The genome sequence of the Burnished Brass, Diachrysia chrysitis (Linnaeus, 1758)

We present a genome assembly from an individual male Diachrysia chrysitis (the Burnished Brass; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 386 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,320 protein coding genes.


Background
The Burnished Brass Diachrysia chrisitis (Linnaeus, 1758) is one of the most striking noctuid moths found in UK, characterised by shimmering metallic golden patches on the forewings. The adult is on the wing from June to September in the UK in two overlapping generations; the second generation has become more frequent since 1970(Randle et al., 2019. Larvae feed primarily on nettle (Urtica dioica) and sometimes other herbaceous plants. The species is widespread across the UK and found throughout much of Europe and Russia (GBIF Secretariat, 2021).
The iridescent gold sheen on the forewings is a structural colour generated by light scattering and interference rather than a chemical pigment. Indeed, wing scales in the gold regions are devoid of melanin pigment and form a nanoscale multilayer structure enclosing a sandwich of irregular spheres (Savić-Šević et al., 2018). The spectrum of reflected light from golden regions of the wing is a close match to that generated by true metallic gold (Pantelić et al., 2017). These remarkable optical properties have stimulated efforts to mimic the structure in a laboratory setting, and a successful proof of concept has been achieved using layers of polysaccharide sandwiching spherical nanoparticles of variable size (Savić-Šević et al., 2018). Similar multilayer structures may ultimately prove useful in solar energy collection and other applications.
The typical form of the Burnished Brass moth has two separate bands of gold on the forewing separated by a broad region of brown scales, while a variant has a 'bridge' between the golden regions forming a letter 'H' pattern (form juncta). Although intermediate forms exist, there has been discussion over whether the two extreme wing pattern morphs in the UK represent different species, with the juncta form potentially being D. stenochrysis, a moth found across the Eastern Palaeartic Region and much of mainland Europe (Hammond, 2022;Plant, 2010). Application of reflectance spectroscopy to wings of D. chrisitis and D. stenochrysis collected in Poland revealed significant differences related to chemical composition and scale structure, suggestive of species-level distinction (Dyba et al., 2022). These methods have not yet been applied to UK specimens. Molecular phylogenetic analysis using the mitochondrial COI gene also divides specimens from mainland Europe into distinct clades for D. chrisitis and D. stenochrysis. The taxonomic situation is less clear in the UK, since DNA barcodes from several UK specimens with the juncta wing pattern cluster with D. chrisitis rather than with D. stenochrysis (P.W.H. Holland and P.O. Mulhair analysis at the Barcode of Life Database (BOLD, 2023)). This suggests either that there is a single species of burnished brass moth in the UK (D. chrysitis) or that the two species exist but the juncta trait has introgressed across the species boundary. A recent preliminary report of UK moths with barcodes comparable to D. stenochrysis (Hammond, 2022) needs to be followed up with further phylogenetic analyses and inclusion of more sequences from additional UK individuals, ideally from multiple genetic loci.
A genome sequence from Diachrysia chrisitis will prove useful as a reference genome for resolving the taxonomy of this genus and for probing the basis of species differentiation. It may also lay a foundation for understanding the developmental genetic basis of the unusual photonic scale structures. The complete genome sequence presented here is generated from an individual burnished brass moth with a juncta wing pattern and a C. chrisitis-type CO1 DNA barcode.

Genome sequence report
The genome was sequenced from one male D. chrysitis ( Figure 1) collected from Wytham Woods, UK (latitude 51.77, longitude -1.34). A total of 34-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.
The final assembly has a total length of 386.4 Mb in 41 sequence scaffolds with a scaffold N50 of 13.4 Mb (Table 1). Most (99.89%) of the assembly sequence was assigned to 31 chromosomal-level 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 2- Figure 5; Table 2). The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 99.1% (single 98.8%, duplicated 0.2%) using the lepidoptera_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.

Genome annotation report
The D. chrysitis GCA_932294365.1 genome assembly was annotated using the Ensembl rapid annotation pipeline (

Sample acquisition and nucleic acid extraction
One male Diachrysia chrysitis (ilDiaChry1) specimen was collected in Wytham Woods, Oxfordshire (biological vicecounty: Berkshire), UK (latitude 51.77, longitude -1.34) on 8 September 2020, using a light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford) and snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The ilDiaChry1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Thorax tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. 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.

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 the Pacific Biosciences SEQUEL II (HiFi) instrument. Hi-C data were also generated from head tissue of ilDiaChry1 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020). The assembly was 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), which performed annotation using MitoFinder (Allio et al., 2020). The genome was analysed and BUSCO scores were generated  Table 3 contains a list of all software tool versions used, where appropriate.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Diachrysia chrysitis assembly (GCA_934047225.1) in Ensembl Rapid Release.

Ethics and compliance issues
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. 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,   The genome sequence is released openly for reuse. The Diachrysia chrysitis genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. Raw data and assembly accession identifiers are reported in Table 1.