The genome sequence of a ground beetle, Nebria brevicollis (Fabricius, 1792)

We present a genome assembly from an individual female Nebria brevicollis (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence is 242 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules, with the X sex chromosome assembled. The mitochondrial genome has also been assembled and is 25.2 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,021 protein-coding genes.


Background
Nebria brevicollis (Coleoptera, Carabidae) is a relatively large ground beetle, measuring 10-14 mm, closely resembling other members of the Nebria Latreille, 1802 and Leistus Frölich, 1799 genera.N. brevicollis is distinguished from others by a uniformly dark brown or black habitus; always with completely brown antennae.Humeral angles of the elytra are discontinuous and with a small protruding tooth, though this tooth can sometimes appear more as simply distinctly angled.The basal abdominal sternite is punctured laterally (Luff, 2007).It can be easily separated from its close relative N. salina by a fine pubescence of the dorsal surface of the hind tarsi, which are not present in N. salina.
Nebria brevicollis is a ubiquitous, widely distributed and commonly found beetle throughout the UK.It prefers the moister habitats of woodland, heathland, moorland and parkland, venturing into stable coastal (but not saline) areas.It can also be found in wasteland, industrial areas and gardens.It lives under rocks, logs and moist debris.Though native to temperate Europe, ranging through the Caucasus and Asia Minor, its range has expanded to North America, where it is considered an invasive species (LaBonte, 2011).This species is an opportunistic, omnivorous nocturnal predator.It has been recorded as feeding on Mollusca, earthworms, various arachnids, and other small insects, including other beetles, in both larval and imaginal stages of their lifecycles (Larochelle, 1990).This species can be found throughout the year but is most active from June to August.After an intensive feeding period they enter diapause, emerging to mate in the Autumn (Penney, 1969).Larvae are winter active, with the first adults appearing in late winter to early spring.
The Nebria genus is amongst the ground beetles capable of surviving at high altitudes (Gobbi, 2020).This ability, along with a eurytopic life-history, makes this genus of interest for climatechange studies.The genome sequence of the Nebriine described here is useful for investigations into species' ability to withstand and adapt to depauperate environments, in a world of increasing climatic instability (Butterfield, 1996), and its potential impact on native populations of other invertebrates as climate change and anthropogenic effects allow it to expand its ecological and geographical range.

Genome sequence report
The genome was sequenced from one female Nebria brevicollis specimen (icNebBrev1: Figure 1) collected from Wytham Woods (latitude 51.77, longitude -1.34).A total of 70-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 76-fold coverage in 10X Genomics read clouds was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 304 missing joins or mis-joins and removed three haplotypic duplications, reducing the scaffold number by 38.73%, and increasing the scaffold N50 by 246.17%.
The final assembly has a total length of 241.9 Mb in 424 sequence scaffolds with a scaffold N50 of 13.8 Mb (Table 1).Most (86.87%) of the assembly sequence was assigned to 15 chromosomal-level scaffolds, representing 14 autosomes and the X sex chromosome (Figure 2-Figure 5; Table 2).Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size.The order and orientation of scaffolds within the centromeric region of chromosomes 1, 3, 4, 8 and 10 is uncertain (Figure 5).The assembly has a BUSCO v5.3. 2 (Manni et al., 2021) completeness of 98.4% (single 97.9%, duplicated 0.5%), using the OrthoDB v10 endopterygota reference set.While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.

Genome annotation report
The N. brevicollis genome assembly was annotated using the Ensembl rapid annotation pipeline (Table 1; GCA_944738965.1).The resulting annotation includes 20,797 transcribed mRNAs from 11,021 protein-coding and 3,253 non-coding genes.

Sample acquisition and nucleic acid extraction
A female Nebria brevicollis (icNebBrev1) was collected in woodland habitat of the Great Wood, Wytham, Berkshire, UK (latitude 51.773, longitude -1.338) on 9 October 2019, using a pitfall trap.The specimen was collected and identified by Liam Crowley (University of Oxford), and preserved on dry ice using a CoolRack.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute.The icNebBrev1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Head and thorax tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing.
HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30.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 and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and HiSeq X Ten (10X) instruments.Hi-C data were also generated from abdomen tissue of icNebBrev1 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.et al., 2020).Table 3 contains a list of all software tool versions used, where appropriate.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the N. brevicollis assembly (GCA_944738965.1).Annotation was created primarily through

Sean Schoville
Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA Crowley and colleagues present the first genome sequence of Nebria brevicollis, an widespread and well studied ground beetle.The genome is an important contribution to our knowledge of beetle genomic diversity and the resources developed in the paper are of high quality.I found the paper to be well written and the graphics are nicely composed.
Among the existing beetle genomes, this is one of the smaller assemblies and perhaps worth discussing.It is also of note that a previous estimate of chromosome number in N. brevicollis is widely different (N 30): Serrano, J., 1982 1 .
Possible contamination: I was surprised, given previous genome reports, that no microbial contaminants/symbionts were found.However, the blobplot does have some unusual scatter.Perhaps a second approach, based on k-mer matching, might be helpful for a comprehensive check.

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Minor revisions: 2nd sentence of background: Typical convention is that "Nebria" should be spelled out if it starts a sentence, even if the full taxonomic name has been mentioned previously.

Are the datasets clearly presented in a useable and accessible format? Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Population genomics and comparative genomics of insects 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 Nebria brevicollis, icNebBrev1.1: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 241,934,194 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 (20,209,999 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (13,798,286 and 301,996 bp), respectively.The pale grey spiral shows the cumulative sequence 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/icNebBrev1.1/dataset/ CALYJB01/snail.

Figure 5 .
Figure 5. Genome assembly of Nebria brevicollis, icNebBrev1.1:Hi-C contact map.Hi-C contact map of the icNebBrev1.1 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=Uq6H4s_FTWuI6hhSy2sL3A.

Open Peer Review Current Peer Review Status: Version 1
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.
Sandro Patroca da SilvaEvandro Chagas Institute, Ananindeua, Brazil The research paper, titled "The Genome Sequence of Nebria brevicollis (Fabricius, 1792)," comprehensively elucidates the nuclear genome and mitogenome sequences of Nebria brevicollis, available in the public database.It meticulously outlines the methodology employed, providing a clear roadmap for potential replication and further exploration of this groundbreaking genomic study on this ground beetle species.

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.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
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.