The genome sequence of the Willow Beauty, Peribatodes rhomboidaria (Denis & Schiffermüller, 1775)

We present a genome assembly from an individual male Peribatodes rhomboidaria (the Willow Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 499.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,486 protein coding genes.


Background
The Willow Beauty (Peribatodes rhomboidaria) is a moth in the family Geometridae, a group in which many species have wings patterned with wavy lines, dots, and speckling, providing crypsis when settled with wings flat against the bark of a tree.The Willow Beauty has a pale brown ground colour, dark speckles, and a pair of black transverse lines converging sharply together at the trailing edge of the forewing.The species exhibits variation in ground colour, including a uniformly black melanic form thought to be due to a dominant allele and a grey variant (Ford, 1967;South, 1961;Waring et al., 2017).The wingspan is typically 35 to 45 mm in mainland Europe or 40 to 48 mm in the UK (Skinner & Wilson, 2009), with smaller specimens often seen late in the season.The larvae are polyphagous, feeding on the leaves of many broadleaved plants including hawthorn, privet, ivy and conifers (Henwood et al., 2020).The common name Willow Beauty, therefore, is a misnomer as the species does not favour willow and is not particularly beautiful.In Italy, France and Romania, P. rhomboidaria has been reported as an intermittent pest of vineyards; major damage can be caused by larvae which have overwintered feeding on the new buds of grapevine in spring (Busato et al., 2000;de Meirleire, 1979;Filip, 1998;Julei, 1984).This moth is widely distributed throughout Europe, including inland and coastal habitats in western Europe, and is primarily found in coastal locations in Scandinavia and around the Black Sea and Caspian Sea (GBIF Secretariat, 2022).In the UK, the Willow Beauty is common in gardens, woodlands, and scrub habitats in England and Wales, but less frequently recorded in Scotland (NBN Atlas Partnership, 2022;Randle et al., 2019).
The flight season and voltinism has been observed to be changing, with one generation per year and adult moths on the wing from June to August in the north of the UK and in Ireland, and a recent increase to two overlapping flight seasons from May to October in southern England (Waring et al., 2017).
Molecular cytogenetic analyses have revealed a particularly large and heterochromatic W chromosome in females (Hejníčková et al., 2021), with low-depth genome sequencing and chromosome hybridization showing that the W chromosome is rich in female-enriched DNA repeats (Hejníčková et al., 2022).The assembled genome sequence for P. rhomboidaria will facilitate the study of the genetic basis of cryptic colouration, polymorphism, and polyphagy, and contribute to the growing dataset of genomic resources for understanding lepidopteran biology.

Genome sequence report
The genome was sequenced from one male Peribatodes rhomboidaria (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 44-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 74-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 17 missing or mis-joins and removed one haplotypic duplication, reducing the assembly length by 0.17% and the scaffold number by 16.28%. The final assembly has a total length of 499.7 Mb in 36 sequence scaffolds with a scaffold N50 of 17.1 Mb (Table 1).Most (99.96%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes and the Z 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/190356.

Sample acquisition and nucleic acid extraction
A male Peribatodes rhomboidaria (specimen number Ox000663, individual ilPerRhom1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.77, longitude -1.34) on 20 July 2020.The specimen was collected and identified by Douglas Boyes (University of Oxford).The specimen was taken from woodland habitat using a light trap.The specimen was snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilPerRhom1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Abdomen 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   as described previously (Howe et al., 2021).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., 2022), which performed annotation using MitoFinder (Allio et al., 2020).The genome was analysed and BUSCO scores generated within the BlobToolKit environment (Challis et al., 2020).Table 3 contains a list of all software tool versions used, where appropriate.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the P. rhomboidaria assembly (GCA_934047225.1) in Ensembl Rapid Release.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: The genome assembly report for the Willow Beauty is well written and describes in detail the process of sequencing and assembling the genome.The authors use a "well oiled" pipeline to assemble this high quality genome.The couple of minor suggestions that authors may or may not accept are listed below: In the sentence ":The common name Willow Beauty, therefore, is a misnomer as the species does not favour willow and is not particularly beautiful" , the part that state "...and is not particularly beautiful" should be removed.Beauty is in the eyes of the beholder, and we do not know the etymology of the name.Therefore, I believe that pointing out that this insect does not favour Willow is sufficient.

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The sentence "The genome was sequenced from one male Peribatodes rhomboidaria (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.34)" in the Genome Sequence Report section and the sentence "A male Peribatodes rhomboidaria (specimen number Ox000663, individual ilPerRhom1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.77, longitude -1.34) on 20 July 2020" in the methods section duplicates the same information and may be revised.Reviewer Expertise: Genetics, molecular biology, population genetics 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 Peribatodes rhomboidaria, ilPerRhom1.1: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 499,728,750 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 (24,949,269 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (17,104,115 and 12,037,098 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 lepidoptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilPerRhom1.1/dataset/CAJVRP01.1/snail.
Legal and ethical review process for Darwin Tree of Life Partner submitted materialsThe 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.

Figure 5 .
Figure 5. Genome assembly of Peribatodes rhomboidaria, ilPerRhom1.1:Hi-C contact map.Hi-C contact map of the ilPerRhom1.1 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=Sa1ZSyVfQ96U6daRyLhLOA,

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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.

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.