
==== Front
Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
F1000 Research Limited London, UK

38779053
10.12688/wellcomeopenres.20338.1
Data Note
Articles
The genome sequence of a rove beetle, Othius punctulatus (Goeze, 1777)
[version 1; peer review: 5 approved]

McCulloch James Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing 1
University of Oxford and Wytham Woods Genome Acquisition Lab
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life programme
Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 Department of Biology, University of Oxford, Oxford, England, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

13 11 2023
2023
8 5192 11 2023
Copyright: © 2023 McCulloch J et al.
2023
https://creativecommons.org/licenses/by/4.0/ 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.

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.

Othius punctulatus
rove beetle
genome sequence
chromosomal
Coleoptera
Wellcome Trust206194 Wellcome Trust218328 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (218328). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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pmcSpecies taxonomy

Eukaryota; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Staphyliniformia; Staphylinoidea; Staphylinidae; Staphylininae group; Staphylininae; Othiini; Othius; Othius punctulatus (Goeze, 1777) (NCBI:txid347424).

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, –1.34). 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%.

Figure 1. Photograph of the Othius punctulatus (icOthPunc1) specimen used for genome sequencing.

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.

Table 1. Genome data for Othius punctulatus, icOthPunc1.1.

Project accession data	
Assembly identifier	icOthPunc1.1	
Assembly release date	2023-06-02	
Species	Othius punctulatus	
Specimen	icOthPunc1	
NCBI taxonomy ID	347424	
BioProject	PRJEB61848	
BioSample ID	SAMEA112232778	
Isolate information	icOthPunc1: whole organism (DNA sequencing and Hi-C data)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	59.6	≥ 50	
k-mer completeness	100%	≥ 95%	
BUSCO **	C:98.8%[S:97.3%,D:1.5%],
F:0.3%,M:0.9%,n:2,124	C ≥ 95%	
Percentage of assembly mapped
to chromosomes	96.91%	≥ 95%	
Sex chromosomes	X chromosome	localised homologous pairs	
Organelles	Mitochondrial genome assembled	complete single alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR11413976	
Hi-C Illumina	ERR11439632	
Genome assembly	
Assembly accession	GCA_951805005.1	
Accession of alternate haplotype	GCA_951805015.1	
Span (Mb)	870.5	
Number of contigs	669	
Contig N50 length (Mb)	7.7	
Number of scaffolds	470	
Scaffold N50 length (Mb)	97.1	
Longest scaffold (Mb)	GCA_951805015.1	
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from ( Rhie et al., 2021).

** BUSCO scores 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.

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 3. Genome assembly of Othius punctulatus, icOthPunc1.1: BlobToolKit GC-coverage plot.

Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Othius%20punctulatus/dataset/icOthPunc1_1/blob.

Figure 4. Genome assembly of Othius punctulatus, icOthPunc1.1: BlobToolKit cumulative sequence plot.

The grey line shows cumulative length for all scaffolds. Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Othius%20punctulatus/dataset/icOthPunc1_1/cumulative.

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.

Table 2. Chromosomal pseudomolecules in the genome assembly of Othius punctulatus, icOthPunc1.

INSDC accession	Chromosome	Length (Mb)	GC%	
OX638138.1	1	132.67	32.5	
OX638139.1	2	120.21	32.5	
OX638140.1	3	100.14	32.5	
OX638141.1	4	97.11	32.5	
OX638142.1	5	91.76	33.0	
OX638143.1	6	77.3	33.0	
OX638144.1	7	71.12	32.5	
OX638145.1	8	63.07	33.0	
OX638146.1	9	50.11	34.5	
OX638147.1	X	40.18	35.5	
OX638148.1	MT	0.02	22.0	

The estimated Quality Value (QV) of the final assembly is 59.6 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 completeness of 98.8% (single = 97.3%, duplicated = 1.5%), using the endopterygota_odb10 reference set ( n = 2,124).

Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://tolqc.cog.sanger.ac.uk/darwin/insects/Othius_punctulatus/.

Methods

Sample acquisition and nucleic acid extraction

An Othius punctulatus (specimen ID Ox002592, ToLID icOthPunc1) 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.

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).

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.

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 and corrected as described previously ( Howe et al., 2021). 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.

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). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.

Table 3 contains a list of relevant software tool versions and sources.

Table 3. Software tools: versions and sources.

Software tool	Version	Source	
BlobToolKit	4.2.1	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.3.2	https://gitlab.com/ezlab/busco	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
Merqury	MerquryFK	https://github.com/thegenemyers/MERQURY.FK	
MitoHiFi	2	https://github.com/marcelauliano/MitoHiFi	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
purge_dups	1.2.5	https://github.com/dfguan/purge_dups	
sanger-tol/genomenote	v1.0	https://github.com/sanger-tol/genomenote	
sanger-tol/readmapping	1.1.0	https://github.com/sanger-tol/readmapping/tree/1.1.0	
YaHS	1.2a.2	https://github.com/c-zhou/yahs	

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.

