The genome sequence of a ground beetle, Ophonus ardosiacus (Lutshnik, 1922)

We present a genome assembly from an individual female Ophonus ardosiacus (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 911.9 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 40,995 protein coding genes.


Background
Ophonus ardosiacus is a ground beetle of the family Carabidae, order Coleoptera.Adults grow to 14 mm in length, and the grooved elytra vary in colour from dark brown to black, with a metallic blue sheen, and reddish-brown appendages (UK Beetles, no date).
Ophonus ardosiacus has a wide Palearctic distribution, and is common across central and southern Europe, as far east as Czechia, and also in northern Africa (GBIF Secretariat, 2022), with rare records in Czechia and the Netherlands.It is regarded as nationally scarce (category B) in Britain (Hyman, 1992;Telfer, 2016).However, O. ardosiacus has become more common here over the past few decades, occurring more widely inland.This shift may be a response to climate change, or to an increase in favourable habitats (Harvey, 2004).It occurs from the midlands of England to the south (Giglio et al., 2008).
The typical habitats of O. ardosiacus include open grassland and some agricultural or coastal areas in areas with chalky, limestone or clay soils (Harvey, 2004).These ground beetles consume the seeds of many annual plants, especially carrot seed heads.Both the larvae and adults are phytophagous (UK Beetles, no date).
The genome of O. ardosiacus has now been 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 O. ardosiacus, based on one female specimen from Wytham Woods, Oxfordshire.The genome sequence will prove useful in studies assessing invertebrate communities for agricultural areas as part of integrated pest management.

Genome sequence report
The genome was sequenced from one female Ophonus ardosiacus (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 25-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 13-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 94 missing joins or mis-joins and removed 20 haplotypic duplications, reducing the assembly length by 0.95%, and the scaffold number by 45.52%, and increasing the scaffold N50 by 96.53%. The final assembly has a total length of 911.9 Mb in 73 sequence scaffolds with a scaffold N50 of 52.1 Mb (Table 1).Most (99.69%) of the assembly sequence was assigned to 19 chromosomal-level scaffolds, representing 18 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).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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/247415.

Sample acquisition and nucleic acid extraction
The specimen selected for genome sequencing was a female Ophonus ardosiacus (specimen ID Ox000754, individual icOphArdo1) collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.33) on 2020-08-04 by potting.Liam Crowley (University of Oxford) collected and identified the specimen.The specimen was snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The icOphArdo1 sample was weighed    A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019)     genome was analysed within the BlobToolKit environment (Challis et al., 2020) andBUSCO scores (Manni et al., 2021;Simão et al., 2015) were calculated.
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 Ophonus ardosiacus assembly (GCA_943142095.1) 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

Ping Wang
Yangtze University, Jingzhou,, China Dear Authors, I have put forward some views that are only my own in the following sections respectively, thank you.This is an interesting manuscript that provides information on the genome sequencing of Ophonus ardosiacus.The manuscript presents a comprehensive genome assembly of Ophonus ardosiacus, a ground beetle, as part of the Darwin Tree of Life Project.The assembly appears to be of high quality, with a significant portion of the genome scaffolded into chromosomal pseudomolecules and a detailed annotation of protein-coding genes.The use of advanced sequencing technologies and the integration of Hi-C data for scaffolding are commendable.

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The background information on O. ardosiacus is informative, but it could be enhanced by discussing the ecological and evolutionary significance of ground beetles in general, and how this specific species contributes to the ecosystem.This would provide a broader context for the importance of the genome sequence.

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The authors have provided detailed information on the sequencing and assembly methods, which is excellent.However, it would be beneficial to include a brief explanation of the technologies (e.g., Pacific Biosciences HiFi, 10X Genomics) for readers who may not be familiar with these terms.

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The BUSCO scores indicate a high completeness of the assembly, which is commendable.It would be helpful to briefly discuss any potential limitations or areas for improvement in the assembly process.

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The annotation of 40,995 protein-coding genes is a significant achievement.It would be beneficial to provide insights into the functional diversity of these genes, perhaps by comparing them to other related species or discussing potential novel genes that could be ○ of interest.
The manuscript mentions the potential use of the genome sequence in studies assessing invertebrate communities for agricultural areas.It would be helpful to expand on this, discussing specific research questions or applications that could benefit from this resource.

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The conclusion could be strengthened by summarizing the key contributions of this genome assembly to the field of entomology and ecology, and how it fits into the broader goals of the Darwin Tree of Life Project.

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The manuscript is well-prepared and presents a valuable resource for the scientific community.With the suggested improvements, I believe it would be a strong contribution to Wellcome Open Research.Reviewer Expertise: Population genetics, evolutionary genomics, taxonomy of Carabidae.
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 Ophonus ardosiacus, icOphArdo1.1: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 911,917,119 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 (89,420,107 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (52,059,326 and 31,939,453 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/icOphArdo1.1/dataset/CALPBS01/snail.

Figure 5 .
Figure 5. Genome assembly of Ophonus ardosiacus, icOphArdo1.1:Hi-C contact map of the icOphArdo1.1 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=HVSPI2KAS8WA2aeR28Wf2w.

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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: Taxonomy; Entomology 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 14 September 2023 https://doi.org/10.21956/wellcomeopenres.21982.r65599© 2023 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.Yi-Ming WengDepartment of Entomology, University of Wisconsin Madison, Madison, WI, USA This paper reports a very complete genome assembly for a carabid beetle, Ophonus ardosiacus.The number of coding gene was quite high comparing to many other ground beetle species, despite of the fact that only protein was used to train the model (usually more genes with RNA data to jointly train the gene model with proteins).I wonder which protein database was used to in modeling the gene in the braker2 pipeline.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?PartlyAre the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.

Table 1 . Genome data for Ophonus ardosiacus, icOphArdo1.1. Project accession data
* Assembly metric benchmarks are adapted from column VGP-2020 of "Table1: 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/icOphArdo1.1/dataset/CALPBS01/busco. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer

Peer Review Current Peer Review Status: Version 1
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.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.