The genome sequence of a rove beetle, Othius punctulatus (Goeze, 1777)

We present a genome assembly from an individual female Othius punctulatus (a rove beetle; Arthropoda; Insecta; Coleoptera; Staphylinidae). The genome sequence is 870.5 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 20.71 kilobases in length.


Background
Beetles in the highly speciose Staphylinidae (rove beetles) are characterised by short elytra leaving several segments of the abdomen exposed, although there are exceptions.The subfamily Staphylininae is not one of those exceptions, but can be distinguished from other subfamilies by the structure and placement of the antennae which lack a terminal club and are placed distinctly in front of the eyes and medial to the base of the mandibles.The tribe Othiini within Staphylininae is recognised by the evenly curved pronotal side margin at the front angle, coupled with a dorsal series of pronotal punctures extending from the apical margin beyond the transverse midline.Within this tribe, Othius punctulatus can be easily distinguished from other UK species by the red elytra (Lott & Anderson, 2011).
The native distribution of O. punctulatus extends across much of the Western Palearctic.The species has also been introduced to the Pacific Northwest, where it was first recorded in 2011 in Washington and is now established, and likely introduced to the Canary Islands (Rood et al., 2015).It is widespread across the British Isles, but less common in the north and west.This species prefers woodland habitats, and can be found both in the forest interior and edge zones (Tóthmérész et al., 2014).Delany (1960) noted an adult of O. punctulatus feeding on prey ranging in size from Collembola to other rove beetles, generally feeding on larger items than its smaller congener O. angustus.While adults can be found throughout the year, the peak of activity is in spring, with a further peak in late autumn.Most copulation and oviposition appear to occur in the autumn, with larvae pupating during the following summer, although the reproductive cycle may be flexible (Kasule, 1970).
Here we present a chromosomally complete genome sequence for Othius punctulatus, based on one female specimen from Oxfordshire, UK, sequenced as part of the Darwin Tree of Life Project.

Genome sequence report
The genome was sequenced from one female Othius punctulatus (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 26-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 47 missing joins or mis-joins and removed 10 haplotypic duplications, reducing the assembly length by 0.6% and the scaffold number by 4.07%, and increasing the scaffold N50 by 1.34%. The final assembly has a total length of 870.5 Mb in 470 sequence scaffolds with a scaffold N50 of 97.1 Mb (Table 1).The snailplot 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 (96.91%) of the assembly sequence was assigned to 10 chromosomal-level scaffolds, representing 9 autosomes and the X sex chromosome.The X chromosome was assigned based on synteny to Philonthus cognatus (GCA_932526585.2) (Crowley et al., 2023) and Ocypus olens (GCA_910593695.2) (Crowley et al., 2021).Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).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.

Sample acquisition and nucleic acid extraction
An Othius punctulatus (specimen ID Ox002592, ToLID icO-thPunc1) was collected using a sweep net in Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2022-07-29.The specimen was collected and identified by James McCulloch (University of Oxford) and preserved on dry ice.

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 (HiFi) instrument.Hi-C data were also generated from remaining tissue of icOthPunc1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.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    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

Liang Lü
Hebei Normal University, Shijiazhuang, China I am happy to see one more rove beetle species with a high-quality genome.Actually, the author presents a simple article with a standard and widely accepted methodology, but not simple results, which were actually described in a very simple form.I recommend the editorial office consider its acceptance with minor or no revision.My only worry is about the identity of ths sample specimen, because the manuscript shows only in a lateral view, which does not expose many definite traits of Othius punctulatus.The author should show in dorsal view if it is still possible.

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

Are the datasets clearly presented in a useable and accessible format? Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: rove beetle taxonomy and evolution I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Robert M Waterhouse
University of Lausanne, and the Swiss Institute of Bioinformatics, Lausanne, Switzerland This Data Note for the rove beetle presents a clear and comprehensive description of all the steps taken to generate the Othius punctulatus genome assembly spanning 870 Mb with 97% assigned to 10 chromosomal-level scaffolds including the X sex chromosome.The rationale behind the production of these reference data resources is clearly described, explaining the importance of genomic data and their contribution to improving our understanding of the biology, ecology, and evolution of O. punctulatus and other rove beetles.The results also include the mitochondrial genome assembly, I had not realized that it was now common to include the mitochondrial genome as a scaffold within the multifasta of a nuclear genome submission.The described data collection and analysis methods follow the best practices in the field and have delivered a highquality complete and accurate chromosome-level reference genome.The manuscript methods provide detailed descriptions of the protocols employed for sample acquisition, DNA extractions, and sequencing of long reads and Hi-C data generation.The genome assembly is of one haplotype, with contigs corresponding to the second haplotype also deposited.The results are clearly presented along with the standard quality control analyses and summary statistics to be able to easily verify the high quality of the generated reference resources, which are freely accessible along with appropriate metadata in community open access genomic data repositories (the ENA and INSDC global mirrors).

