The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761)

We present a genome assembly from an individual male Ypsolopha scabrella (the Wainscot Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 853.6 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 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,594 protein coding genes.


Background
Ypsolopha scabrella (Wainscot Smudge) is a common micromoth in the family Ypsolophidae.The species has a southerly distribution in Britain and is found throughout Europe apart from Portugal and Greece (GBIF Secretariat, 2022).
Y. scabrella has one generation a year and flies between June and October.It readily comes to light and is found in woodland, scrub and gardens (Sterling et al., 2012).The small (wingspan 15-21 mm) adult moth rests with its wings curled around its body.The forewing colour is whitish, with pale and dark brown streaks.There are three tufts of raised, darkened scales along the back (Emmet, 1996).The egg is usually laid on hawthorn or apple, but occasionally on cotoneaster where it overwinters.The larvae feed in a rather insignificant web and pupate during June and July in a boat-shaped cocoon on the ground (Langmaid et al., 2018).
A genome sequence from Y. scabrella will be useful for comparative studies across the Lepidoptera.The genome of Y. scabrella 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 Y. scabrella based on a male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one male Ypsolopha scabrella (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 36-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 40-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 35 missing joins or misjoins, reducing the scaffold number by 38.46%, and increasing the scaffold N50 by 1.37%. The final assembly has a total length of 853.6 Mb in 40 sequence scaffolds with a scaffold N50 of 29.9 Mb (Table 1).Most (99.97%) of the 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).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/1870435.

Sample acquisition and nucleic acid extraction
Two Ypsolopha scabrella specimens were collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2020-07-20 using a light trap.The specimens were collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.The specimen used for genome sequencing was specimen ID Ox000642, ToLID ilYpsScab1, while the specimen used for Hi-C scaffolding was specimen ID Ox000643, ToLID ilYpsScab2.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilYpsScab1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Tissue from the whole organism 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  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., 2017) DSL2 pipelines 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 Ypsolopha scabrella assembly (GCA_910592155.1) in Ensembl Rapid Release.

Software tool Version
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

Jerome H L Hui
The Chinese University of Hong Kong, Hong Kong, Hong Kong In this Data Note, Boyes and colleagues sequenced and assembled the genome of moth Ypsolopha scabrella (Linnaeus, 1761), commonly known as wainscot hooktip or wainscot smudge.According to the UKmoths and iNaturalist, this species can be found in both England and Wales.Molecular data of this species are scarce prior to this report, and are mainly mitochondrial cytochrome oxidase subunit 1 (COI) gene sequences deposited to the NCBI database.Therefore, this new genome resource will be useful for further studies, ranging from understanding the effect and impact of climate change on them, revealing their population structures, to understanding their evolution with other insects.
This genome resource is excellent from the summary statistics, with high BUSCO number scores, high sequence continuity, and majority of sequences contained on the 30 pseudochromosomes (plus sex chromosome and mitochondrion).All in all, this is another valuable contribution.

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: 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.

Kai Li
Donghua University, Shanghai, China The genome sequence obtained from Y. scabrella will serve as a valuable resource for conducting comparative studies within the Lepidoptera order.The author provides a relatively clear description of sample acquisition, DNA library preparation, high-throughput sequencing, bioinformatics, and other related aspects.Therefore, judging from the key points of the journal review, it is a qualified study, and the relevant sequences are helpful for other researchers.

Feng Zhang
Nanjing Agricultural University, Nanjing, China This manuscript presents a high-quality genome assembly but a low-quality annotation.See detailed comments below: "The genome was sequenced from one male Ypsolopha scabrella (Figure 1) collected from Wytham Woods, Oxford-shire, UK (51.77, -1.34)." ○ Add the 'E, N' and measurement unit for the longitude and latitude.
○ I don't think that it is a good idea to annotate the insect genome using BRAKER2, which usually generate more gene models than other pipelines.Those models are often of shorter gene length (mean < 500 aa) and lower BUSCO completeness.In this case, the gene number 20,594 is much higher than those of most lepidopteran published genomes, including world-wide pests.In addition, it doesn't make much sense to annotate the genome while the RNA-seq data is lacking.Reviewer Expertise: Insect genomics and phylogenomics.
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, however I have significant reservations, as outlined above.

Figure 2 .
Figure 2. Genome assembly of Ypsolopha scabrella, ilYpsScab1.1: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 853,595,150 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 (52,420,632 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (29,858,840 and 19,866,168 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/ilYpsScab1.1/dataset/CAJUZF01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Ypsolopha scabrella, ilYpsScab1.1:Hi-C contact map of the ilYpsScab1.1 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=MEkHt8scQR6xmc-6DNy3Gg.

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Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?PartlyAre 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.

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.
Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.https://doi.org/10.21956/wellcomeopenres.21969.r86877© 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.

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.