The genome sequence of the Round-winged Muslin, Thumatha senex (Hübner, 1804)

We present a genome assembly from an individual female Thumatha senex (the Round-winged Muslin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 810.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.


Background
The Round-winged Muslin, Thumatha senex, is a small moth in the subfamily Arctiinae, family Erebidae, closely related to the Footman and Tiger moths.The genus Thumatha includes approximately 20 species, most restricted to sub-Saharan Africa; T. senex is the only representative found in Europe (Volynkin, 2021).While many members of the Arctiinae have brightly coloured wings, advertising unpalatability, T. senex has grey-brown wings with a thin covering of scales giving the moth a papery, translucent and delicate appearance.
In Britain, the moth is widely distributed in marshy areas, fenland and damp woodland in the south-east of England especially East Anglia, but it is less common in central and northern England, Wales and Northern Ireland; it is scarce in Scotland (NBN Atlas Partnership, 2021).In Ireland, the moth has been recorded from central and eastern regions (MothsIreland, 2022).In mainland Europe, the species is also associated with wetland habitats, with many records from the Netherlands, Scandinavia and France; there are scattered records further east across Eurasia including from Russia (GBIF Secretariat, 2022).The larvae are usually described as moss and lichen feeders although a study in marshy ground in southern Germany found the larvae more commonly in the detritus layer feeding on decaying vegetation from sedge Carex sp.(Wagner, 2023).The adults, which fly in summer, have been described as swarming in large numbers at dusk on warm, still nights in suitable habitats (South, 1961;Wagner, 2023).
The genome sequence of Thumatha senex was determined as part of the Darwin Tree of Life project.The assembled genome sequence will facilitate research into adaptations to wetland habitats and contribute to the growing set of resources for studying insect ecology and evolution.

Genome sequence report
The genome was sequenced from one female Thumatha senex (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.34).A total of 48-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 11 missing joins or mis-joins and removed two haplotypic duplications.
The final assembly has a total length of 810.3 Mb in 78 sequence scaffolds with a scaffold N50 of 28.4 Mb (Table 1).Most (99.48%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 28 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).The order and orientation of W chromosome contigs is unknown as the Hi-C data used for scaffolding was derived from a male sample (PacBio HiFi data used for de novo assembly is from a female sample).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/997290.

Sample acquisition and nucleic acid extraction
The specimen used for genome sequencing was a female Thumatha senex (specimen number Ox000618, individual ilThuSene1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2020-07-05, using a light trap.Douglas Boyes (University of Oxford) collected and identified the specimen.The specimen was snap-frozen on dry ice.

A male
T. senex specimen (specimen number NHMUK013805987, ilThuSene2) was collected from Hartslock Nature Reserve latitude 51.51, longitude -1.11) on 2021-07-29.The specimen was collected and identified by Ian Sims (British   Entomological and Natural History Society).This specimen was used for Hi-C scaffolding.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilThuSene1 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.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.
Table 3 contains a list of relevant software tool versions and sources.

Wellcome Sanger Institute -Legal and Governance
The materials that have contributed to this genome 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)  Table 3. Software tools: versions and sources.

Software tool Version
I appreciate the authors for compiling Thumatha senex's whole genome sequence.They employed the appropriate software, genome assembly techniques for the whole genome sequencing.

In the Methods
In the first paragraph, the first sentence can be modified as "A female Thumatha senex (specimen number Ox000618) moth specimen was collected from Wytham Woods, Oxforshire (biological vice-country Berkshire), UK (latitude 51.77 longitude -1.34) on 2020-07-05, using a light trap.Douglas Boyes (University of Oxford) collected and identified the moth species.The specimen was snap-frozen on dry ice until the nucleic acid extraction."

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In the third paragraph the first sentence starts as "The DNA was extracted..." but the second sentence starts as "The whole organism..."?
○ Query: Why have the authors used male and female specimens for the DNA extraction?
○ Overall, the manuscript is written well and it can be Approved for Indexing.

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: Taxonomy and phylogenetic implications of superfamily Noctuoidea moths using mitochondrial genome sequence.
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.
This is a fantastic addition to the genomic resources of the Lepidoptera of Britain and Ireland.I have just a few notes, including some figure errors that require adjustment: Remove "closely related to the Footman and Tiger moths".It is more common for 'tiger moths' to refer to members of Arctiinae (and so Thumatha is a member of the group) and in some cases "Footman" can refer to Lithosiini, to which Thumatha is also a member.

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Is/was the specimen deposited?Is there a voucher remaining?
○ Some justification as to why a male was used for HiFi instead of a female would be welcomed.

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Illumina NovaSeq 6000 read archive information is missing from the "Raw Data Accessions"  Reviewer Expertise: Phylogenomics, evolution, and behavioral ecology of Noctuiodea, especially Erebidae and Arctiinae.
We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above.
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: Genetics and evoluiton of bees 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 Thumatha senex, ilThuSene1.1: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 810,282,324 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 (59,070,461 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (28,419,001 and 16,758,000 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/Thumatha senex/dataset/CAOLNX01/snail.

Figure 3 .
Figure 3. Genome assembly of Thumatha senex, ilThuSene1.1:BlobToolKit GC-coverage plot.Scaffolds are coloured by phylum.Circles are sized in proportion to scaffold length.Histograms show the distribution of scaffold length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Thumathasenex/dataset/CAOLNX01/blob.

Figure 4 .
Figure 4. Genome assembly of Thumatha senex, ilThuSene1.1: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/Thumathasenex/dataset/CAOLNX01/ cumulative.
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.

Figure 5 .
Figure 5. Genome assembly of Thumatha senex, ilThuSene1.1:Hi-C contact map of the ilThuSene1.1 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=ZmhhH1o7TiCmqSVOtyNZcg.

Fig. 2
Fig. 2 missing the BUSCO graph described in figure caption.○

Table 2 . Chromosomal pseudomolecules in the genome assembly of Thumatha senex, ilThuSene1.
www.ncbi.nlm.nih.gov/nuccore/CAOLNX000000000.1) it appears there are 8 associated sequence read archives, but only 4 are included in the "Raw Data Accessions" table.Is there a reason for that?
table, but used to generate Figure 3.○ Based on the GenBank WGS Project page ( ○ https://