The genome sequence of the White-backed Marble, Hedya salicella (Linnaeus, 1758)

We present a genome assembly from an individual male Hedya salicella (the White-backed Marble; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 742.3 megabases in span. Most of the assembly is scaffolded into 25 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,961 protein coding genes.


Background
The White-backed Marble, Heyda salicella (Linnaeus, 1758) is a single brooded, common species of micro moth widely distributed across Europe and introduced in North America (Gilligan et al., 2020).This large and distinctive Heyda species is predominantly white with a mottled chestnut and grey thorax.It has a wingspan of 19-24 mm and has been recorded in flight from the months June through to September.H. salicella inhabits areas where food plants are abundant, with sightings recorded in marshy areas amongst willows, banks of streams, open woodland and occasionally parks and gardens.Larvae feed on spun shoots and folded leaves of Salix (willow, sallow) and Populus (poplar, aspen) species (Kimber, 2023).
The genome of H. salicella 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 complete chromosome-level genome sequence for H. salicella,based on one male specimen from Wytham Woods, Oxfordshire, UK.This high-quality complete genome assembly of H. salicella, among a phylogenetically diverse set of insect orders, will yield genomes from closely related species, permitting valuable insights into genomic change over shorter time frames (Mulhair & Holland, 2022), while resolving the biogeographic origin of morphologically similar populations in Europe and North America.

Genome sequence report
The genome was sequenced from one male Hedya salicella (Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.34).A total of 25-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 43-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected four missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 16.67%.
The final assembly has a total length of 742.3 Mb in 45 sequence scaffolds with a scaffold N50 of 27.3 Mb (Table 1).Most (99.88%) of the assembly sequence was assigned to 25 chromosomal-level scaffolds, representing 24 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/1869985.

Sample acquisition and nucleic acid extraction
A male Hedya salicella (specimen no.Ox000472, individual ilHedSali1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.77, longitude -1.34) on 13 June 2020.The specimen was taken from woodland by Douglas Boyes (University of Oxford) using a light trap.The specimen was identified by the collector, and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilHedSali1 sample was 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.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 HiSeq X Ten (10X) instruments.Hi-C data were also generated from tissue of ilHedSali1 using the Arima2 kit and sequenced on the HiSeq X Ten instrument.et al., 2019).The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016)   Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The Ensembl gene annotation system (Aken et al., 2016) was used to generate annotation for the Hedya salicella assembly (ilHedSali1.2,GCA_905404275.2).Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt (UniProt Consortium, 2019).

Ethics and compliance issues
The

Yes
Competing Interests: No competing interests were disclosed.
Reviewer Expertise: I am a bioinformatician with experience in the assembly and annotation of fungal and insect genomes, but I do not have expertise in the taxonomy of this particular group.I have evaluated the aspects within my competency.
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.

Leonardo Barbosa Koerich
Federal University of Minas Gerais, Belo Horizonte, State of Minas Gerais, Brazil The manuscript entitled " The genome sequence of the White-backed Marble, Hedya salicella (Linnaeus, 1758)", by Boyes and colleagues, presents the basic data for the sequencing, assembly, and annotation of the White-backed Marble moth.
The manuscript presents the genome assembly, with ~740Mb span, reporting on basic statistics on genome and annotation quality.The genome was sequenced following up-to-date protocols, focusing on long-read data (PacBio) to attain complete chromosomes.Although the authors do not provide a comparison of genome and annotation quality with other insect genomes, BUSCOs numbers suggest that the assembly have a good quality (completeness ~98%).Most of the genome statistics is presented in a Snailplot figure, which I find a poor-choice given it is very confusing, specially to readers not used to genomic data.However, the results are well described and easy to follow.The manuscript also reports the annotation of 11,961 protein-coding and 1,706 non-coding genes.However, it is not clear if the annotation is of good quality.For such, I recommend the authors to perform a BUSCO analysis on the annotated genes.

