The genome sequence of the Crescent Bell, Epinotia bilunana (Haworth, 1811)

We present a genome assembly from an individual male Epinotia bilunana (the Crescent Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 659.0 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 15.4 kilobases in length.


Background
Epinotia bilunana (Haworth, 1811) is a moth of the Tortricidae family.This species is widely distributed across the British Isles and northern Eurasia (Bradley et al., 1979;Elliott et al., 2018;GBIF Secretariat, 2022), being found almost anywhere with birch (Betula) woodland.
The larvae feed from September to April within the catkin of birches, sometimes betraying their presence by distorting the catkin (Bradley et al., 1979;Elliott et al., 2018).Pupation occurs in May either within the larval feeding site or in a silken cocoon amongst leaf litter (Bradley et al., 1979;Elliott et al., 2018).Adults are on the wing from late May to September from dusk onwards, but are readily disturbed from birch foliage and trunks by day (Bradley et al., 1979;Elliott et al., 2018).The forewings of the adult moth are typically a light grey or creamy white with black markings, but can show variation in the strength of black colouration (Bradley et al., 1979).
The genome of Epinotia bilunana 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 Epinotia bilunana, based on one male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one male Epinotia bilunana (Figure 1) collected from Wytham Woods, UK (latitude 51.77, longitude -1.34).A total of 28-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 16 missing joins or mis-joins and removed five haplotypic duplications, reducing the assembly length by 0.48% and the scaffold number by 4.17%.
The final assembly has a total length of 659.0 Mb in 46 sequence scaffolds with a scaffold N50 of 247.5 Mb (Table 1).Most (99.82%) 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/1594293.

Sample acquisition and nucleic acid extraction
Two Epinotia bilunana specimens (ilEpiBilu1 and ilEpiBilu2) were collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.77, longitude -1.34) on 16 June 2021.The specimens were taken from woodland habitat by Douglas Boyes (University of Oxford) using a light trap.The specimens were identified by the collector and preserved on dry ice.Specimen ilEpiBilu1 (specimen number Ox001909) was used for genome sequencing, and ilEpiBilu2 (specimen number Ox001910) was used for Hi-C scaffolding.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEpiBilu1 sample was weighed and dissected on dry ice.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.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   then scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023).The assembly was checked for contamination 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),

Software tool Version
This data note describes a long read based, high quality assembly of the Crescent Bell.The genome was sequenced using PacBio HiFi reads and scaffolded to chromosome-level using HiC data.A primary and alternate assembly was produced.The primary assembly has a very high base accuracy and performs well in metrics that measure completeness.
Everything is done according to the high standards of DToL and the methods are clearly described.
I only have one minor comment and a question.
1) I couldn't find the contig N50 value mentioned in the text or in Table 1.This should be added.
2) In the HiC plot, I wonder why the Z chromosome does not show a lighter background color compared to the autosomes.A male should only have one Z copy, while all autosomes are present in two copies.Is this related to the fact that the HiC data came from another individual (which was likely also a male)?
Is the rationale for creating the dataset(s) clearly described?

Guillem Ylla
Laboratory of Bioinformatics and Genome Biology, Uniwersytet Jagiellonski w Krakowie, Kraków, Lesser Poland Voivodeship, Poland This article, authored by Douglas Boyes, and James Hammond, titled "The genome sequence of the Crescent Bell, Epinotia biluana (Haworth, 1811)", as clearly stated in the title describes the release of the chromosome-level genome assembly of the moth Epinotia biluana.The article is concise, well written, and contains the information expected from a genome release publication.
Materials and methods are exhaustively reported, with the software versions reported in Table 3.
The raw data and the final assembly file have been deposited in public repositories and the accession identifiers are duly provided in the article.

I only have a few minor comments:
The rationale for sequencing this genome is not clearly stated.A few lines regarding the relevance of this species and the potential interest of this genome could be interesting.

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The contig N50 is described to be 247.5Mb in the text, but table 1 shows 24.7Mb.I am afraid there must be a typo in the text.Reviewer Expertise: My areas of expertise include bioinformatics, evolution, and insect 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 Epinotia bilunana, ilEpiBilu1.1: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 659,043,568 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 (52,658,368 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (24,745,286 and 16,921,967 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/ilEpiBilu1.1/dataset/CAMRIR01/snail.

Figure 5 .
Figure 5. Genome assembly of Epinotia bilunana, ilEpiBilu1.1:Hi-C contact map of the ilEpiBilu1.1 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=VZ-7jSRjReSf9xze3k6gCw.

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It is not clear to me what point is Figure3intended to make, what information the reader should get from it, and how to interpret it.The figure is not specifically mentioned in the text (only referred to it within "Figure1-Figure5").Also, in the legend, it says that it has been colored by phylum, but it is not clear how the phylum assignment was done.○Is the rationale for creating the dataset(s) clearly described?PartlyAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.

Table 1 . Genome data for Epinotia bilunana, ilEpiBilu1.1. Project accession data
(Rhie et al., 2021)enchmarks are adapted from column VGP-2020 of "Table1: Proposed standards and metrics for defining genome assembly quality" from(Rhie et al., 2021).High Sensitivity Assay kit.Fragment size distribution was evaluated by running the sample on the FemtoPulse system.SequencingPacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Genome assembly, curation and evaluation Assembly was carried out withHifiasm (Cheng et al., 2021)and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020).The assembly was

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.21419.r56145© 2023 Ylla G.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.