The genome sequence of the Straw Underwing, Thalpophila matura (Hufnagel, 1766) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual male Thalpophila matura (the Straw Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 520.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.52 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,185 protein coding genes.


Background
The Straw Underwing moth, Thalpophila matura (Huffnagel, 1766) is an owlet moth belonging to the family Noctuidae with a wide distribution that ranges from Northern Africa to across Europe.They are found in forest edges and grasslands, where larvae feed on a variety of grasses.These moths are predominantly greyish brown with patches of red brown on their forewings.Their hindwings are pale yellow, earning them the common name "straw".Due to their extensive range, they have been included in research on rapid insect decline in Britain (Conrad et al., 2006).Straw underwings are also consideredto be rare habitat specialists, making them an ideal species for studying the diversity in rare and altered habitats (Szalárdi et al., 2021).A genome of the straw underwing is needed for comparative analysis and may contribute to the understanding of biodiversity dynamics and support conservation strategiesin areas where insect populations are declining across Europe.
The genome of the Straw Underwing moth, Thalpophila matura, was sequenced as part of the Darwin Tree of Life 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 Thalpophila matura, based on one male specimen from Wytham Woods, Oxfordshire.

Genome sequence report
The genome was sequenced from one male Thalpophila matura (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 51-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 7 missing joins or mis-joins and removed one haplotypic duplication. The final assembly has a total length of 520.4 Mb in 626 sequence scaffolds with a scaffold N50 of 18.4 Mb (Table 1).The snailplot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (97.99%) of the assembly sequence was assigned to 31 chromosomallevel scaffolds, representing 30 autosomes and the Z sex chromosome.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (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.

Genome annotation report
The Thalpophila matura genome assembly (GCA_948465475.1)was annotated using the Ensembl rapid annotation pipeline (Table 1; https://rapid.ensembl.org/Thalpophila_matura_GCA_948465475.1/Info/Index).The resulting annotation includes 19,392 transcribed mRNAs from 19,185 protein-coding genes.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 DNA sequencing libraries were constructed according to the manufacturers' instructions.DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences SEQUEL II instrument.Hi-C data were also generated from head tissue of ilThaMatu1 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with  et al., 2023).The assembly was checked for contamination and corrected 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., 2023), which runs MitoFinder (Allio 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 Thalpophila A male Thalpophila matura (specimen ID Ox001864, ToLID ilThaMatu1) was collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude -1.34) on 2021-08-11 using a light trap.The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.Protocols developed by the Wellcome Sanger Institute (WSI) Tree of Life core laboratory have been deposited on protocols.io(Denton et al., 2023).The workflow for high molecular weight (HMW) DNA extraction at the WSI includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.In sample preparation, the ilThaMatu1 sample was weighed and dissected on dry ice (Jay et al., 2023).For sample homogenisation, thorax tissue was cryogenically disrupted using the Covaris cryoPREP ® Automated Dry Pulverizer (Narváez-Gómez et al., 2023).

Figure 2 .
Figure 2. Genome assembly of Thalpophila matura, ilThaMatu1.1: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 520,413,395 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 (23,869,902 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (18,353,037 and 10,960,160 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/CAOJZF01/dataset/CAOJZF01/snail.

Figure 3 .
Figure 3. Genome assembly of Thalpophila matura, ilThaMatu1.1: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/CAOJZF01/dataset/CAOJZF01/blob.

Figure 4 .
Figure 4. Genome assembly of Thalpophila matura, ilThaMatu1.1: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/CAOJZF01/dataset/CAOJZF01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Thalpophila matura, ilThaMatu1.1:Hi-C contact map of the ilThaMatu1.1 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=dz68tkCuQ1uUghi9m4M9zw.

Table 1 . Genome data for Thalpophila matura, ilThaMatu1.1. Project accession data
(Bates et al., 2023)) in the WSI Scientific Operations core using the Automated MagAttract v2 protocol(Oatley et al., 2023).HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 31(Bates et al., 2023).Sheared DNA was purified by solid-phase reversible immobilisation(Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA.The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer