The genome sequence of the Red Twin-spot Carpet, Xanthorhoe spadicearia (Denis & Schiffermüller, 1775) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual female Xanthorhoe spadicearia (the Red Twin-spot Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 276.7 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 17.03 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,396 protein coding genes.


Background
The Red Twin-spot Carpet (Xanthorhoe spadicearia) is a geometrid moth that occurs in a wide variety of habitats across Britain.In Ireland it is more scarce, and records are more widely scattered (GBIF Secretariat, 2023).Its caterpillars feed on a wide variety of herbaceous plants (Henwood et al., 2020).There are two generations each year, and adult moths from both generations are now recorded earlier in the year than they were in the 1970s (Randle et al., 2019;Waring et al., 2017).
The genome of the Red Twin-spot Carpet, Xanthorhoe spadicearia, 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 Xanthorhoe spadicearia, based on one female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one female Xanthorhoe spadicearia (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 62-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 3 missing joins or mis-joins and removed one haplotypic duplication. The final assembly has a total length of 276.7 Mb in 32 sequence scaffolds with a scaffold N50 of 10.3 Mb (Table 1).Most (99.99%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes and the Z sex chromosome.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.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).There is half-coverage of the Z chromosome, and the species appears to be a ZO female.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/934904.

Sample acquisition and nucleic acid extraction
A female Xanthorhoe spadicearia (specimen ID Ox001823, ToLID ilXanSpad1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2021-07-24 using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford).(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 Xanthorhoe spadicearia assembly (GCA_947086425.1) 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   Table 3. Software tools: versions and sources.

Software tool Version
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; DNA fragmentation; and fragmented DNA clean-up.The sample was prepared for DNA extraction at the WSI Tree of Life laboratory: the ilXanSpad1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing(Jay et al., 2023).Tissue from the head and thorax was homogenised using a PowerMasher

Figure 2 .
Figure 2. Genome assembly of Xanthorhoe spadicearia, ilXanSpad1.1: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 276,691,867 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 (14,446,717 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (10,252,953 and 5,980,574 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/ilXanSpad1.1/dataset/CAMTYT01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Xanthorhoe spadicearia, ilXanSpad1.1:Hi-C contact map of the ilXanSpad1.1 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=ZFpT9HYSTwajfMQ9VHRHkg.

Table 1 . Genome data for Xanthorhoe spadicearia, ilXanSpad1.1. Project accession data
SequencingPacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers' instructions.Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit.DNA and RNA sequencing was performed by the Scientific Operations core