The genome sequence of the Lilac Beauty, Apeira syringaria (Linnaeus, 1758)

We present a genome assembly from an individual female Apeira syringaria (the Lilac Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 544.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,426 protein coding genes.


Background
The Lilac Beauty, Apeira syringaria (Linnaeus, 1758) is a moth in the family Geometridae, from the 'thorn' subfamily, Ennominae.Adult moths of this species have an unusual resting posture, with the forewings slightly raised, and the leading edge slightly folded (Waring et al., 2017), increasing their resemblance to a crumpled dead leaf.Males are smaller and more brightly coloured than females (South, 1961).
Apeira syringaria has a local distribution in Britain and Ireland, occurring mostly in south and central areas.It was not recorded from Scotland in the early part of the twentieth century (South, 1961), but has extended its distribution there in recent decades (Randle et al., 2019).At monitored sites, the abundance of this species has declined greatly since 1970 (Randle et al., 2019).Internationally, the distribution of A. syringaria extends across Europe and temperate Asia (GBIF Secretariat, 2022).
A genome sequence for Apeira syringaria will contribute to a growing data set of resources for understanding Lepidopteran biology.The genome of Apeira syringaria 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 Apeira syringaria, based on one female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one female Apeira syringaria (Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.34).A total of 49-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.
The final assembly has a total length of 544.4 Mb in 51 sequence scaffolds with a scaffold N50 of 21.0 Mb (Table 1).Most (99.96%) of the 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).The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 98.4% (single 97.7%, duplicated 0.7%), 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 female Apeira syringaria specimen (ilApeSyri1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire) (latitude 51.77, longitude -1.34) on 13 June 2020.The specimen was taken from woodland habitat by Douglas Boyes (University of Oxford) using a light trap.The specimen was identified by Douglas Boyes using field ID and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilApeSyri1 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) instruments.Hi-C data were also generated from tissue of ilApeSyri1 using the Arima v2 kit and sequenced on the HiSeq X Ten instrument.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Apeira syringaria assembly (GCA_934044485.1) in Ensembl Rapid Release.

Ethics and compliance issues
The materials that have contributed to this genome    The article carefully describes the sequencing, assembly and annotation of the genome of a lilac beauty female, following a state-of-the-art workflow.I have only two questions Did the author specifically search for the W chromosome? 1.
In figure 5, we can clearly see that one of the scaffold does not seem to have any contact with the others.This is quite unusual to me.Is there any biological and/or technical reason that my explain this uncommon feature of the Hi-C map? 2.

Are the datasets clearly presented in a useable and accessible format? Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: evolutionary ecology, population 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.Reviewer Expertise: Systematics, biodiversity, taxonomy, bioinformatics, Lepidoptera 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 Apeira syringaria, ilApeSyri1.1: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 544,443,574 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 (37,666,467 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (20,999,187 and 10,846,250 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/ilApeSyri1.1/dataset/CAKOGW01/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

Figure 5 .
Figure 5. Genome assembly of Apeira syringaria, ilApeSyri1.1:Hi-C contact map.Hi-C contact map of the ilApeSyri1.1 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=BdknbMWvQoywaKY2jyxqZA.

Reviewer○
Report 09 November 2023 https://doi.org/10.21956/wellcomeopenres.21290.r69167© 2023 De Prins J.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.Jurate De PrinsRoyal Belgian Institute of Natural Sciences, Brussels, Belgium My review is only from the taxonomic point of view, for molecular details please apply to a molecular specialist.From the taxonomic point of view, this article looks ok.Just a couple of small details:I would suggest to explain in more detail what the authors mean by "an unusual resting posture".What is usual then in Geometridae?Geometridae moths, differently from the majority of other moths, rest with open wings.○Itwould be good to mention that Apeira syringaria (Linnaeus, 1758) is widely distributed in Europe.Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?YesCompeting Interests: No competing interests were disclosed.