The genome sequence of the Small Angle Shades, Euplexia lucipara (Linnaeus, 1758)

We present a genome assembly from an individual male Euplexia lucipara (the Small Angle Shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 661.8 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 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,395 protein coding genes.


Background
The Small Angle Shades (Euplexia lucipara) is a noctuid moth with a wide distributed in a variety of habitats across Britain and Ireland (Randle et al., 2019).Globally, its range extends across temperate Europe and Asia to Japan (GBIF Secretariat, 2023).In appearance, it varies little across its range, and has a distinct resting posture with folder forewings that resemble a dead leaf (Waring et al., 2017).This is one of a relatively small set of British and Irish insects that feeds frequently on bracken (Pteridium aquilinum (L.) Kuhn) and other ferns (Lawton, 1982); its larvae also feed on a wide variety of angiosperms (Henwood et al., 2020).This species has a single generation in the UK, over-wintering as a pupa.
The genome of the Small Angle Shades, Euplexia lucipara, 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 Euplexia lucipara, based on one male specimen from Wytham Woods, Oxfordshire.

Genome sequence report
The genome was sequenced from one male Euplexia lucipara (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 26-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 51-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 27 missing joins or mis-joins and removed 4 haplotypic duplications, reducing the assembly length by 0.46% and the scaffold number by 22.83%, and increasing the scaffold N50 by 1.13%. The final assembly has a total length of 661.8 Mb in 71 sequence scaffolds with a scaffold N50 of 22.7 Mb (Table 1).Most (99.62%) 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.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (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/987933.

Sample acquisition and nucleic acid extraction
A male Euplexia lucipara (specimen ID Ox000606, ToLID ilEupLuci1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2020-07-05 using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEupLuci1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Abdomen 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.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 Illumina NovaSeq 6000 (10X) instruments.Hi-C data were also generated from head and thorax tissue of ilEupLuci1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.
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 Euplexia lucipara assembly (GCA_921972225.1) 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

Vlad Dincă
University of Oulu, Oulu, Finland In this study, the authors have successfully generated a chromosome-level genome assembly of a male Euplexia lucipara (Lepidoptera, Noctuidae).The mitochondrial genome has been assembled as well.
Although I am not an expert in several of the methodological approaches used, as far as I can tell, the manuscript is technically sound and uses methodologies and pipelines that are fairly wellestablished through use by the Sanger Institute.
The genome appears to be of high quality and has a BUSCO v5.3.2 completeness of 99.0%.
It is a pity that the W sex chromosome is lacking (a male was sequenced).
Reference genomes such as this one represent a valuable resource for the scientific community and each new addition provides new opportunities for research.

Other comments:
I wonder how much is known in terms of genetic structure for E. lucipara.Even if limited data is available (e.g.mtDNA, a few nDNA markers etc), if any notable aspect is known (e.g.diverged lineages), it could be worth briefly mentioning it in the Background.It may also be worth mentioning whether the species can have more than one generation in other parts of its range.
Species taxonomy, third line: Euplexia lucipara should be written in italics Background, first line: "with a wide distribution" or "widely distributed" Is the rationale for creating the dataset(s) clearly described?

Jerome H L Hui
The Chinese University of Hong Kong, Hong Kong, Hong Kong Boyes, Lewis, and colleagues report the genome sequence of a male moth Euplexia lucipara (Linnaeus, 1758).According to the UKmoths (www.ukmoths.org.uk), this species is common and widespread over most of the British Isles.Prior to this report, molecular data of this species was rather limited (mainly mitochondrion COI gene sequences deposited to the NCBI database).
This new genome resource will be useful for further studies such as understanding their population genetic structure, identify cryptic/sub-species, as well as understanding their evolutionary relationships with other moths.
This genome resource is excellent from the summary statistics, with high BUSCO number, high sequence continuity, and majority of sequences contained on the 30 pseudochromosomes (plus Z chromosome and mitochondrion).To sum up, this is another valuable contribution by the Darwin Tree of Life.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?

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: I have published with Peter Holland more than three years ago, and confirm that this potential conflict of interest did not affect my ability to write an objective and unbiased review of the article.
Reviewer Expertise: Genomics, evolution, invertebrates 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.

like E. lucipara
The total length of the mitochondrial genome sequence must be provided in the text.
Above all, I confirm that the manuscript meets the necessary scientific standards and is suitable for indexing.
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: Molecular biology
We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 2 .
Figure 2. Genome assembly of Euplexia lucipara, ilEupLuci1.1: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 661,825,765 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 (37,151,478 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (22,669,833 and 15,555,094 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/Euplexia%20lucipara/dataset/CAKLHH01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Euplexia lucipara, ilEupLuci1.1:Hi-C contact map of the ilEupLuci1.1 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=e6psxBA4RJqdiQYZcvsoiw.

Table 3 . Software tools: versions and sources. Software tool Version 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 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.
https://doi.org/10.21956/wellcomeopenres.22417.r83573© 2024 Hui 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.