharinae; Rhagonycha; Rhagonycha lutea (Müller, 1764) (NCBI:txid1553715)
Background
Rhagonycha lutea (O.F. Müller, 1764) is a member of the Cantharidae, commonly known as “soldier beetles”. Genome notes for seven members of the same family have already been published, including one on another member of the same genus ( Crowley et al., 2021). The genus Rhagonycha Eschscholtz, 1830 is one of four British genera of the subfamily Cantharinae, along with Cantharis Linnaeus, 1758, Podabrus Westwood, 1838 and Ancistronycha Märkel, 1852 ( Duff, 2018). The genus Rhagonycha is distributed primarily across the Palaearctic and Nearctic regions, with a few species reaching into tropical South-East Asia ( Delkeskamp, 1977). Overall, well over 300 species have been described ( Kazantsev, 2023; Kazantsev & Brancucci, 2007; Ramsdale, 2002; Xiao et al., 2023). Seven species of Rhagonycha occur on the British Isles ( Duff, 2018).
British members of Cantharidae can be identified using the key by Duff and Schmidt (2020), and for members of the subfamily Cantharinae there is an easy-to-use picture guide by Gurney (2019). Within the British fauna, Rhagonycha is distinguished from all related genera by having both claws on each tarsus deeply split. Within the genus, R. lutea resembles R. fulva (Scopoli, 1763) in colour, by having a red pronotum and pale brown elytra, usually with a black tip (the amount of black is variable), but is easily distinguished by the entirely black head. Adults of R. lutea range from 6 to 9 mm in length, about the same size as R. fulva ( Duff & Schmidt, 2020).
R. lutea is a widely distributed species found across most of Europe, reaching Ireland in the north-west, northern Spain in the south-west, the Tatarstan republic of Russia in the East, and the European part of Turkey in the south-east ( Kazantsev, 2011; Kazantsev & Brancucci, 2007). Within the UK, it is recorded from much of England except the West and Cumbria, and from a few localities in Wales. Alexander (2003) lists no records from Scotland, Northern Ireland or the Isle of Man. There are, however, two recent Scottish records shown on the online NBN map, suggesting that the species has recently expanded its range northwards ( NBN Atlas Partnership, 2024). Due to its apparent rarity and the lack of recent records from many known sites, Alexander (2014) has assigned it “Nationally Scarce” status within the UK fauna.
R. lutea inhabits woodlands, hedgerows and forest edges, with adults typically found by beating foliage ( Alexander, 2003). In Germany, it is said to prefer montane altitudes ( Bretzendorfer, 2017). As usual for Cantharidae, it is a univoltine species. Adults are active from early June to mid-July, overlapping with other members of the genus. Karyotypes of R. lutea were studied and illustrated by James and Angus (2007).
In general, the biology and ecology of Cantharidae larvae is still poorly understood. Usually, they are predatory and found in leaf litter, often during winter ( Fitton, 1976). There is a key to the genera of British Cantharidae by Fitton (1976), which did not list R. lutea among the examined species. Later, Klausnitzer (1997) provided a key to the larvae of six European Rhagonycha species, which includes R. lutea and the other British species except R. elongata (Fallén, 1807) and R. translucida (Krynicki, 1832).
We present a chromosome-level genome sequence for Rhagonycha lutea, based on a male specimen from Great Bookham Common, England, United Kingdom ( Figure 1). It 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.
Figure 1. Photographs of the Rhagonycha lutea (icRhaLute1) specimen used for genome sequencing.
Genome sequence report
The genome of Rhagonycha lutea ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating a total of 21.58 Gb (gigabases) from 1.89 million reads, providing an estimated 46-fold coverage. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data, which produced 121.76 Gb from 806.36 million reads. Specimen and sequencing details are summarised in Table 1.
