The genome sequence of the Diamond-back Marble, Eudemis profundana (Denis & Schiffermüller, 1775)

We present a genome assembly from an individual male Eudemis profundana (the Diamond-back Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.


Background
Eudemis profundana (Denis & Schiffermüller, 1775) is a moth of the Tortricidae family.A large and robust species for its family, profundana shows a wide range of variation in colouration of the forewing, particularly in the strength of its white markings (Bradley et al., 1979).The species frequents oak (Quercus) woodland, and adult moths fly high up amongst foliage before sunset, resting on branches and trunks of oak trees by day, The larva feeds on oak leaves, rolling the leaf around the leaf's midrib, between May and June.Pupation occurs either in the larval habitation or amongst leaf litter on the ground.Adults can be found between June and September (Bradley et al., 1979;Elliott et al., 2018).This species is widespread across the British Isles, reaching southern Scotland, and being common in the oak woodlands of southern Ireland (Bradley et al., 1979;Elliott et al., 2018).Globally the moth is found across Eurasia eastwards to at least the Caucasus (Maharramova & Ayberk, 2017).The species is also reported from Hokkaido, and the Korean peninsula, being known to feed on Prunus ssiori in Hokkaido, alongside Quercus (Bae & Sakamaki, 1995).However, specimens formerly identified as profundana in the Korean peninsula are now regarded as Eudemis lucina or E. brevisetosa (Sohn et al., 2015), so these records may not necessarily refer to profundana.
The genome of Eudemis profundana was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence the named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.Here we present a chromosomally complete genome sequence for Eudemis profundana, based on one male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one male Eudemis profundana (Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.31).A total of 37-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 56 missing joins or mis-joins and removed 17 haplotypic duplications, reducing the assembly length by 0.59% and the scaffold number by 56%.
The final assembly has a total length of 691.3 Mb in 44 sequence scaffolds with a scaffold N50 of 25.2 Mb (Table 1).Most (99.94%) of the assembly sequence was assigned to 28 chromosomal-level scaffolds, representing 27 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/1100989.

Sample acquisition and nucleic acid extraction
A male Eudemis profundana (specimen number: Ox001669, ToLID: ilEudProf1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.31) on 17 July 2021.The specimen was taken from woodland habitat by Douglas Boyes (University of Oxford) using a light trap.The specimen was identified by the collector and snap-frozen on dry ice.The ilEudProf1 sample was prepared at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The sample weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Whole organism tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.DNA was extracted at the WSI Scientific Operations core using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.

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 on Pacific Biosciences SEQUEL II (HiFi) instrument.Hi-C data were also generated from tissue of ilEudProf1 that was set aside for this purpose, using the Arima v2 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 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.To evaluate the assembly, MerquryFK was used to estimate consensus quality (QV) scores and k-mer completeness (Rhie et al., 2020).The genome was analysed within the BlobToolKit environment (Challis et al., 2020) and BUSCO scores (Manni et al., 2021;Simão et al., 2015) were calculated.Table 3 contains a list of software tool versions and sources.

Ethics and compliance issues
The

Balaji Chattopadhyay
Ashoka University, Sonipat, Haryana, India The manuscript presents a high-quality genome assembly of the Diamond-back Marble.
The methods and results are fairly detailed and can serve as a methodological reference for many researchers who are implementing genome sequencing projects.I feel that the methods section can be improved slightly.The authors can add brief justifications for using specific programs.Additionally, they can provide parameters used for the analyses and brief clarification for using these specific parameters.
The figure legends can include brief details about the results displayed.

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? Partly
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Genomics, NGS, Biodiversity, Evolution 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.

Merid Negash Getahun
International Centre of Insect Physiology and Ecology, Nairobi, Kenya In this short report, the authors present the genome from a single male of Eudemis Profundana, an Eurasian Lepidopteran specie.The article represents a good genome note although the findings have not been fully discussed.While the method and analyses are well done in general.We can take as a good resource if someone wants to know more about the species by analyzing the available data.Define the hypothesis why you are doing this work?Paragraph 2 of background need improvement it is confusing.The methodology does not clarify how the collected specimen was identified to the species level.This should be mentioned in the method.Also better photo of the insect with better describing features A bit more description of each figure to make it simple or understandable.There is also an additional line that need to be removed or described.Except the identical comparison we cannot see any difference between other chromosomes.Add a legend describing the heatmap.Is it possible to conduct some phylogenomic analysis using selected gene and available data on the lepidopteran genome?It will be interesting to have some functional annotations (unless this was beyond the scope of the study).
All The figures could be improved to make it readable for non-experts.Figure 5 needs a legend describing the heatmap.

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

Are sufficient details of methods and materials provided to allow replication by others? Partly
Are the datasets clearly presented in a useable and accessible format?No Boyes and colleagues report the genome sequence of a male diamond-back marble moth Eudemis profundana (Denis and Schiffermuller, 1761).This species of moth can be commonly found in Britain.Molecular data of this species are scarce prior to this report, and are mainly confined to COI sequences deposited to the NCBI database.This new genome resource will be useful for further studies, such as identifying potential cryptic species, understanding its roles in the ecosystem, revealing its evolutionary relationships with other lepidopterans, and understanding their variable coloration in relations to the environment and perhaps also to climate change.
This genome resource is excellent from the summary statistics, with high BUSCO numbers (98.5%), high sequence continuity (scaffold N50), and majority of sequences contained on the 28 pseudochromosomes (plus mitochondrion).To sum up, 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: No competing interests were disclosed.

Figure 2 .
Figure 2. Genome assembly of Eudemis profundana, ilEudProf1.1: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 691,289,278 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold in the assembly (51,369,493 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (25,204,545 and 16,195,774 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/ilEudProf1.1/ dataset/CAMQQK01/snail.
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.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

Figure 5 .
Figure 5. Genome assembly of Eudemis profundana, ilEudProf1.1:Hi-C contact map of the ilEudProf1.1 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=ZrVQpBgYT9utmKxSIJBcyQ.

Reviewer Report 13
February 2024 https://doi.org/10.21956/wellcomeopenres.21457.r72291© 2024 Getahun 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.
Can we divide fig 3 in to 3 panels (A-C) and describe better each, what is the total we do not see it on the figure we can see it in the next figure.

Figure 5
put the chromosome name and the scale bar showing how strong is the correlation.

Table 3 . Software tools: versions and sources. Software tool Version for
, and supplied to, the Darwin Tree of Life Project.All efforts are undertaken to minimise the suffering of animals used for sequencing.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.