The genome sequence of a ground beetle, Leistus spinibarbis (Fabricius, 1775)

We present a genome assembly from an individual male Leistus spinibarbis (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 235.1 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 15.82 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,576 protein coding genes.


Background
The genus Leistus Frölich, 1799 is divided into six subgenera, and includes more than 250 species of medium sized, fast running predatory ground beetles, mainly distributed in the Palaearctic region (Anichtchenko et al., 2021).Leistus spinibarbis is the type species of the subgenus Pogonophorus Latreille, 1802, and is itself divided into three subspecies (Löbl & Löbl, 2017).The British population forms part of the nominate subspecies Leistus spinibarbis spinibarbis, which has a restricted distribution in the centre and west of Europe, being listed for only nine countries: Great Britain, Belgium, the Netherlands, Luxembourg, France, Austria, Germany, Monaco and Italy (Löbl & Löbl, 2017).Other subspecies occur to the south and east of this range.In the British Isles the species is widespread in England and Wales, local in Scotland and apparently absent from Ireland.
Leistus are specialist predators of springtails (Collembola) and have expanded mandibles used for catching this prey, and are hence sometimes called 'plate-jaws' (e.g.Telfer & Walters, 2010).These authors use the name 'Prussian Plate-Jaw' for L. spinibarbis, because of the metallic 'Prussian blue' reflection on the black cuticle.It is a conspicuous beetle, on average larger and more brightly coloured than any of the other five species of Leistus that occur in Britain.
Leistus spinibarbis is 8 to 10.5 mm in length, winged and able to fly, and can be found in woods, gardens and near the coast (Luff, 2007).In the author's experience, it can often be found in degraded and human-modified habitats in and around cities, and is usually encountered singly and by chance rather than by deliberate searching.The specimen used for the genome was collected on a wall adjoining a busy London road, surrounded by housing and gardens.The genome of a ground beetle, Leistus spinibarbis, 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 Leistus spinibarbis, based on one male specimen from Fulham, London, UK.

Genome sequence report
The genome was sequenced from one male Leistus spinibarbis (Figure 1) collected from Fulmead Street, Fulham, London, UK (51.48,.A total of 66-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 19 missing joins or mis-joins and removed two haplotypic duplications, reducing the scaffold number by 5.43%, and increasing the scaffold N50 by 16.49%.
The final assembly has a total length of 235.1 Mb in 87 sequence scaffolds with a scaffold N50 of 11.6 Mb (Table 1).Most (96.9%) of the assembly sequence was assigned to 23 chromosomal-level scaffolds, representing 22 autosomes and the X sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-Figure 5; Table 2.This appears to be a male assembly denoted by read coverage for Chromosome X being half that of the autosomes.Despite the presence of unassigned repetitive scaffolds, it was not possible to identify a Y chromosome.As there is no way to reliably determine if this sample is XY or XO the assembly has been submitted with a single X allosome assignment.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 54.4 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.3.2 completeness of 99.2% (single =98.7%, duplicated = 0.4%), using the endopterygota_odb10 reference set (n = 2,124).
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/878056.

Sample acquisition and nucleic acid extraction
A male Leistus spinibarbis (specimen ID NHMUK014400244, individual icLeiSpin1) was collected from Fulham, London, UK (latitude 51.48, longitude -0.19) on 2021-05-12.The specimen was collected and identified by Maxwell Barclay (Natural History Museum) and preserved by dry-freezing at -80°C.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The icLeiSpin1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Abdomen tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW  SEQUEL II (HiFi) instrument.Hi-C data were also generated from head and thorax tissue of icLeiSpin1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Leistus spinibarbis assembly (GCA_933228885.1) in Ensembl Rapid Release.

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 The one comment that we had was the unavailability of code for their computational pipelines (for assembly, annotation, QC, and other steps).I recommend that the authors make this publicly available via GitHub or some similar platform, especially to ensure reproducibility/reusability of their data.

