The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis & Schiffermüller, 1775)

We present a genome assembly from an individual male Cosmia pyralina (the Lunar-spotted Pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 803.3 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 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,901 protein coding genes.


Background
The Lunar-spotted Pinion (Cosmia pyralina) is a noctuid moth, commonly found in central Europe, but its territory extends all the way through the Palaearctic to Korea and Japan (Fauna Europea, 2023).In Britain this is a species of central and southern England and (albeit more scarcely) Wales, particularly the south-east.
With a wingspan of 28-32 mm, the Lunar-spotted Pinion could be confused with the Lesser-spotted Pinion, Cosmia affinis (Linnaeus, 1767), but has paler hindwings and broader forewings (Waring et al., 2017).Cosmia pyralina has a variety of colour morphs, with dull or bright red-brown forewings, with a contrasting white edge in the outer line, that eventually joins the white streak before the submarginal line.Similarly, larvae are pale green with white lines.The larvae are polyphagous and feed on deciduous trees, such as blackthorn (Prunus spinosa) and hawthorn (Crataegus monogyna) as well as English elm (Ulmus procera) and wych elm (U. glabra) (Waring et al., 2017) The species is declining in Britain (Conrad et al., 2006), most likely due to Dutch elm disease.Caused by the fungus Ophiostoma novo-ulmi, Dutch elm disease is one of the most severe tree diseases in the world, causing foliage and tip dieback in all of Britain's major native elms (Potter et al., 2011).Ten beetle species from the genus Scotylus (a genus of bark beetle) are known to feed on elms and a key insect vector for the disease to spread.The beetles frequently visit or inflict wounds in healthy elms; thus, depositing any spores directly into the damaged tree (Peacock et al., 1981).Other Cosmia species which have suffered due to this disease include the White-spotted Pinion, Cosmia diffinis, which is now listed as 'Nationally Scarce' (Fox et al., 2019).The fourth British Cosmia species, C. trapezina (the Dun-bar), still has a healthy population despite the described challenges, perhaps due to its trait of eating the larvae of other moth species as well as cannibalising its own (Turčáni & Patočka, 2011;Ward, 1903).
We present a chromosomally complete genome sequence for the Lunar-spotted Pinion (Cosmia pyralina) as part of the Darwin Tree of Life Project.This project is a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago, encompassing Britain and Ireland.

Genome sequence report
The genome was sequenced from one male Cosmia pyralina (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.34).A total of 22-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 26 missing joins or mis-joins and removed 1 haplotypic duplication, reducing the scaffold number by 18.01% and increasing the scaffold N50 by 1.63%.
The final assembly has a total length of 803.3 Mb in 50 sequence scaffolds with a scaffold N50 of 27.4 Mb (Table 1).Most (99.89%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes and the Z sex chromosome.A summary of the assembly statistics is shown in Figure 2, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Chromosomescale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).Comparators Cosmia trapezina (GCA_905163495.2) (Boyes et al., 2022) and Amphipoea oculea (GCA_945859645.1)(Boyes et al., 2023) were used for Z chromosome identification.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/987909.

Genome annotation report
The Cosmia pyralina genome assembly (GCA_946251885.1)was annotated using the Ensembl rapid annotation pipeline (Table 1; https://rapid.ensembl.org/Cosmia_pyralina_GCA_946251885.1/Info/Index).The resulting annotation includes 20,077 transcribed mRNAs from 19,901 protein-coding genes.RNA was extracted from abdomen tissue of ilCosPyra2 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer's instructions.RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit.Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers' instructions.Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit.DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments.Hi-C data were also generated from remaining head and thorax tissue of ilCosPyra2 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 scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023).The assembly was checked for contamination and   Table 3. Software tools: versions and sources.

Software tool Version
corrected as described previously (Howe et al., 2021).Manual curation was performed using HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022).The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2022), which runs MitoFinder (Allio 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 work was done using Nextflow (Di Tommaso et al  et al., 2021;Simão et al., 2015) were calculated.
Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Cosmia pyralina assembly (GCA_946251885.1) in Ensembl Rapid Release.

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome note have been supplied by a 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', which can be found in full on the Darwin Tree of Life website here.By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, 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

Jose Martinez
University of Florida, Florida, USA Boyes and Januszczak present a highly complete and meticulously assembled genome of a male Lunar-spotted Pinion, Cosmia pyralina (Denis & Schiffermüller, 1775).The assembly, distinguished by an outstanding BUSCO score, is arranged into 31 chromosomal pseudomolecules, including the fully recovered Z sex chromosome.The comprehensive quality of this genomic resource reflects the use of cutting-edge sequencing technologies and rigorous assembly methodologies.This high-quality dataset provides an invaluable tool for evolutionary studies, offering deep insights into the species' genetic makeup and laying a strong foundation for future research on systematics, population genomics, and the broader evolutionary history of Lepidoptera.
The development of this dataset is founded on a clear, well-structured rationale, supported by concise and accessible descriptions that enhance its usability.The carefully selected protocols and methodologies are meticulously designed to ensure both accuracy and reproducibility, adhering to the highest standards of scientific rigor.The dataset is highly standardized, allowing for seamless integration into various research frameworks.Accompanied by comprehensive and detailed illustrations, it provides a visually rich resource that enhances understanding and facilitates data interpretation.Furthermore, its accessibility ensures that it can be readily utilized by researchers across multiple disciplines, making it a versatile and invaluable asset for advancing knowledge in numerous scientific fields.
Finally, the authors tackle a critical issue in natural ecosystems: "insect declines."The species in question, along with others in its genus, appears to be disappearing from Britain, likely due to the spread of Dutch elm disease.This genomic study provides valuable insights into the biology of this species and could play a pivotal role in its conservation.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?The rationale for creating the dataset(s) is clearly described.However, while the protocols used are appropriate and the work is technically sound to some extent, there are areas where improvements could be made.The paper notes that the transcriptome sequencing was performed on the insect's abdomen.It might be worth considering whether gene annotation based solely on this abdominal transcriptome could fully capture all coding genes, as additional transcriptome data from other tissues might offer a more comprehensive annotation.
Furthermore, the authors did not address the annotation of repetitive sequences in the genome, which could be an important aspect to include in the analysis.The methods and materials are

Figure 2 .
Figure 2. Genome assembly of Cosmia pyralina, ilCosPyra2.1: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 803,276,861 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 (39,281,260 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (27,366,473 and 18,734,863 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/ilCosPyra2.1/dataset/CAMIUC01/snail.

Figure 5 .
Figure 5. Genome assembly of Cosmia pyralina, ilCosPyra2.1:Hi-C contact map of the ilCosPyra2.1 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=TpGzUdJFRHyRe3gFUR058w.

©
2024 Wu N et al.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.Ningning Wu 1 China Agricultural University Education Foundation, Beijing, Beijing, China 2 College of Plant Protection, China Agricultural University College of Plant Protection, Beijing, Beijing, China Shaolong Qiu China Agricultural University College of Plant Protection, Beijing, Beijing, ChinaIn this study, the authors assembled the genome of the forestry insect Cosmia pyralina.They utilized a single adult male specimen and integrated PacBio HiFi sequencing, Hi-C sequencing, and transcriptome sequencing to produce a chromosome-level genome and achieve comprehensive annotation of protein-coding genes.The high quality of the assembly is demonstrated by the favorable QV and BUSCO values.

Open Peer Review Current Peer Review Status: Version 1
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.

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.
Reviewer Report 15 August 2024 https://doi.org/10.21956/wellcomeopenres.22310.r91944