The genome sequence of the Dingy Skipper, Erynnis tages (Linnaeus, 1758) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual male Erynnis tages (the Dingy Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 329.3 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 15.51 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,237 protein coding genes.


Background
The Dingy Skipper, Erynnis tages (Linnaeus, 1758), is a small butterfly of the family Hesperiidae with a Palearctic distribution.It is present in most of Europe and in Asia up to the Amur region (Tolman & Lewington, 1997).It is widely distributed in the UK, being found throughout most of England, and also has some populations in northern Scotland, and Ireland.
The upper side of Dingy Skipper wings is dark brown and lacks clearly defined bands.It also presents small, white marginal spots, adjacent to the fimbriae.This species has a slight sexual dimorphism: males have a costal fold in the forewings; females a scent organ near the tip of the abdomen (de Jong, 1975).
Erynnis tages inhabits open and sunny grasslands and many other habitats with sparse vegetation, across a wide range of altitudes (Gutiérrez et al., 1999).It is an oligophagous species that mainly oviposits on the legume species Lotus corniculatus and Hippocrepis comosa, although it can also use other Fabaceae.Females lay eggs singly on the upper side of leaves.In the southern part of its range, the species is typically bivoltine, with one generation between April and May and another between July and August.At higher altitudes and in northern populations, the second generation is partial.It overwinters as a last instar larva (Tolman & Lewington, 1997).The species is classified as Least Concern both in the European Red List of Butterflies (Van Swaay et al., 2010) and in the UK Red List (Fox et al., 2022).In parts of the Mediterranean region this species is declining in range (e.g. in Catalonia, Vila et al., 2018), apparently due to the loss of open habitats and also to the increasingly intense and frequent summer droughts.Its haploid chromosome number is 31 (Lorković, 1941;Lukhtanov, 2014).

Genome sequence report
The genome was sequenced from one male Erynnis tages (Figure 1) collected from Gheorgheni,Romania (46.65,25.37).A total of 29-fold coverage in Pacific Biosciences singlemolecule HiFi long reads and 112-fold coverage in 10X Genomics read clouds was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 56 missing joins or misjoins and removed 6 haplotypic duplications, reducing the assembly length by 0.88% and the scaffold number by 45.21%, and increasing the scaffold N50 by 1.49%.
The final assembly has a total length of 329.3 Mb in 40 sequence scaffolds with a scaffold N50 of 11.9 Mb (Table 1).Most (99.93%) 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 mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Sample acquisition and nucleic acid extraction
A male Erynnis tages (ilEryTage1) was collected from Gheorgheni, Romania (latitude 46.65, longitude 25.37) on 2018-07-21 using a net.The collectors were Konrad Lohse, Alex Hayward, Dominik Laetsch and Roger Vila, and Roger Vila identified the specimen.The specimen was frozen from live in a dry shipper.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEryTage1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Tissue from the whole organism was disrupted using a Nippi Powermasher fitted with a Bio-Masher 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 HiSeq X Ten (10X) instruments.Hi-C data were also generated from tissue of ilEryTage1 using the Arima2 kit and sequenced on the HiSeq X Ten instrument.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.
A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020).To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury (Rhie et al., 2020).This

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Erynnis tages assembly (GCA_905147235.1) in Ensembl Rapid Release.

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a Tree of Life collaborator.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 • Legality of collection, transfer and use (national and international) Each transfer of samples is undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Tree of Life collaborator, Genome Research Limited (operating as the Wellcome Sanger Institute) and in some circumstances other Tree of Life collaborators.

Figure 1 .
Figure 1.Forewings and hindwings of the Erynnis tages (RO_ ET_1014, ilEryTage1) specimen from Gheorgheni, Romani, from which the genome was sequenced.(A) Dorsal surface view of wings (B) Ventral surface view of wings.

Figure 2 .
Figure 2. Genome assembly of Erynnis tages, ilEryTage1.1: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 329,358,918 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 (17,495,979 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (11,903,105 and 7,488,951 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/ilEryTage1.1/dataset/ CAJHUV01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Erynnis tages, ilEryTage1.1:Hi-C contact map of the ilEryTage1.1 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=SCajeZwCRXap6yP_XemUOQ.