The genome sequence of a click beetle, Melanotus villosus (Geoffroy in Fourcroy, 1785)

We present a genome assembly from an individual female Melanotus villosus (click beetle; Arthropoda; Insecta; Coleoptera; Elateridae). The genome sequence is 803.5 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.91 kilobases in length.

complete genome sequence based on one male specimen (NHMUK014111204) collected by DS on 20/04/2021 from Bookham Commons and identified by MB and HM.This genome note will provide a molecular description of this species and will be useful for separating M. villosus from its close relative M. castanipes in future research projects.

Genome sequence report
The genome was sequenced from one female Melanotus villosus (Figure 1) collected from Bookham Commons, England, UK (51.29,.A total of 29-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 30 missing joins or mis-joins and removed 5 haplotypic duplications, reducing the assembly length by 0.91% and the scaffold number by 20.20%, and increasing the scaffold N50 by 28.53%. The final assembly has a total length of 803.5 Mb in 78 sequence scaffolds with a scaffold N50 of 80.2 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 (98.25%) of the assembly sequence was assigned to 10 chromosomal-level scaffolds, representing 9 autosomes and the X sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named

Background
Melanotus villosus is a large black click beetle, 13-20 mm long, which is associated with mature woodland where the larvae develop in rotting wood (Duff, 2020;James, 2018;Laibner, 2000).The adult beetles are typically found on tree trunks, inside wood, in flight during the evening, or can be swept from vegetation.They can potentially be seen in all months of the year (du Chatenet, 2000;Duff, 2020).
Melanotus villosus and its close relative M. castanipes used to be regarded as one species in Britain until they were reviewed and separated by Mendel (2004).The length of the antennae and the shape of the pronotum are useful characters for identification, though separation of adults is difficult, and larval characters may also be helpful (Mendel, 2004).Pre-2004 records of M. villosus may therefore refer to M. castanipes and should be treated with caution.The names Melanotus rufipes (Herbst, 1784) non (De Geer, 1774) and M. erythropus (Gmelin, 1790), now treated as synonyms of M. villosus, were frequently applied to both species in the older British literature (Duff, 2020).
It appears that M. villosus mostly occurs in the south-east of England while M. castanipes is widespread across Britain (Duff, 2020;Mendel, 2004).On mainland Europe this situation is reversed, with M. villosus being the more widespread species while M. castanipes tends to occur at higher elevations (du Chatenet, 2000;Laibner, 2000).
There are some ecological differences between these species that are worth noting.James (2018) reports that in Hertfordshire M. villosus is closely associated with woodland, while M. castanipes tends to occur in more open habitats (while still requiring dead wood).He states that there is only one site in Hertfordshire where both beetles are known to coexist.Some authors have suggested that in continental Europe, M. villosus adults are diurnal whereas M. castanipes are crepuscular or nocturnal and sometimes come to light traps (Laibner, 2000;Leseigneur, 1972).Such differences have not yet been observed in Britain.The global distributions of these species differ, as M. villosus is Palaearctic whereas M. castanipes is Holarctic, also occurring in North America (Laibner, 2000).
The genome of Melanotus villosus 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 in order of size (Figure 5; Table 2).Chromosome X was assigned by alignment to the genome assembly for Agrypnus murinus (GCA_929113105.1)(Crowley et al., 2023).While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
The estimated Quality Value (QV) of the final assembly is 67.2 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 99.3% (single = 97.5%,et al., 2023).Tissue from the abdomen 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 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 head tissue of icMelVill1 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  (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Table 3 contains a list of relevant software tool versions and sources.

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner.The submission of materials by a Darwin Tree of Life Partner is subject Table 3. Software tools: versions and sources.

Software tool Version
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  The genome report of a click beetle endemic to Britain presented here is well written and provides the necessary details for assembly reproduction.The authors describe the relevance of this specimen in an ecological and historical context, ie the past 'lumping' of this species with another click-beetle, the methods used to generate the assembly, and its importance for the larger Darwin Tree of Life Project goal to sequence all eukaryotes of Britain and Ireland.The figures and results provided are informative and help emphasize the high-quality product.This genome assembly has relevant applications for coleopterists, taxonomists and evolutionary biologists.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

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

Figure 2 .
Figure 2. Genome assembly of Melanotus villosus, icMelVill1.1: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 803,481,935 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 (147,383,313 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (80,210,941 and 59,994,649 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/CAUJBP01/dataset/CAUJBP01/snail.

Figure 3 .
Figure 3. Genome assembly of Melanotus villosus, icMelVill1.1: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/CAUJBP01/dataset/CAUJBP01/blob.

Figure 4 .
Figure 4. Genome assembly of Melanotus villosus, icMelVill1.1: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/CAUJBP01/dataset/CAUJBP01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Melanotus villosus, icMelVill1.1:Hi-C contact map of the icMelVill1.1 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=YzPOQ6dBT_qs6yvQPYKXWA.

©
2024 Palmieri L. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Luciano Palmieri 1 Free University of Bolzen-Bolzano, Bolzano, Italy 2 University of Wisconsin-Madison, Madison, WI, USAThe study presents a genome assembly of a female Melanotus villosus, a click beetle (Coleoptera; Elateridae).The genome sequence spans 803.5 Mb, scaffolded into 10 chromosomal pseudomolecules, including the X sex chromosome.The mitochondrial genome is also assembled, measuring 15.91 kb.This work clarifies the taxonomy of M. villosus and its ecological significance, providing a valuable resource for future research.Protocols followed best practices in genomics.The integration of PacBio HiFi long reads, Hi-C scaffolding, and quality checks ensures a highquality assembly.Data deposition in public repositories and detailed methodological descriptions enhance reproducibility.Gene annotation is not available, but future annotation is planned.Overall, it is a valuable resource for research.Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?YesCompeting Interests: No competing interests were disclosed.Reviewer Expertise: Entomology, 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.Reviewer Report 06 August 2024 https://doi.org/10.21956/wellcomeopenres.23327.r90153© 2024 Cohen Z.This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Zachary P Cohen USDA Agricultural Research Service, College Station, TX, USA