Data availability

European Nucleotide Archive: Othius punctulatus. Accession number PRJEB61848; https://identifiers.org/ena.embl/PRJEB61848 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Othius punctulatus 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. 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 Table 1.

Author information

Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7125292.

Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.

Members of the Wellcome Sanger Institute Tree of Life programme are listed here: https://doi.org/10.5281/zenodo.4783585.

Members of Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective are listed here: https://doi.org/10.5281/zenodo.4790455.

Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.

Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.

10.21956/wellcomeopenres.22521.r76021
Reviewer response for version 1
Lü Liang 1Referee https://orcid.org/0000-0001-7533-6244

1 Hebei Normal University, Shijiazhuang, China
20 5 2024 Copyright: © 2024 Lü L
2024
https://creativecommons.org/licenses/by/4.0/ 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.
Version 1recommendationapprove
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.

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:

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.

10.21956/wellcomeopenres.22521.r80944
Reviewer response for version 1
Waterhouse Robert M 1Referee https://orcid.org/0000-0003-4199-9052

1 University of Lausanne, and the Swiss Institute of Bioinformatics, Lausanne, Switzerland
15 5 2024 Copyright: © 2024 Waterhouse RM
2024
https://creativecommons.org/licenses/by/4.0/ 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.
Version 1recommendationapprove
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 high-quality 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).

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:

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.

10.21956/wellcomeopenres.22521.r70462
Reviewer response for version 1
Weng Yi-Ming 1Referee https://orcid.org/0000-0002-8243-5061

1 Department of Entomology, University of Wisconsin Madison, Madison, WI, USA
11 5 2024 Copyright: © 2024 Weng YM
2024
https://creativecommons.org/licenses/by/4.0/ 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.
Version 1recommendationapprove
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.

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:

entomology, population genetics, evolutionary 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.

10.21956/wellcomeopenres.22521.r80938
Reviewer response for version 1
Van Belleghem Steven M 1Referee https://orcid.org/0000-0001-9399-1007

1 University of Puerto Rico, KU Leuven, Puerto Rico, Brazil
7 5 2024 Copyright: © 2024 Van Belleghem SM
2024
https://creativecommons.org/licenses/by/4.0/ 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.
Version 1recommendationapprove
The paper presents a genome assembly for the rove beetle Othius punctulatus ith very high quality: Total Assembly Length: 870.5 megabases

Number of Scaffolds: 470

Scaffold N50: 97.1 megabases

Number of Contigs: 669

Contig N50: 7.7 megabases

Quality Value (QV): 59.6, indicating a high-quality assembly

k-mer Completeness: 100%, suggesting excellent coverage of the genome

BUSCO Completeness: 98.8% (with 97.3% single copy and 1.5% duplicated), using the endopterygota_odb10 BUSCO set, indicating that nearly all expected gene content is present

Mitochondrial Genome: Also assembled and included within the genome data

Chromosomal Assignment: 96.91% of the assembly sequence is assigned to 10 chromosomal-level scaffolds, representing 9 autosomes and the X sex chromosome.

The authors outline the significance of the dataset in enhancing our understanding of the beetle's evolutionary biology, ecological adaptations, and biodiversity.

The protocols used for sample acquisition, nucleic acid extraction, sequencing, and genome assembly are thoroughly outlined and appropriate for the study. The methods incorporate advanced techniques like PacBio single-molecule HiFi long reads and Hi-C data, ensuring a robust and reliable genomic assembly. The work is technically sound, employing current best practices in genomic research.

The paper provides detailed descriptions of the methods and materials used, including specific protocols for each stage of sample processing and data generation

The datasets are clearly presented and accessible in a format that is usable for further analysis by the scientific community. The authors provide comprehensive assembly statistics, quality metrics, and chromosomal-level scaffolds.

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.

10.21956/wellcomeopenres.22521.r76025
Reviewer response for version 1
Palmieri Luciano 12Referee https://orcid.org/0000-0002-4813-2614

1 Faculty of Agricultural Environmental and Food Sciences, Free University of Bolzen-Bolzano, Bolzano, Bolzano, 39100, Italy
2 Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
18 3 2024 Copyright: © 2024 Palmieri L
2024
https://creativecommons.org/licenses/by/4.0/ 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.
Version 1recommendationapprove
The 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.

The datasets are provided in a usable and accessible format, enabling further analysis and exploration by the scientific community. Assembly statistics, quality metrics, and chromosomal-level 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.

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:

Coleoptera, Systematics, Biogeography, Biodiversity, Taxonomy, Entomology, Systematic Entomology, Insect Taxonomy, Evolution, Natural History, Molecular Phylogenetics, Invertebrate Zoology, Parasitoids, Macroevolution, Genome Assembly, and Phylogenomics.

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.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
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