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.

Yi-Ming Weng
Department of Entomology, University of Wisconsin Madison, Madison, WI, USA The genome report entitled "The genome sequence of a rove beetle, Othius punctulatus (Goeze, 1777)" is reviewed.This report includes brief and clear introduction about the species, followed by the result of genome assembly work.Despite of the high completeness according to BUSCO and Merqury, more (470) scaffolds were in the final assembly than I expected.Considering that the longest 10 scaffolds have accounted for the 10 chromosomes, I wonder if it is possible with more sequences to improve the assembly in the future to assemble the remaining scaffolds into the existing chromosomes.
Is the rationale for creating the dataset(s) clearly described?The datasets are provided in a usable and accessible format, enabling further analysis and exploration by the scientific community.Assembly statistics, quality metrics, and chromosomallevel scaffolds are clearly presented, providing insights into the genomic composition of O.
punctulatus.The inclusion of metadata, barcode results, sequencing runs, and assembly statistics enhances the transparency and accessibility of the genomic dataset.The authors' meticulous approach to experimental design, execution, and data dissemination contributes to the advancement of knowledge in entomology and genomic biology.
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 Othius punctulatus, icOthPunc1.1: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 870,474,623 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 (132,666,048 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (97,110,198 and 50,107,992 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/Othius%20punctulatus/dataset/icOthPunc1_1/snail.

Figure 5 .
Figure 5. Genome assembly of Othius punctulatus, icOthPunc1.1:Hi-C contact map of the icOthPunc1.1 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=ZN8O9EITQkqDzh9YuTUbIA.

Reviewer Report 15
May 2024 https://doi.org/10.21956/wellcomeopenres.22521.r80944© 2024 Waterhouse R.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.
Expertise: Arthropod 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 11 May 2024 https://doi.org/10.21956/wellcomeopenres.22521.r70462© 2024 Weng Y.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.

©
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 Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA 2 Faculty of Agricultural Environmental and Food Sciences, Free University of Bolzen-Bolzano, Bolzano, Bolzano, 39100, ItalyThe text outlines the creation of a chromosomally complete genome sequence for Othius punctulatus, a species of rove beetle belonging to the Staphylinidae family.The rationale for creating the dataset is clearly described, emphasizing the importance of understanding the genomic makeup of O. punctulatus for advancing research in evolutionary biology, ecology, and biodiversity.The manuscript describes the species' distribution, habitat preferences, and behavioral patterns, underscoring the relevance of genomic data in unraveling the genetic basis of its ecological adaptations and evolutionary history.The protocols employed in sample acquisition, nucleic acid extraction, and sequencing are appropriate.The text provides detailed descriptions of the methodologies used, including sample preparation, DNA extraction, library construction, and sequencing.The integration of PacBio single-molecule HiFi long reads and Hi-C data for genome assembly and scaffold correction reflects a robust approach to genomic analysis.The manuscript also highlights the availability of publicly accessible protocols, ensuring transparency and reproducibility in experimental procedures.Sufficient details of methods and materials are provided, facilitating replication by other researchers.References to publicly available protocols and software tools enhance the comprehensibility and replicability of the experimental procedures outlined in the study.

Table 1 . Genome data for Othius punctulatus, icOthPunc1.1. Project accession data
(Rhie et al., 2021)enchmarks are adapted from column VGP-2020 of "Table1: Proposed standards and metrics for defining genome assembly quality" from(Rhie et al., 2021).**BUSCOscores based on the endopterygota_odb10 BUSCO set using v5.3.2.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/Othius%20punctulatus/dataset/icOthPunc1_1/busco.The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation; DNA extraction; HMW DNA fragmentation; and fragmented DNA clean-up.The sample was prepared for DNA extraction at the WSI Tree of Life laboratory: the icOthPunc1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing (https://dx.doi.org/10.17504/protocols.io.x54v9prmqg3e/v1).Tissue from the whole organism was disrupted using a Nippi Powermasher fitted with a BioMasher pestle (https://dx.doi.org/10.17504/protocols.io.5qpvo3r19v4o/v1).DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.All protocols used by the Tree of Life laboratory are publicly available on protocols.io(https://dx.doi.org/10.17504/protocols.io.8epv5xxy6g1b/v1).

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.

the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
https://doi.org/10.21956/wellcomeopenres.22521.r76025