The genome sequence of a weevil, Polydrusus cervinus (Linnaeus, 1758)

We present a genome assembly from an individual female Polydrusus cervinus (a weevil; Arthropoda; Insecta; Coleoptera; Curculionidae). The genome sequence is 713.4 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 18.22 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,058 protein coding genes.


Background
The genome of the weevil, Polydrusus cervinus, 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 Polydrusus cervinus, based on one female specimen from Fulham, London, UK.

Genome sequence report
The genome was sequenced from one female Polydrusus cervinus (Figure 1) collected from Fulham, London, UK (51.48, -0.18).A total of 38-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 21 missing joins or mis-joins and removed 7 haplotypic duplications, reducing the assembly length by 0.55% and the scaffold number by 48.15%.
The final assembly has a total length of 713.4 Mb in 14 sequence scaffolds with a scaffold N50 of 72.8 Mb (Table 1).Most (99.99%) of the assembly sequence was assigned to 11 chromosomal-level scaffolds, representing 10 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).A large heterozygous indel was observed on chromosome 6 (8-17.3Mb).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/202137.

Sample acquisition and nucleic acid extraction
A female Polydrusus cervinus (specimen ID NHMUK014400214, individual icPolCerv1) was collected from Fulham, London, UK (latitude 51.48, longitude -0.18) on 2021-05-09.The specimen was collected and identified by Maxwell Barclay (Natural History Museum) and dry-frozen at -80°C.
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 icPolCerv1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing (as per the protocol at https://dx.doi.org/10.17504/protocols.io.x54v9prmqg3e/v1).For sample homogenisation, thorax tissue was cryogenically disrupted using the Sample Homogenisation: Covaris cryoPREP® Automated Dry Pulverizer protocol (https://dx.doi.org/10.17504/protocols.io.eq2lyjp5qlx9/ v1).HMW DNA was extracted by means of the Automated   was purified by manual solid-phase reversible immobilisation (SPRI) (as per the protocol at https://dx.doi.org/10.17504/protocols.io.kxygx3y1dg8j/v1).In brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA.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 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) instruments.Hi-C data were also generated from head and thorax tissue of icPolCerv1 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).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    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 Polydrusus cervinus assembly (GCA_935413205.1) 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 The one point where the provided information is perhaps not complete is regarding the gene annotation procedure.This was performed as part of Ensembl's Rapid Annotation pipeline and not described in detail here.The link provided ( https://rapid.ensembl.org/Polydrusus_cervinus_GCA_935413205.1/Info/Index)does have some additional information, but lacks detail on which database versions and exact taxonomic divisions were used as protein evidence to run BRAKER2.I believe this information could be easily added to the methods.

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? Partly
Are the datasets clearly presented in a useable and accessible format?Yes

Figure 2 .
Figure 2. Genome assembly of Polydrusus cervinus, icPolCerv1.1: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 713,374,358 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 (114,676,269 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (72,832,772 and 43,617,443 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/icPolCerv1.1/dataset/CAKXYR01/snail.
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.

Figure 5 .
Figure 5. Genome assembly of Polydrusus cervinus, icPolCerv1.1:Hi-C contact map of the icPolCerv1.1 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=LKZX3gxoRFm36P4kf8iabg.
for Science and Technology, Riyadh, Saudi ArabiaBarclay et al. conducted  this study to present the weevil Polydrusus cervinus genome sequence as part of the Darwin Tree of Life Project, aiming to sequence all named eukaryotic species in the Atlantic Archipelago.This work generated a high-quality genome assembly of 713.4 megabases, including 11 chromosomal pseudomolecules and the mitochondrial genome, with 23,058 proteincoding genes identified.The assembly achieved a BUSCO completeness of 99.2%, utilizing Pacific Biosciences single-molecule HiFi long reads and meticulous manual curation.This effort contributes significantly to biodiversity research and the understanding of eukaryotic genomes, highlighting the importance of this study in the broader scientific community.The study could benefit from comparing its genome with those of similar species or other weevils to gain insights into evolutionary relationships.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.Reviewer Expertise: bioinformatics, genomics, and evolutionary biology I confirm that I have read this submission and believe that I have an appropriate level of