Table 1. Specimen and sequencing data for Rhagonycha lutea.
| Project information | |||
|---|---|---|---|
| Study title | Rhagonycha lutea | ||
| Umbrella BioProject | PRJEB59296 | ||
| Species | Rhagonycha lutea | ||
| BioSample | SAMEA14448414 | ||
| NCBI taxonomy ID | 1553715 | ||
| Specimen information | |||
| Technology | ToLID | BioSample accession | Organism part |
| PacBio long read sequencing | icRhaLute1 | SAMEA14448798 | thorax |
| Hi-C sequencing | icRhaLute1 | SAMEA14448799 | abdomen |
| Sequencing information | |||
| Platform | Run accession | Read count | Base count (Gb) |
| Hi-C Illumina NovaSeq 6000 | ERR10818320 | 8.06e+08 | 121.76 |
| PacBio Sequel IIe | ERR10812860 | 1.89e+06 | 21.58 |
Assembly errors were corrected by manual curation, including 15 missing joins or mis-joins and two haplotypic duplications. This reduced the scaffold number by 6.84% and increased the scaffold N50 by 68.3%. The final assembly has a total length of 479.80 Mb in 108 sequence scaffolds, with 88 gaps, and a scaffold N50 of 71.0 Mb ( Table 2).
Table 2. Genome assembly data for Rhagonycha lutea, icRhaLute1.1.
| Genome assembly | ||
|---|---|---|
| Assembly name | icRhaLute1.1 | |
| Assembly accession | GCA_958510855.1 | |
| Accession of alternate haplotype | GCA_958510815.1 | |
| Span (Mb) | 479.80 | |
| Number of contigs | 197 | |
| Number of scaffolds | 108 | |
| Longest scaffold (Mb) | 106.35 | |
| Assembly metrics * | Benchmark | |
| Contig N50 length (Mb) | 7.5 | ≥ 1 Mb |
| Scaffold N50 length (Mb) | 71.0 | = chromosome N50 |
| Consensus quality (QV) | 67.0 | ≥ 40 |
| k-mer completeness | primary: 91.69%; alternate:
78.41%; combined: 98.86% |
≥ 95% |
| BUSCO ** | C:98.7%[S:94.9%,D:3.8%],
F:0.6%,M:0.7%,n:2,124 |
S > 90%, D < 5% |
| Percentage of assembly
mapped to chromosomes |
90.1% | ≥ 90% |
| Sex chromosomes | XO | localised homologous pairs |
| Organelles | Mitochondrial genome: 20.08 kb | complete single alleles |
| Genome annotation of assembly GCA_958510855.1 at Ensembl | ||
| Number of protein-coding
genes |
24,745 | |
| Number of gene transcripts | 25,147 | |
* Assembly metric benchmarks are adapted from Rhie et al. (2021) and the Earth BioGenome Project Report on Assembly Standards September 2024.
** 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/icRhaLute1_1/dataset/icRhaLute1_1/busco.
The snail plot in Figure 2 provides a summary of the assembly statistics, indicating the distribution of scaffold lengths and other assembly metrics. Figure 3 shows the distribution of scaffolds by GC proportion and coverage. Figure 4 presents a cumulative assembly plot, with separate curves representing different scaffold subsets assigned to various phyla, illustrating the completeness of the assembly.
Figure 2. Genome assembly of Rhagonycha lutea, icRhaLute1.1: metrics.
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 equal-sized 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 is available at https://blobtoolkit.genomehubs.org/view/icRhaLute1_1/dataset/icRhaLute1_1/snail.
Figure 3. Genome assembly of Rhagonycha lutea, icRhaLute1.1: BlobToolKit GC-coverage plot.
BlobToolKit GC-coverage plot showing sequence 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 at https://blobtoolkit.genomehubs.org/view/icRhaLute1_1/dataset/icRhaLute1_1/blob.
Figure 4. Genome assembly of Rhagonycha lutea icRhaLute1.1: 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/icRhaLute1_1/dataset/icRhaLute1_1/cumulative.
