The genome sequence of the oak pinhole borer, Platypus cylindrus Fabricius, 1792

We present a genome assembly from an individual male Platypus cylindrus (the oak pinhole borer; Arthropoda; Insecta; Coleoptera; Curculionidae). The genome sequence is 147.5 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,468 protein coding genes.


Background
The genome of the oak pinhole borer, Platypus cylindrus, 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 Platypus cylindrus, based on one male specimen from Bookham Commons, England, UK.

Genome sequence report
The genome was sequenced from one male Platypus cylindrus (Figure 1) collected from Bookham Commons, England, UK (51.29, -0.39).A total of 181-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 34 missing joins or mis-joins and removed 4 haplotypic duplications, reducing the assembly length by 0.38% and the scaffold number by 16.13%, and increasing the scaffold N50 by 6.57%.
The final assembly has a total length of 147.5 Mb in 25 sequence scaffolds with a scaffold N50 of 15.2 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 (96.77%) of the assembly sequence was assigned to 8 chromosomal-level scaffolds, representing 6 autosomes and the X and Y sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).Y chromosome scaffolds were identified but were not scaffolded, as Hi-C data are from a female sample.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.

Sample acquisition and nucleic acid extraction
The specimen used for genome sequencing, a male Platypus cylindrus (specimen ID NHMUK014439781, ToLID icPla-Cyli4), was collected from Bookham Commons, England, UK (latitude 51.29, longitude -0.39) on 2021-09-19.The specimen was collected by Maxwell Barclay, Michael Geiser, Danaë Vassiliades, Will Bayfield Farrell and Joana Cristovao (Natural History Museum) and identified by Maxwell Barclay (Natural History Museum), and then preserved by dry freezing at -80°C.
The specimen used for Hi-C sequencing was a female Platypus cylindrus (specimen ID Ox001653, ToLID icPlaCyli3) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.33) on 2021-07-08.The specimen was collected and identified by Mark Telfer (independent researcher) 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, fragmentation, and clean-up.In sample preparation, the icPlaCyli4 sample was weighed and dissected on dry ice (Jay et al., 2023).Tissue from the head and thorax was homogenised using a PowerMasher II tissue disruptor (Denton et al., 2023a).
HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol (Oatley et al., 2023).The DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 31 (Bates et al., 2023).Sheared DNA was purified by solid-phase reversible immobilisation (Strickland et al., 2023): 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  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

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Platypus cylindrus assembly (GCA_949748235.1) 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.

Software tool Version
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

Luciano Palmieri
Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, BZ, Italy This manuscript presents the genome assembly of Platypus cylindrus, as part of the Darwin Tree of Life Project, which aims to sequence all named eukaryotic species in Britain and Ireland.The assembled genome spans 147.5 Mbases, with most of the sequence scaffolded into 8 chromosomal pseudomolecules, including the X and Y sex chromosomes.Additionally, the mitochondrial genome (19.29 Kbases) was successfully assembled, and automatic gene annotation identified 13,468 protein-coding genes.The genome was sequenced using PacBio HiFi long reads from a male specimen, and scaffolded with Hi-C data.The assembly is of high quality, with a BUSCO completeness score of 96.2%.
This study is part of a growing body of work from the same group, which has developed and refined an efficient pipeline for generating high-quality genome assemblies.This pipeline has been used to describe the genomes of dozens of insect species, making significant contributions to our understanding of insect genomics.The rationale for creating this dataset is not often clear, while it provides valuable data for understanding the genetics of P. cylindrus, the broader ecological and evolutionary context of this species is less emphasized.Nonetheless, the described genome provides a foundational resource for further research into the genetics, evolution, and ecological role of this species.

Sophie Tandonnet
Universitat de Barcelona, Barcelona, Catalonia, Spain In this note, the authors present a highly complete and continuous genome assembly for the species Platypus cylindrus.It is an addition to the growing database of high quality genomes coming from the Darwin Tree of Life project.The note is well written and the data correctly referenced and available.The annotation is available containing 13,468 protein coding genes.
Below are some suggestions, questions and general comments minor comment: I missed reading more background on this species: ecology, special characteristics, lifestyle, habitat, etc…

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The abstract states that "Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X and Y sex chromosomes."but later in the report it is said "Y chromosome scaffolds were identified but were not scaffolded".Looking at the PRJEB60808 project page on ENA, I did find the Y chromosome as a single sequence.So I'm confused: is the Y chromosome on ENA only a part of the Y? Or were all the scaffolds tagged as Y collated together?Could the authors clarify this point?
○ Related to the previous point: how were the X and Y chromosome material identified?Was a coverage analysis performed?Was it based on synteny?If so, with which species?I think it is very cool to have the Y chromosome (which is usually hard to assemble well) and it may be useful for other researchers to have more information on how the Y was identified.

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Add "from an additional female specimen" in the sentence "Primary assembly contigs were scaffolded with chromosome conformation Hi-C data." in the report section.This is because ○ other assemblies have both the HiC and the Pacbio/10X sequencing from the same individual.
For the genome annotation: please add the protein database or transcriptome data used as this can influence the completeness of the annotation.Is 13,468 protein coding genes around the expected number of genes for a beetle?What is the proteome BUSCO score?

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The PRJEB59383 page states that "This project collects the genomic and transcriptomic data generated for Platypus cylindrus".However I couldn't locate the transcriptomic data.

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The MT genome is 19.29 kilobases in length: did the authors check for internal duplication in this sequence?Reviewer Expertise: Evolutionary Biology, Genetics, sex determination, bioinformatics, non-model organisms 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, however I have significant reservations, as outlined above.

Figure 1 .
Figure 1.Photographs of the Platypus cylindrus (icPlaCyli4) specimen used for genome sequencing: a) dorsal view, b) lateral view, c) ventral view.

Figure 2 .
Figure 2. Genome assembly of Platypus cylindrus, icPlaCyli4.1: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 147,483,955 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 (53,441,370 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (15,234,454 and 11,925,517 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/icPlaCyli4_1/dataset/icPlaCyli4_1/snail.

Figure 3 .
Figure 3. Genome assembly of Platypus cylindrus, icPlaCyli4.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icPlaCyli4_1/dataset/icPlaCyli4_1/blob.

Figure 4 .
Figure 4. Genome assembly of Platypus cylindrus, icPlaCyli4.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/icPlaCyli4_1/dataset/icPlaCyli4_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Platypus cylindrus, icPlaCyli4.1:Hi-C contact map of the icPlaCyli4.1 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=b-vYOkPgQiCy-EjqgJSJdQ.

○Figure 5 :
Figure 5: Why are there "white bands" (no contacts) in the Hi-C contact map? ○

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

the rationale for creating the dataset(s) clearly described? Partly 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.
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.