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: Genomics of insects vector of diseases 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.The authors present a chromosome-level assembly for the moth species Hedya salicella.They used PacBio HiFi long-read sequencing and Illumina 10X Genomic reads sequencing to perform the initial assembly.For chromosomal-level scaffolding, they used Hi-C data.In this report, the authors show the quality data of this genome as well as an annotation of the gene models.
The sequencing techniques used are appropriate as demonstrated by the high contiguity of the scaffolds.Therefore, the data presented here represents a high-quality genome that has great potential to answer questions related to genome evolution, molecular systematics, population genomics and conservation of Lepidoptera.
However, I found some points that I would like to clarify: Separate "H.salicella, based."

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The use of "complete" when describing the contiguity of the genome ("This high-quality complete genome assembly of H. salicella") is not accurate.I agree that is a highly contiguous genome but the assembly still has gaps.Please, delete the word "complete".

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It would be also interesting to report the number of gaps across the final genome assembly.

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It is claimed in the manuscript that the assembly is not fully phased.It would be necessary a clearer explanation of this point in the text.

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I am unclear about the idea behind these sentences: "This high-quality complete genome assembly of H. salicella, among a phylogenetically diverse set of insect orders, will yield genomes from closely related species, permitting valuable insights into genomic change over shorter time frames."Suppose the intention was to point out that this genome can help assemble other genomes of closely related species.In that case, I think it is debatable, considering that closely related species within the same family seem to have some degree of variation in the number of chromosomes (see Table 1 in Traut, Sahara, and Marec, 2008).
If the intention was to point out that its comparison with closely related species is of interest for genomic analysis, etc., then, I think it might be necessary to rephrase the sentence.The sentence could be rephrased as: This high-quality genome for the species H. salicella constitutes a valuable resource for studying genomic evolution over short periods among closely related species.The use of the term sequencing depth instead of coverage could be more appropriate when the authors refer to it in the text.Both terms are interchangeable, but I think in this case it refers to the sense of sequencing depth, and therefore it would be more precise (Sims, et al, 2014 [Ref-2]).

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It is mentioned that transcriptomic information was used for genome annotation, but whether these transcriptomes were sequenced from the same individual or from other individuals is not specified.It is also not specified which tissue was used to sequence the transcriptomes.I believe this section needs further clarification.

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The genome's BUSCO score is reported, but not the BUSCO of the annotation.It would be interesting to know this value for the annotation.

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As described in the article, the genome annotation was performed following the Ensembl gene annotation system.Like most current genome annotations, this method requires the annotation of repetitive elements in the genome.Information on repeats such as microsatellites or transposons is highly relevant since it often constitutes a large amount of genomic material in the species, with direct implications during development or evolution.If possible, I think it would be very informative if this report provides information on the annotation of repetitive elements such as the percentage of total elements found and the most frequent transposon families.Although the suggested addition could be out of the scope of this data note, this information is commonly reported in genome analyses.In the case of this H. salicella, it might be of great interest considering the disproportionate size of the Z chromosome, which is five times larger than the average of the other pseudochromosomes.

Xiangyu Hao
College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China The manuscript presents a comprehensive genome assembly and annotation of Hedya salicella, commonly known as the White-backed Marble.The assembly spans 742.3 megabases, with 25 chromosomal pseudomolecules, including the Z sex chromosome, and a fully assembled mitochondrial genome.This study provides valuable genomic resources for understanding the biology and evolution of this species.

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: Zoology, Entomology, 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.

Figure 2 .
Figure 2. Genome assembly of Hedya salicella, ilHedSali1.2: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 742,325,546 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 (128,845,201 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (27,275,373 and 17,835,027 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/ilHedSali1.2/dataset/CAJQFL02.1/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 for, and supplied to, the Darwin Tree of Life Project.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.

Figure 5 .
Figure 5. Genome assembly of Hedya salicella, ilHedSali1.2:Hi-C contact map of the ilHedSali1.2assembly, 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=dVzSopIPQm2BTrcTNwkrZw.

Reviewer Report 05
June 2024 https://doi.org/10.21956/wellcomeopenres.21532.r85357© 2024 Pardos-Blas 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.Jose Ramon Pardos-Blas Department of Chemistry, Hunter college, Research Foundation of the City University of New York (Ringgold ID: 460801), Belfer Research Building, 413 E 69th St, NY., New York, 10021, USA