The genome sequence of the Pebble Hook-tip, Drepana falcataria (Linnaeus, 1758)

We present a genome assembly from an individual male Drepana falcataria (the Pebble Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 326.7 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.


Background
Drepana falcataria, the Pebble Hook-tip, is the largest and commonest of the hook-tip moths (family Drepanidae) in Britain and Ireland.The English name of these moths reflects the distinctive hooked appearance of their forewings.In the case of D. falcataria, the pebble-like central spot on the forewing, combined with a purplish-brown blotch near the wing tip, distinguish this species from the other six Drepanidae species recorded in Britain and Ireland (Waring et al., 2017).This species occurs in woodlands, gardens, heathland and similar habitats across much of Britain and more locally in Ireland (Randle et al., 2019;Waring et al., 2017).It has expanded its distribution significantly since 1970, but has also declined in abundance (Randle et al., 2019).Drepana falcataria has a wide distribution across western and central Europe and Siberia (GBIF Secretariat, 2022).
The main larval foodplants of D. falcataria are birches (Betula spp.) and alder (Alnus glutinosa) (Henwood et al., 2020).It overwinters as a pupa, and adults fly at night from late April to June, with a second brood which peaks in August (Randle et al., 2019).The spring generation now appears significantly earlier in the year than it did in the 1970s (Randle et al., 2019).In the north, this species has a single annual generation, and in the northern half of Scotland occurs as a distinct subspecies, scotica, which has a paler ground colour (Waring et al., 2017).
A genome sequence for Drepana falcataria will contribute to a growing data set of resources for understanding lepidopteran biology.The genome of Drepana falcataria 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 Drepana falcataria, based on one male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one male Drepana falcataria (Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.34).A total of 73-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual curation corrected two missing joins or misjoins.
The final assembly has a total length of 326.7 Mb in 31 sequence scaffolds with a scaffold N50 of 11.7 Mb (Table 1).The whole 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).The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 98.6% (single 98.4%, duplicated 0.2%) using the lepidoptera_odb10 reference set.While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and nucleic acid extraction
A male Drepana falcataria (ilDreFalc1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire) (latitude 51.77, longitude -1.34) on 24 July 2021.The specimen was taken from grassland habitat by Douglas Boyes (University of Oxford) using a light trap.The specimen was identified by Douglas Boyes and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilDreFalc1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.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 a Pacific Biosciences SEQUEL II (HiFi) instrument.Hi-C data were also generated from tissue of ilDreFalc1 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly
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 scaffolded with  performed annotation using MitoFinder (Allio et al., 2020).The genome was analysed and BUSCO scores generated within the BlobToolKit environment (Challis et al., 2020).Table 3 contains a list of all software tool versions used, where appropriate.

Ethics and compliance issues
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    Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.

Data availability
European Nucleotide Archive: Drepana falcataria (pebble hooktip).Boyes and Lewis present a genome assembly of the Pebble Hook-tip, Drepana falcataria (Linnaeus, 1758), which demonstrates a high degree of completeness, as evidenced by the elevated BUSCO score.The assembly is organized into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome.This, combined with other well-described methodologies, has produced highquality genomic data.
The rationale behind creating the dataset is standard, with clear and easily understandable descriptions, making it straightforward to follow.The protocols and procedures are appropriate, and the methods and materials are presented in a manner that facilitates replication.Ultimately, the dataset is highly standardized, accompanied by comprehensive illustrations, and easily accessible, rendering it exceptionally valuable for various applications.
Additionally, the quality of the genome can be enhanced through manual adjustments, making it a valuable reference for studying the systematics and evolution of the Drepanidae family.It can also facilitate the annotation of important genes associated with these groups of moths.This is particularly crucial considering that the family Drepanidae is among the least studied groups of moths.

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 Biology, Ecology, Integrative Biology, Entomology 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.This data note reports another high quality genome assembly of a lepidopteran species.All method, including version numbers of the software tools are clearly described, and the genome will certainly be valuable for lepidopteran comparative genomics.
I only have one question on why a male (the homogametic sex, lacking chr W) was picked for sequencing?If this species is common, was it not possible to pick a female?

Leonardo Barbosa Koerich
Federal University of Minas Gerais, State of Minas Gerais, Brazil I find the report of Boyes and Lewis, entitled: "The genome sequence of the Pebble Hook-tip, Drepana falcataria (Linnaeus, 1758)" to be of high quality.In the study, the authors present the genome assembly of the Peeble-hook-tip (Drepana falcataria), assembled in 31 scaffolds at chromosome level.
The genome sequencing process, outlined in detail, demonstrates a rigorous and well-executed approach.The use of Pacific Biosciences single-molecule HiFi long reads, complemented by chromosome conformation Hi-C data for scaffolding, ensures high-quality assembly.The manual curation efforts to correct misjoins further enhance the reliability of the assembly.The assembly statistics, including total length, scaffold N50, and chromosomal-level scaffolds, indicate a robust and comprehensive genome assembly.The high BUSCO completeness score validates the quality of the assembly, reinforcing its suitability for downstream analyses.
As an overall assessment, the rationale for the study is clearly articulated, the methodologies are appropriate and well-described, and the datasets are presented in a clear and accessible manner.

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.
Overall, the presented assembly will be of great value to study genome architecture as well as genome size evolution in Lepidoptera.However, as with other genome notes of the Darwin Tree of Life project, the genome is not yet annotated.Instead the data availability statement highlights that "The genome will be annotated using available RNA-Seq data and presented through the Ensemble pipeline at the European Bioinformatics Institute."It would be important to update this genome note with the data identifier once the data is made public.

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: Speciation Genomics I confirm that I have read this submission and believe that I have an appropriate level of

Figure 2 .
Figure 2. Genome assembly of Drepana falcataria, ilDreFalc1.1: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 326,745,212 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 (14,982,236 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (11,692,006 and 7,634,482 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/ilDreFalc1_1/dataset/ilDreFalc1_1/snail.

Figure 3 .
Figure 3. Genome assembly of Drepana falcataria, ilDreFalc1.1:GC coverage.BlobToolKit GC-coverage plot.Scaffolds are coloured by phylum.Circles are sized in proportion to scaffold length.Histograms show the distribution of scaffold length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilDreFalc1_1/dataset/ilDreFalc1_1/blob.

Figure 4 .
Figure 4. Genome assembly of Drepana falcataria, ilDreFalc1.1:cumulative sequence.BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all scaffolds.Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilDreFalc1_1/dataset/ilDreFalc1_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Drepana falcataria, ilDreFalc1.1:Hi-C contact map.Hi-C contact map of the ilDreFalc1.1 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=f_ybUAspTj2zY-keVs2uqQ.

Reviewer
Report 25 May 2024 https://doi.org/10.21956/wellcomeopenres.21295.r72031© 2024 Hiller M. 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.Michael HillerLOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Frankfurt Am Main, Germany

Table 2 . Chromosomal pseudomolecules in the genome assembly of Drepana falcataria, ilDreFalc1. INSDC accession Chromosome Size (Mb) GC%
Drepana falcataria 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 Table1.

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.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
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.