The genome sequence of the Rose-flounced Tabby, Endotricha flammealis (Denis & Schiffermüller, 1775)

We present a genome assembly from an individual female Endotricha flammealis (the Rose-flounced Tabby; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 473.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,578 protein coding genes.


Background
Endotricha flammealis, also known as the Rose-flounced Tabby, is a species of snout moth of the family Pyralidae.This species is found in western, central, and southern Europe, extending to Turkey, Crimea, Cyprus, Iran, Lebanon, Syria, and north Africa's Maghreb region, which includes Algeria and Tunisia.While it is widespread in southern Britain, it is absent in Ireland (GBIF Secretariat, 2022).This species is known to inhabit gardens, heathland, woodland and grassland.It has an unusual resting posture, with the front of its body elevated by its forelegs and its wings held at an angle, touching the surface it rests on.It is also identifiable by distinct physical features, such as two thin white cross-lines, dark spots in the middle of its wings, and a reddishpurple hue (Sterling & Parsons, 2018).
The moths fly from July to August in Britain and Ireland, and are attracted to light.They mainly feed on nectar of Calluna vulgaris, Tanacetum vulgare, Chamerion angustifolium, Buddleja davidii, Heracleum sphondylium and Jacobaea vulgaris.The females lay their eggs in summer on the underside of leaves.The caterpillars typically feed on common agrimony (Agrimonia eupatoria) and bilberries (Vaccinium), as well as on various plant remains and on dry leaves of willows (Salix) and oaks (Quercus).This polyphagous species is not threatened in any part of its range (Sterling & Parsons, 2018).
The genome of the Rose-flounced Tabby, Endotricha flammealis, 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.A genome assembly for the Rose-flounced Tabby will give us access to valuable genomic resources that can be used to improve our understanding of lepidopteran biology, as well as provide insights into trait and function evolution in Lepidoptera superfamily (Zhu et al., 2018).

Genome sequence report
The genome was sequenced from one female Endotricha flammealis (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 19-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 86-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 172 missing joins or misjoins and removed 37 haplotypic duplications, reducing the assembly length by 1.71% and the scaffold number by 64.6%, and increasing the scaffold N50 by 6.33%. The final assembly has a total length of 473.9 Mb in 40 sequence scaffolds with a scaffold N50 of 16.2 Mb (Table 1).Most 99.92%) of the assembly sequence was assigned to 32 chromosomal-level scaffolds, representing 30 autosomes and the W and Z sex chromosomes.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/1101095.
The resulting annotation includes 17,781 transcribed mRNAs from 17,578 proteincoding genes.

Sample acquisition and nucleic acid extraction
A female Endotricha flammealis (specimen ID Ox000062, individual ilEndFlam1) was collected from Wytham Woods, Oxfordshire (biological vice-country Berkshire), UK (latitude 51.77, longitude -1.33) on 2019-07-17 using a light trap.The   specimen was collected and identified by Douglas Boyes (University of Oxford) and was snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEndFlam1 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 Pacific Biosciences SEQUEL II (HiFi) and HiSeq X Ten (10X) instruments.Hi-C data were also generated from tissue of ilEndFlam1 using the Arima2 kit and sequenced on the HiSeq X Ten instrument.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.
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 Endotricha flammealis assembly (GCA_905163395.2) 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

Kay Lucek
University of Basel, Basel, Switzerland The authors present the chromosome level genome assembly of a male specimen of the Roseflounced Tabby moth Endotricha flammealis.The assembly consists of 32 chromosomes including both sex chromosomes.The assembly is highly complete as revealed by the high BUSCO score but not fully phased.Sequencing and genome assembly follow the current state of the art and use established methods.
Overall, the presented assembly will be of great value to study genome architecture as well as genome size evolution in Lepidoptera.It is very interesting to see that a 19X long read coverage is enough to resolve a chromosome level assembly in this holocentric species group.Although I was wondering if this could explain the additional larger scaffolds that were not part of the chromosome assembly.
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: Speciation 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 Endotricha flammealis, ilEndFlam1.2: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 473,948,990 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 (24,152,721 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (16,153,102 and 10,965,917 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/ilEndFlam1.2/dataset/CAJHZK02.1/snail.

Figure 5 .
Figure 5. Genome assembly of Endotricha flammealis, ilEndFlam1.2:Hi-C contact map of the ilEndFlam1.2assembly, 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=JxsPDaCSQIGNGfqEzxAHdQ.

Table 3 . Software tools: versions and sources. Software tool Version 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: entomology, biodiversity, bioinformatics 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.
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