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

Are sufficient details of methods and materials provided to allow replication by others? Partly
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Genetics, genomics, computational biology We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.Its also an example of convergence, as it is one of three lineages who demoinstrate specialized feeding on Collembola: Baulechner, D., Jauker, F., Neubauer, T.A. and Wolters, V., 2020.Convergent evolution of specialized generalists: implications for phylogenetic and functional diversity of carabid feeding groups.Ecology and Evolution,10(20), pp.11100-11110.
My favorite descriptor that I have heard/read is that Leistus has a "Collembola basket".The preycapture technique has been described well by: Bauer, Thomas."Beetles which use a setal trap to hunt springtails: The hunting strategy and apparatus of Leistus (Coleoptera, Carabidae)."Pedobiologia (1985): n. pag.
Leistus is often found in cool, damp and rock habitats.Interestingly, it seems to prefer foraging on sloped and elevated features when foraging, such as vegetation, on large boulders or sloped banks, similar to your rock wall.

Figure 2 .
Figure 2. Genome assembly of Leistus spinibarbis, icLeiSpin1.1:metrics.The BlobToolKit Snailplot 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 235,131,629 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 (18,248,107 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (11,648,774 and 4,697,515 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/icLeiSpin1.1/dataset/ CAKOGD01/snail.
Manual curation was performed using HiGlass(Kerpedjiev et al., 2018) and Pretext (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.

Figure 5 .
Figure 5. Genome assembly of Leistus spinibarbis, icLeiSpin1.1:Hi-C contact map of the icLeiSpin1.1 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=FKGrm21hTo6nvptbBrWYKw.

Reviewer Report 23
October 2023 https://doi.org/10.21956/wellcomeopenres.22143.r68998© 2023 Amaral D. 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.Danilo T Amaral Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de Sao Carlos, São Carlos, State of São Paulo, Brazil I had the pleasure of reviewing the manuscript by Barclay et al., titled "The genome sequence of a ground beetle, Leistus spinibarbis(Fabricius, 1775)."This study presents the a new chromosomelevel genome assembly for a member of the Carabidae family, offering valuable insights into the genome structure of this group.The high-quality assembly of genomes, particularly at the chromosome level, is pivotal in advancing scientific research.Mainly with the chromosome X definition and mitochondrial genome characterization accurately deciphering the complete genetic blueprint of an organism enables researchers to gain a comprehensive understanding of its structure, function, and evolutionary history.The manuscript provided well-written and detailed methodologies and results.As a reader, I have a minor suggestion.While the figures and tables effectively demonstrate the assembly quality, it may be beneficial to include Figure4as supplementary material, based on the sequencing and assembly methodologies.Additionally, it would be interesting to know if any previous studies have performed the karyotyping of this species (or closely related species) to determine the number of chromosomes.Including this information in the text would further enhance the study's context and significance.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: Genomic and bioinformaticI 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 26 September 2023 https://doi.org/10.21956/wellcomeopenres.22143.r67439© 2023 Schoville S. 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.Sean Schoville Department of Entomology, University of Wisconsin-Madison, Madison, Wisconsin, USA This is a nice resource for beetle (especially Carabid beetle) phylogenomics research, and the assembly is of high quality.Now that several genomes are available for Nebria, I wonder if an analysis of synteny across Nebria and Leistus could be added to this analysis.The lack of a clear Y chromosome is interesting, so my thoughts were based on if that might yield insights to the XO vs XY hypothesis (one would expect synteny at all autosomes in your dataset).Suggestions on Background:As part of your justification, you might consider the important phylogenetic placement of Leistus within the diverse tribe Nebriini: Kavanaugh, D.H., Maddison, D.R., Simison, W.B., Schoville, S.D., Schmidt, J., Faille, A., Moore, W., Pflug, J.M., Archambeault, S.L., Hoang, T. and Chen, J.Y., 2021.Phylogeny of the supertribe Nebriitae (Coleoptera, Carabidae) based on analyses of DNA sequence data.ZooKeys, 1044, p.41.