The genome sequence of the Oak-tree Pug, Eupithecia dodoneata (Guenée, 1858)

We present a genome assembly from an individual male Eupithecia dodoneata (the Oak-tree Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 353.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.


Background
The Oak-tree Pug Eupithecia dodoneata is a small and delicately-patterned moth in the family Geometridae found widely across Europe, with scattered records from Asia Minor and North Africa (GBIF Secretariat, 2022). The forewings have a light grey ground colour, crossed by bands of brown and dark grey, with a prominent black discal spot. In the UK, the moth is common is woodlands and suburban areas in the south of England and Wales where oaks are present (Riley & Prior, 2003). The moth is univoltine in the UK, with adults on the wing in May and June, larvae developing through summer, and pupae overwintering. The commonest larval food plants in the north of Europe are pedunculate oak Quercus robur and holm oak Q. ilex, with indications from rearing that larvae also eat the fleshy sepals around the fruits of hawthorn Crataegus monogyna (Haggett, 1992). In Turkey, downy oak Q. pubescens is also used as a food plant (Torun & Seven Çalişkan, 2016) and in Italy E. dodoneata was found to be the commonest oak-feeding species in woodlands of cork oak Q. suber (Scalercio, 2022).
A genome sequence for E. dodoneata will facilitate studies investigating molecular adaptations to oak feeding and will contribute to the growing set of genomic resources for Lepidoptera.

Genome sequence report
The genome was sequenced from one male Eupithecia dodoneata ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.32). A total of 53-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 five missing or mis-joins, reducing the scaffold number by 5.71%.
The final assembly has a total length of 353.7 Mb in 33 sequence scaffolds with a scaffold N50 of 12.6 Mb (Table 1). Most (99.98%) 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 estimated Quality Value (QV) of the final assembly is 70.8 with k-mer completeness of 100%, and the assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 98.0% (single 97.6%, duplicated 0.4%) using the lepidoptera_odb10 reference set (n = 5,286).

Sample acquisition and nucleic acid extraction
A male Eupithecia dodoneata (ilEupDodo1) was collected from Wytham Woods, Oxfordshire, UK (biological vicecounty: Berkshire) (latitude 51.77, longitude -1.32) on 28 May 2021. The specimen was taken from woodland habitat by Douglas Boyes (University of Oxford) using a light trap. 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 ilEupDodo1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Whole organism 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. 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 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) instrument. Hi-C data were also generated from tissue of ilEupDodo1 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
To evaluate the assembly, MerquryFK was used to estimate consensus quality (QV) scores and k-mer completeness (Rhie et al., 2020). The genome was analysed and BUSCO scores (Simão et al., 2015;Manni et al., 2021) were generated within the BlobToolKit environment (Challis et al., 2020).     The genome sequence is released openly for reuse. The Eupithecia dodoneata genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1. 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.