The genome sequence of the Phoenix, Eulithis prunata (Linnaeus, 1758)

We present a genome assembly from an individual male Eulithis prunata (the Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 263.1 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 15.9 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,023 protein coding genes.


Background
The Phoenix, Eulithis prunata, is a moth in the family Geometridae distributed widely across northern Europe and Scandinavia, with scattered records from Eastern Europe and across Russia to Mongolia, China and Japan.There are also a few records and museum specimens from Canada and the United States, including some from the 1930s, suggesting occasional accidental importation (GBIF Secretariat, 2022).The species is common across most of southern Britain, although never abundant, and is found most frequently in gardens or cultivated areas where the larval food plants grow (Randle et al., 2019;South, 1961).E. prunata is larger than most members of the Geometridae found in Europe (wingspan 30-35 mm) and has a chocolatebrown deeply-lobed cross band on the forewings, outlined in white.In northern Europe, the adult moth is on the wing primarily in July and August, and will come to light.Eggs are laid on the bark of the food plant, usually blackcurrant (Ribies nigrum), redcurrant (R. rubrum) or gooseberry (R. uva-crispa), but embryonic development is delayed and the first instar larvae does not hatch until the following April.The larvae then feed on leaves of the currant or gooseberry bushes, pupating around June in a web spun between leaves (Newman, 1869;South, 1961;Waring et al., 2017).
A genome sequence for E. prunata will facilitate research into embryonic diapause and adaptations for host plant specificity, and will also contribute to the growing set of genomic resources for Lepidoptera.

Genome sequence report
The genome was sequenced from one male Eulithis prunata (Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.31).A total of 69-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 177-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected one missing join, reducing the scaffold number by one.
The final assembly has a total length of 263.1 Mb in 30 sequence scaffolds with a scaffold N50 of 9.4 Mb (Table 1).The whole 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 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/934839.

Sample acquisition and nucleic acid extraction
A male Eulithis prunata (ilEulPrun1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.31) on 25 June 2020.The specimen was taken from fen habitat by Douglas Boyes (University of Oxford) by netting.The specimen was identified by the collector and snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEulPrun1 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 spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

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 NovaSeq 6000 (10X) instruments.Hi-C data were also generated from head and thorax tissue of ilEulPrun1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.performed annotation using MitoFinder (Allio et al., 2020).To evaluate the assembly, MerquryFK was used to estimate k-mer completeness and consensus quality (QV) (Rhie et al., 2020).The genome was analysed, and BUSCO scores (Manni et al., 2021;Simão et al., 2015) were generated within the BlobToolKit environment (Challis et al., 2020).Table 3 provides a list of 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 Eulithis prunata assembly (GCA_918843925.1). in Ensembl Rapid Release.

Ethics and compliance issues
The materials that have contributed to this genome

Muzafar Riyaz
St Xavier's College, Palayamkottai, Tamil Nadu, India The paper titled "The genome sequence of the Phoenix, Eulithis prunata" by Douglas Boyes and Peter W.H. Holland, along with their collaborators, provides the genome assembly of Eulithis prunata, commonly known as the Phoenix, a species of moth belonging to the Geometridae family.The authors have meticulously carried out genome sequencing, assembly, and annotation, offering a detailed insight into the genetic makeup of this fascinating moth.The inclusion of detailed methods and data availability information in the paper demonstrates transparency and facilitates reproducibility for future researchers interested in exploring this genome.

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: Genomics; Phylogenomics; Moths 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.
The article reports the Eulithis prunata (the Phoenix; Arthropoda; Insecta; Lepidoptera; Geometridae).It is a merely descriptive article that reports the complete genome of this insect.
There is no extra scientific contribution, only the description of this insect's genome components and mitochondria.The methodology used explains how the genome sequencing was carried out.

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: Molecular biology of baculoviruses as insect biocontrol agents 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 Eulithis prunata, ilEulPrun1.1: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 263,147,802 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest sequence present in the assembly (12,422,325 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (9,415,980 and 6,527,104 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/ilEulPrun1.1/dataset/ ilEulPrun1_1.1/snail.
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.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

Figure 5 .
Figure 5. Genome assembly of Eulithis prunata, ilEulPrun1.1:Hi-C contact map.Hi-C contact map of the ilEulPrun1.1 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=JyygYVU5TBmpYhjfwKQK-Q.

Open 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.