The genome sequence of the Light Emerald, Campaea margaritaria (Linnaeus, 1761)

We present a genome assembly from an individual male Campaea margaritaria (the Light Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 335.2 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,403 protein coding genes.


Background
The Emerald moths are a large group of moths which belong to two distinct sub-families of the Geometridae family: most belong to Geometrinae, while the Light Emerald, Campaea margaritaria, belongs to Ennominae (Murillo-Ramos et al., 2019).A newly emerged C. margaritaria has a pale green colour that fades to white within days, as the green wing pigment geoverdin is unstable (Cook et al., 1994).This Geometrid moth also has a distinctive hooked red tip to the forewing (Waring et al., 2017).
A common resident that is well distributed and frequently found throughout the Atlantic Archipelago of Britain and Ireland (GBIF Secretariat, 2023), C. margaritaria is not currently a species under threat (Butterfly Conservation, 2023).It is most abundant in broadleaved woodland but also found in scrub, hedgerows, parks, gardens and in urban areas, often disturbed while resting under leaves.There is one generation in northern England, Scotland and Ireland and two generations in the southern half of Britain, with the moth being seen from late May to early October (Waring et al., 2017).The C. margaritaria larva, which has a distinctive fringe on the underside of its body, feeds on a variety of deciduous trees, including apple, beech, birch, elm, hawthorn, hazel and oak as well as several species of Prunus (Waring et al., 2017).The larva lives on the foliage of deciduous trees, overwintering along the stems of the foodplant (Kimber, 2023).
A pilot study analysing the diet of bats in Belgium orchards applied DNA metabarcoding to find evidence of C. margaritaria in Plecotus auritus faecal samples (Dekeukeleire et al., 2020).The completed genome sequence might be used in areas of research such as this, continuing work to identify biological pest suppressors such as bats on invasive agricultural pests.We present a chromosomally complete genome sequence for Campaea margaritaria based on one male specimen from Wytham Woods, Oxfordshire as part of the Darwin Tree of Life Project.

Genome sequence report
The genome was sequenced from one male Campaea margaritaria (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 48-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 115-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 6 missing joins or mis-joins, reducing the scaffold number by 16.22%. The final assembly has a total length of 335.2 Mb in 31 sequence scaffolds with a scaffold N50 of 12.1 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.The whole 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 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/934813.

Sample acquisition and nucleic acid extraction
A male Campaea margaritaria (specimen ID Ox000674, ToLID ilCamMarg1) 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 was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilCamMarg1 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 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

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with

Saskia Wutke
Department of Environmental and Biological Sciences, University or Eastern Finland, Joensuu, Finland This data note reports the genome of the Light Emerald (Campaea margaritaria), a geometrid moth.Genome sequencing, assembly and annotation is based PacBio HiFi, 10X Genomics and Hi-C data.Overall, the dataset is presented clearly and concisely.The methods are state-of-the-art.Yet, reproducibility would benefit from further details concerning the settings of the employed software tools.Moreover, the relevance of this genome report could be explained more in the background section.For example, it is mentioned briefly that the genome can be used for work on invasive agricultural pests but it is not mentioned anywhere if Campaea margaritaria falls into this category.Nevertheless, this genome provides a valuable data resource for future research on insect comparative genomics, biodiversity and evolution.
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 Competing Interests: No competing interests were disclosed.
Reviewer Expertise: evolutionary genetics, insect genomics, phylogenomics 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 Campaea margaritaria, ilCamMarg1.1: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 335,226,495 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 (18,728,427 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (12,093,622 and 8,177,772 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/ilCamMarg1.1/dataset/ilCamMarg1_1.1/snail.

Figure 5 .
Figure 5. Genome assembly of Campaea margaritaria, ilCamMarg1.1:Hi-C contact map of the ilCamMarg1.1 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=fCFg_877SRicnS1Ytr6jWQ.

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

Table 3 . Software tools: versions and sources. Software tool Version Darwin
Tree of Life (DToL) project.All raw sequence data and the assembly have been deposited in INSDC databases.Raw data and assembly accession identifiers are reported in Table 1.

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.
Jaakko L.O.PohjoismäkiDepartment of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland I have no reservations regarding the presented work.The genome assembly and annotation follows the DToL pipeline.The species is a great addition to the growing list of moth genomes.However, it would have been great to have the heterogametic female sex sampled.

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.