Most of the assembly sequence (90.1%) was assigned to 7 chromosomal-level scaffolds, representing 6 autosomes and the X sex chromosome. These chromosome-level scaffolds, confirmed by the Hi-C data, are named in order of size ( Figure 5; Table 3). During manual curation, chromosome X was identified based on read coverage statistics. The species appears to be an XO male. The following regions of the assembly are of uncertain order and orientation: Chromosome 2: 22.7–42.8 Mb and Chromosome 3: 26.7–36.1 Mb.
Figure 5. Genome assembly of Rhagonycha lutea icRhaLute1.1: Hi-C contact map of the icRhaLute1.1 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=R_Dfgt2VTsuhhKE7xiw_0g.
Table 3. Chromosomal pseudomolecules in the genome assembly of Rhagonycha lutea, icRhaLute1.
| INSDC accession | Name | Length (Mb) | GC% |
|---|---|---|---|
| OY294036.1 | 1 | 106.35 | 31.5 |
| OY294037.1 | 2 | 81.42 | 30.5 |
| OY294038.1 | 3 | 71.01 | 32.5 |
| OY294039.1 | 4 | 52.81 | 32.5 |
| OY294040.1 | 5 | 45.93 | 33.0 |
| OY294041.1 | 6 | 42.19 | 33.0 |
| OY294042.1 | X | 32.65 | 32.0 |
| OY294043.1 | MT | 0.02 | 19.0 |
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, and as a separate fasta file with accession OY294043.1.
The final assembly has a Quality Value (QV) of 67.0 and k-mer completeness of 98.86% for the combined assembly. BUSCO (v5.4.3) analysis using the endopterygota_odb10 reference set ( n = 2,124) indicated a completeness score of 98.7% (single = 94.9%, duplicated = 3.8%). The assembly achieves the EBP reference standard of 6.C.67. Other quality metrics are given in Table 2.
Genome annotation report
The Rhagonycha lutea genome assembly (GCA_958510855.1) was annotated at the European Bioinformatics Institute (EBI) on Ensembl Rapid Release. The resulting annotation includes 25,147 transcribed mRNAs from 24,745 protein-coding genes ( Table 2; https://rapid.ensembl.org/Rhagonycha_lutea_GCA_958510855.1/Info/Index). The average transcript length is 4,062.04, with an average of 4.22 exons per transcript.
Methods
Sample acquisition and DNA barcoding
A male specimen of Rhagonycha lutea (specimen ID NHMUK014400307, ToLID icRhaLute1) was hand-collected from Great Bookham Common, England, United Kingdom (latitude 51.29, longitude -0.39) on 2021-06-08 in flight. The specimen was collected and identified by Maxwell Barclay (Natural History Museum) and preserved by dry freezing at –80 °C.
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 specimens and stored in ethanol, while the remaining parts were shipped on dry ice to the Wellcome Sanger Institute (WSI). 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 have been deposited on protocols.io ( Beasley et al., 2023).
Nucleic acid extraction
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of procedures: sample preparation and homogenisation, DNA extraction, fragmentation and purification. Detailed protocols are available on protocols.io ( Denton et al., 2023b). The icRhaLute1 sample was prepared for DNA extraction by weighing and dissecting it on dry ice ( Jay et al., 2023). Tissue from the thorax was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a).
HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol ( Oatley et al., 2023). The DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation, using AMPure PB beads to eliminate shorter fragments and concentrate the DNA ( Strickland et al., 2023). 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.
Hi-C preparation
Tissue from the abdomen of the icRhaLute1 sample was processed at the WSI Scientific Operations core, using the Arima-HiC v2 kit. Tissue (stored at –80 °C) was fixed, and the DNA crosslinked using a TC buffer with 22% formaldehyde. After crosslinking, the tissue was homogenised using the Diagnocine Power Masher-II and BioMasher-II tubes and pestles. Following the kit manufacturer's instructions, crosslinked DNA was digested using a restriction enzyme master mix. The 5’-overhangs were then filled in and labelled with biotinylated nucleotides and proximally ligated. An overnight incubation was carried out for enzymes to digest remaining proteins and for crosslinks to reverse. A clean up was performed with SPRIselect beads prior to library preparation.
