The genome sequence of the Early Thorn, Selenia dentaria (Fabricius, 1775)

We present a genome assembly from an individual male Selenia dentaria (the Early Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 1,030.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,390 protein coding genes.


Background
Selenia dentaria, the Early Thorn, belongs to the Geometridae family of moths, with a forewing length of 14-23 mm (Waring et al., 2017).The key diagnostic feature for S. dentaria is its resting position, unlike other British Thorn moths, it holds its wings pressed together and upwards behind the back, resembling a butterfly (Lewis, 2023;Waring et al., 2017).The Early Thorn is variable in colour between generations and occurrence locations, but generally has 3 crosslines on the forewings with a dark staining colouration by the forewing apex (Lewis, 2023;Waring et al., 2017).
Selenia dentaria is a bivoltine species, with one generation from mid-February to May and a second from July to September, can be seen on the wing at dusk and readily comes to light.The larvae feed on a variety of woody broadleaved plants, including hawthorn, blackthorn, hazel and bog myrtle.The Early Thorn overwinters as a pupa spun between plant debris or leaves (Waring et al., 2017).
In the UK, Selenia dentaria is distributed in a variety of habitats from woodland and scrubs to urban areas and gardens; it is a common and widespread species, frequent in England, Wales, Scotland and Ireland (Waring et al., 2017).Globally, S. dentaria is distributed throughout northern Europe, across the Palearctic to Mongolia and the Russian far East (GBIF Secretariat, 2023).
The larvae of Selenia dentaria mimic the twigs of hostplant species, e.g.hawthorn (Crataegus monogyna).Previous studies have shown this is effective to avoid predation from avian predators, test trials showed that chicks who had been exposed to S. dentaria caterpillars and twigs of the mimicked species showed a greater latency to predate upon the caterpillar, increasing in their caution with handling twig-mimics (Cuthill, 2019;Edmunds, 1974;Skelhorn & Ruxton, 2013;Yu et al., 2022).The full genome for S. dentaria will give us insights into how species genetically developed these kinds of mimicry and which gene expressions or timing in gene expressions lead to their physical appearance.This genome of Selenia dentaria 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 Selenia dentaria, based on two specimens collected from Wytham Woods, Oxfordshire.

Genome sequence report
The genome was sequenced from one male Selenia dentaria (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.34).A total of 25-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 34-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 80 missing joins or mis-joins and removed 5 haplotypic duplications, reducing the assembly length by 0.19% and the scaffold number by 41.23%.
The final assembly has a total length of 1,030.8Mb in 67 sequence scaffolds with a scaffold N50 of 35.3 Mb (Table 1).A summary of the assembly statistics is shown in Figure 2, 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 (99.92%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes and the Z 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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/934894.

Sample acquisition and nucleic acid extraction
A male Selenia dentaria (specimen ID Ox000698, ToLID ilSelDent1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2020-07-20 using a light trap.The specimen  DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilSelDent1 sample was weighed and dissected on dry ice with head and thorax 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 using the 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

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 Illumina HiSeq 4000 and Illumina NovaSeq 6000 (10X) instruments.Hi-C data were also generated from head and thorax tissue of ilSelDent1 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).One round of polishing was performed by aligning 10X Genomics read data to the assembly with Long Ranger ALIGN, calling variants with FreeBayes (Garrison & Marth, 2012).The assembly was then scaffolded   Table 3. Software tools: versions and sources.

Software tool Version
with Hi-C data (Rao et al., 2014) using SALSA2 (Ghurye et al., 2019).The assembly was checked for contamination and corrected 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., 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.
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 Selenia dentaria assembly (GCA_917880725.1) 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

Kuppusamy Sivasankaran
Entomology Research Institute, Loyola College, Chennai, Tamil Nadu, India I appreciate the authors for assembling the genome sequence of Early Thorn, Selenia dentaria (Fabricius, 1775).Using 67 scaffolds, the authors sequenced approximately 1030.8 mega bases of the genome assembly.They have used standard methods for DNA isolation and followed appropriate software for the sequence assembly and annotations.
The minor clarification is given below.
In the background of the article authors have given the genus name Selenia dentaria full name and short name continuously.First time the genus name can be given in full name then subsequently can be given in short form like S. dentaria.
In the background third line "can be seen on the wing at dusk and readily comes to light".This message is not appropriate here and confusing.The sentence can be deleted or elaborate meaningfully.
In the page no 6 para second the sentence can be modified as DNA was extracted at the Darwin Tree of Life laboratory and Wellcome Sanger Institute (WSI).
Overall, I confirm that the article is accepted for scientific standard

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.
Reviewer Expertise: Phylogenetic analysis of Noctuoidea moths using mitogenome sequence 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.

Jullien M Flynn
Whitehead Institute for Biomedical Research, Cambridge, MA, USA In this Data Note, the authors present a genome assembly for Selenia dentaria, as part of the Darwin Tree of Life Project.The genome assembly is of high quality and the figures shown are informative.The assembly is publicly available.I only have a couple of minor suggestions for clarity: 1) It is mentioned that the assembly is based on two specimens, but DNA extraction and sequencing is described to be only from a single male.Please clarify.
2) The last part of this sentence is unclear: "Selenia dentaria is a bivoltine species, with one generation from mid-February to May and a second from July to September, can be seen on the wing at dusk and readily comes to light."It is not clear what can be seen on the wing at dusk.Please separate this last idea into a new sentence or show how it is clearly connected.

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.
Reviewer Expertise: Evolutionary genomics 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 Selenia dentaria, ilSelDent1.1: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 1,030,772,253 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 (54,712,836 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (35,319,394 and 24,754,819 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/Selenia%20dentaria/dataset/CAKJUM01.1/snail.
was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

Figure 5 .
Figure 5. Genome assembly of Selenia dentaria, ilSelDent1.1:Hi-C contact map of the ilSelDent1.1 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=bMrvoXgaTr6WoTUe_xF-aQ.

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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.