The genome sequence of the Buff Footman, Eilema depressum (Esper, 1787)

We present a genome assembly from an individual male Eilema depressum (the Buff Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 622.0 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,038 protein coding genes.


Background
The Buff Footman moth, Eilema depressum (Esper 1787) is a drab-coloured moth in the family Erebidae.It has a Eurasiatic distribution that ranges throughout Europe to Japan (Grassi & Zilli, 2005).There are over 160 described species in this genus.Eilema depressum is sexually dimorphic: females are larger and darker in colour with a yellow border along the edge of their forewings, while males are smaller and paler in colouration (Kobayashi, 1969).
The Buff Footman belongs to a group of lichen and algal feeding moths, feeding on species such as Parmelia and Pleurococcus.Because of their unique feeding, Eilema species have been used to research community dynamics, and an abundant population of lichen feeding Eilema species may indicate environmental health or recovery (Seymour et al., 2020).Some species of Eilema have been studied for their ability to feed and sequester lichen compounds like parietin, divaricatic acid, and usnic acid (Hesbacher et al., 1995).
A genome of E. depressum is needed to better understand community dynamics and the sequestration of secondary compounds in lichen feeding moths.Here we present a chromosomally complete genome sequence for E. depressum, based on one male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one male Eilema depressum (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.34).A total of 54-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 109-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 misjoins, reducing the scaffold number by 6.25%.
The final assembly has a total length of 622.0 Mb in 30 sequence scaffolds with a scaffold N50 of 22.1 Mb (Table 1).The whole assembly sequence was assigned to 30 chromosomallevel scaffolds, representing 29 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/987419.

Sample acquisition and nucleic acid extraction
A male Eilema depressum (specimen ID Ox000804, individual ilEilDepe1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2020-08-01 using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilEilDepe1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Thorax 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.
RNA was extracted from abdomen tissue of ilEilDepe1 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer's instructions.RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using

INSDC accession Chromosome Length (Mb) GC%
OU612027  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 Eilema depressum assembly (GCA_914767945.1) 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 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 • Legality of collection, transfer and use (national and international) 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.

Species Identification:
The authors should cite the literature used for species identification.

2.
Mitochondrial Genome: I strongly recommend submitting the mitochondrial genome separately with an independent accession number.Moreover, while the authors described the methods, they did not provide information about the mitochondrial genome annotation (coding genes, rRNAs, and tRNAs).It is expected that the authors submit the annotations obtained by MITOS separately.

Annotation:
The authors should identify and quantify the transposable elements in the genome.

4.
Command Lines: It is common practice to include the command lines used with all software.Providing this information would be very useful for readers.

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: genomic transcriptomics and proteomics 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 manuscript is well-structured, with data and methodologies that are both appropriate and reliable.In my opinion, this work is well-suited for indexing in Wellcome Open Research.
That said, there are a few minor concerns that merit clarification: specifically, why was a male (ZZ karyotype) sample chosen for sequencing instead of a female (ZW karyotype)?
Is the rationale for creating the dataset(s) clearly described?

Sivasankaran Kuppusamy
Entomology Research Institute, Loyola College, Chennai, India Authors have sequenced and assembled the whole genome of Buff Footman moth Eilema depressum (Esper, 1787).A total length of 622 mb sequence was assembled.A total of 30 chromosomes were confirmed through the assembly.Totally 20, 038 protein coding genes and 20, 236 gene transcripts were observed through the assembly and annotation.

Minor comments on the manuscripts:
Authors have given the genus name of the species Eilema depressum full form throughout the article.And given a short form somewhere.First time the genus name can be given in full form then subsequently can be given in short form like E. depressum.

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In the background the first sentence can be modified as "The Buff Footman moth, Eilema depressum (Esper, 1787) is a drab-coloured moth belonging to the family Erebidae".

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In the genome sequence report (subheading), the first line can be modified as "The genome was sequenced from a male Eilema depressum specimen (Figure 1)".The collection details need not be given here.Because the collection details were given in the methods.

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The table 3 legend was given inside text.The legend can be changed as a text "A list of relevant software tool versions and sources are given in the Table 3".

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Above all, the manuscript was well prepared, and I confirm that the manuscript meets the necessary scientific standard and is suitable for indexing.Reviewer Expertise: phylogenetic analysis of moths using mitogenome 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 Eilema depressum, ilEilDepe1.1: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 622,022,279 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 (46,029,750 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (22,085,244 and 14,221,244 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/Eilema depressum/dataset/ilEilDepe1_1.1/snail.

Figure 4 .
Figure 4. Genome assembly of Eilema depressum, ilEilDepe1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all scaffolds.Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Eilemadepressum/dataset/ilEilDepe1_ 1.1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Eilema depressum, ilEilDepe1.1:Hi-C contact map of the ilEilDepe1.1 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=dMhsDho0SFypSA4I_HI3eQ.

Reviewer Report 23
August 2024 https://doi.org/10.21956/wellcomeopenres.21940.r93172© 2024 Mei Y.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.Yang Mei State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou, Zhejiang, China This manuscript presents the genome assembly of the Buff Footman moth, Eilema depressum.The authors employ a rigorous approach to sample collection, nucleic acid extraction, and sequencing, incorporating advanced techniques such as HiFi and Hi-C.Using robust assembly methods, they have successfully generated a high-quality genome, achieving an impressive BUSCO completeness score of 98.8% and a scaffold N50 of 22.1 Mb.

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Is the rationale for creating the dataset(s) clearly described?YesAre 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?Partly Competing Interests: No competing interests were disclosed.

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 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.21940.r88932© 2024 Kuppusamy S. 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.