Library preparation and sequencing
Library preparation and sequencing were performed at the WSI Scientific Operations core. Pacific Biosciences HiFi circular consensus DNA sequencing libraries were prepared using the PacBio Express Template Preparation Kit v2.0 (Pacific Biosciences, California, USA) as per the manufacturer's instructions. The kit includes the reagents required for removal of single-strand overhangs, DNA damage repair, end repair/A-tailing, adapter ligation, and nuclease treatment. Library preparation also included a library purification step using AMPure PB beads (Pacific Biosciences, California, USA) and size selection step to remove templates shorter than 3 kb using AMPure PB modified SPRI. DNA concentration was quantified using the Qubit Fluorometer v2.0 and Qubit HS Assay Kit and the final library fragment size analysis was carried out using the Agilent Femto Pulse Automated Pulsed Field CE Instrument and 165kb gDNA and 55kb BAC analysis kit. Samples were 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, as well as perform primary and secondary analysis of the data upon completion.
For Hi-C library preparation, DNA was fragmented to a size of 400 to 600 bp using a Covaris E220 sonicator. The DNA was then enriched, barcoded, and amplified using the NEBNext Ultra II DNA Library Prep Kit following manufacturers’ instructions. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp on an Illumina NovaSeq 6000 instrument.
Genome assembly, curation and evaluation
Assembly
The HiFi reads were first 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 were mapped to the primary contigs using bwa-mem2 ( Vasimuddin et al., 2019). The contigs were further scaffolded using the provided Hi-C data ( Rao et al., 2014) in YaHS ( Zhou et al., 2023) using the --break option for handling potential misassemblies. The scaffolded assemblies were evaluated using Gfastats ( Formenti et al., 2022), BUSCO ( Manni et al., 2021) and MERQURY.FK ( Rhie et al., 2020).
The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Assembly curation
The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants (ASCC) pipeline (article in preparation). Flat files and maps used in curation were generated in TreeVal ( Pointon et al., 2023). Manual curation was primarily conducted using PretextView ( Harry, 2022), with additional insights provided by JBrowse2 ( Diesh et al., 2023) and HiGlass ( Kerpedjiev et al., 2018). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). Any identified contamination, missed joins, and mis-joins were corrected, and duplicate sequences were tagged and removed. The sex chromosome was identified by read coverage analysis. The curation process is documented at https://gitlab.com/wtsi-grit/rapid-curation (article in preparation).
Evaluation of the final assembly
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). These genome evaluation pipelines were developed using nf-core tooling ( Ewels et al., 2020) and MultiQC ( Ewels et al., 2016), relying on the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), as well as the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions. The genome was also analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021) were calculated.
Table 4 contains a list of relevant software tool versions and sources.
Table 4. Software tools: versions and sources.
Genome annotation
The BRAKER2 pipeline ( Brůna et al., 2021) was used in the default protein mode to generate annotation for the Rhagonycha lutea assembly (GCA_958510855.1) in Ensembl Rapid Release at the EBI.
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.
Funding Statement
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.
[version 1; peer review: 2 approved, 1 not approved]
Data availability
European Nucleotide Archive: Rhagonycha lutea. Accession number PRJEB59296; https://identifiers.org/ena.embl/PRJEB59296. The genome sequence is released openly for reuse. The Rhagonycha lutea 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. Raw data and assembly accession identifiers are reported in Table 1 and Table 2.
Metadata for specimens, BOLD barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/1553715.
Author information
Members of the Natural History Museum Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.12159242.
Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.12158331.
Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.12162482.
Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.12165051.
Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.12160324.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.12205391.
Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.
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