The genome sequence of a ground beetle, Pterostichus niger (Schaller, 1783)

We present a genome assembly from an individual male Pterostichus niger (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 674.1 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 17.16 kilobases in length.


Background
The ground beetle Pterostichus niger (Schaller, 1783) is the largest of 18 species of the genus Pterostichus Bonelli, 1810 occurring in Britain and Ireland, and the only British member of the subgenus Platysma Bonelli, 1810.It is common and generally distributed throughout the British Isles, including in the Orkneys, the Shetlands, and most of the smaller islands.Like many larger Carabidae in Britain, adults and larvae are terrestrial predators, and P. niger can be abundant in a range of habitats from forests to moorlands and mountains, usually favouring damper biotopes.Globally, the Palaearctic Catalogue lists P. niger for 39 European and 7 Asian countries, most frequently in the north but extending southwest to Spain and east to West Siberia and Western China, but it is apparently absent from Portugal and North Africa (Löbl & Löbl, 2017).
Pterostichus niger is a distinctive insect, and in Britain could only be confused with the similarly sized carabids Pterostichus melanarius (Illiger, 1798) and Abax parallelepipedus (Piller & Mitterpacher, 1783), both of which can be abundant in the same habitats, but which can be easily differentiated by the shape of the pronotum.Species identification is straightforward using Luff (2007) or Lindroth (1974).P. niger is a nocturnal predator primarily of slugs, worms and insect larvae on the ground and in forest litter.Adults can be collected almost all year, by night-searching, looking under logs and loose bark, or by pitfall trapping.It has flight wings, but it appears that most individuals do not have the flight muscles developed and the species is rarely if ever observed to fly.
The genome of Pterostichus niger 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 Pterostichus niger, based on one male specimen collected in September 2021 by a small Natural History Museum team at Bookham Common, Surrey, England.

Genome sequence report
The genome was sequenced from one male Pterostichus niger (Figure 1) collected from Bookham Common, England, UK (51.29, -0.39,Ordnance Survey Grid Reference TQ1256).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 175 missing joins or misjoins and removed 10 haplotypic duplications, reducing the assembly length by 0.75% and the scaffold number by 40.92%, and increasing the scaffold N50 by 18.2%.
The final assembly has a total length of 674.1 Mb in 178 sequence scaffolds with a scaffold N50 of 36.9Mb (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 (97.06%) 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 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.
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes  MagAttract HMW DNA kit, according to the manufacturer's instructions.
RNA was extracted from abdomen tissue of icPteNige1 using the Automated MagMax™ mirVana protocol (https://dx.doi.org/10.17504/protocols.io.6qpvr36n3vmk/v1).The RNA concentration was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit.Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers' instructions.Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit.DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments.Hi-C data were also generated from head tissue of icPteNige1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.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 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

Software tool Version
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

Reviewer Expertise: Genomics, Transcriptomics, Regeneration 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.Reviewer Expertise: Marine invertebrate, Evo-Devo 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 1 .
Figure 1.Photograph of the Pterostichus niger (icPteNige1) specimen used for genome sequencing.a) Dorsal view, b) Lateral view and c) Ventral view.

Figure 2 .
Figure 2. Genome assembly of Pterostichus niger, icPteNige1.1: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 674,098,515 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 (45,804,315 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (36,870,366 and 23,707,136 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/icPteNige1.1/dataset/CANDYQ01/snail.

Figure 3 .
Figure 3. Genome assembly of Pterostichus niger, icPteNige1.1: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/icPteNige1.1/dataset/CANDYQ01/blob.

Figure 4 .
Figure 4. Genome assembly of Pterostichus niger, icPteNige1.1: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/icPteNige1.1/dataset/CANDYQ01/ cumulative.

Figure 5 .
Figure 5. Genome assembly of Pterostichus niger, icPteNige1.1:Hi-C contact map of the icPteNige1.1 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=V0B2AOZYSaae37-GJDYNVg.

Reviewer Report 21
February 2024 https://doi.org/10.21956/wellcomeopenres.22607.r74325© 2024 Morino 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.Yoshiaki MorinoInstitute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan This paper reports the genome sequence of the ground beetle Pterostichus niger.The genome assembly size was 674.1 Mbp, and most of the sequence was assigned to 19 chromosome-level scaffolds.The BUSCO gene completeness score was 97.9%.The quality of this assembly met the standards of the Darwin Tree of Life Project.Therefore, this assembly will be a valuable resource for diverse fields such as entomology, ecotoxicology, and population ecology.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?Yes Competing Interests: No competing interests were disclosed.
a sequence of core procedures: sample preparation; sample homogenisation; DNA extraction; HMW DNA fragmentation; and fragmented DNA clean-up.The icPteNige1 sample was prepared for DNA extraction at the WSI Tree of Life laboratory: it 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).Sample homogenisation was carried on using the Powermasher protocol (https://dx.doi.org/10.17504/protocols.io.5qpvo3r19v4o/v1).DNA was extracted at the WSI Scientific Operations core using the Qiagen