The genome sequence of the Chevron, Eulithis testata (Linnaeus, 1761)

We present a genome assembly from an individual male Eulithis testata (the Chevron; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 308.1 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 16,167 protein coding genes.


Background
The Chevron, Eulithis testata, is a medium sized geometrid moth, quite variable in ground colour, often with a beautiful mixture of yellowish scales frosted with grey on the forewing, distinguished by a series of six strongly angled chevron markings following one another, and a somewhat semicircular brown blotch at the termen (Figure 1).The Chevron emerges in late June or July and flies (at dusk) until mid-September in the UK (Randle et al., 2019), overwintering as an egg.
The Chevron is found in a range of habitats especially moorland and heathland, also marshes and sand dunes (Randle et al., 2019).Its larval foodplants comprise mainly different shrubs particularly Salix species, as well as birch and heather further north (Waring et al., 2017).
E. testata is one of a few geometrid moths that span the Holarctic (GBIF Secretariat, 2022), and it is widespread throughout the United Kingdom (NBN Atlas Partnership, 2021).Populations in the UK show a significant decrease since 1970 in both abundance and distribution (Conrad et al., 2006;Randle et al., 2019).
The genus Eulithis is currently placed in the larentiine tribe Cidariini (Choi, 1997).It is sister to the genus Ecliptopera in the study of Õunap, et al. (2016;Figure 2).Evolution of its wing patterns, including those of its many congeners have been studied, and one species Eulithis convergenata (Bremer, 1864) appears to be mimetic of the aposematic geometrid genus Abraxas (Choi, 2001).
The genome sequence should not only be useful in phylogeny, but also in studies of potentially cryptic species.There are two DNA barcode clusters on BOLD (17 April 2023), the BINs BOLD:AAB0154 and BOLD:ABZ0682 (the former in the USA and Canada, the latter in the Palaearctic including the UK and Europe), and these two discrete clusters are only about 1.47% pairwise divergent from each other.
The genome of Eulithis testata 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 Eulithis testata, based on one male specimen from Beinn Eighe National Nature Reserve, Scotland, UK.

Genome sequence report
The genome was sequenced from one male Eulithis testata.A total of 60-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 12 missing joins or mis-joins, reducing the scaffold number by 12.2%.
The final assembly has a total length of 308.1 Mb in 36 sequence scaffolds with a scaffold N50 of 11.0 Mb (Table 1).Most (99.92%) of the assembly sequence was assigned to 28 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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/326959.

Sample acquisition and nucleic acid extraction
Two Eulithis testata specimens (ilEulTest2 and ilEulTest3) were collected from Beinn Eighe National Nature Reserve, Scotland, UK (latitude 57.63, longitude -5.35) on 10 September  and dry frozen at -80°C.Individual ilEulTest2 (specimen no.NHMUK014543798) was used for genome sequencing, while individual ilEulTest3 (specimen no.NHMUK014543792) was used for Hi-C scaffolding.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEulTest2 sample was weighed and dissected on dry.Head and thorax 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 the Pacific Biosciences SEQUEL II instrument.Hi-C data were also generated from head and thorax tissue of ilEulTest3 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020).The assembly was then

Maurijn van der Zee
Leiden University, Sylviusweg, Leiden, The Netherlands David Lees provides the genome of the the butterfly Eulithis testata.It is a high quality genome, based on PacBio long reads with a 60-fold coverage.This coverage is likely to eliminate sequence reading errors.Particularly powerful is that Hi-C data and manual curation reduced the scaffold number to 36, which practically equals the number of chromosomes (30 autosomes).The Busco score of 98.1% underlines the completeness of the genome.The only weakness I can think of is that annotation is only based on the ENSEMBL rapid annotation pipeline, and that no transcriptomic data have been generated and used.The genome will be useful in many research fields, including phylogeny and taxonomy.
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: comparative genomics, evo-devo 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.
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: Evolutionary developmental biology and comparative genomics 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 testata, ilEulTest2.1: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 308,098,708 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 (13,628,168 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (10,981,015 and 7,954,720 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/Eulithis%20testata/dataset/CANNPX01/snail.

Figure 5 .
Figure 5. Genome assembly of Eulithis testata, ilEulTest2.1:Hi-C contact map of the ilEulTest2.1 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=dYxE9IdaTNu__uKX_RLc4g.

Table 1 . Genome data for Eulithis testata, ilEulTest2.1. Project accession data
2021 using a light trap.The specimens were collected and identified by David Lees(Natural History Museum)