The genome sequence of the Grey Dagger, Acronicta psi (Linnaeus, 1758)

We present a genome assembly from an individual male Acronicta psi (the Grey Dagger; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 405 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases long.


Background
Acronicta psi, Grey Dagger, is a common and widespread moth in Britain and Ireland, found throughout Europe, North Africa, the Near East and Central Asia. The larvae are polyphagous, feeding on a variety of trees and shrubs, but particularly Rosaceae, in woodland, gardens and a variety of other habitats (Waring et al., 2017). The caterpillars feed in the summer and autumn with adults on the wing, at least in Britain, usually from late April through July, although sometimes with a second generation in the autumn.
The Latin and English names both refer to the prominent black streak on the tornal area of the forewing, resembling the Greek ψ (psi), or a dagger shape. Although a distinctive feature at the genus level, A. psi adults are confusingly similar to Dark Dagger, Acronicta tridens (Denis and Schiffermüller). They are only really separable by genitalia examination (nicely illustrated by Townsend et al., 2011). Males of the two species are easily separable by the number of projections on the ventral surface of the valva. The genitalia of the specimen sequenced were checked and retained.
Both species are widespread and polyphagous although, unlike the adults, the larvae of Dark and Grey Dagger are very different in appearance. A. psi has been used as an exemplar generalis moth species in investigating the different responses of specialists and generalists to elevated levels of tannin compounds found in leaves (Roslin & Salminen, 2008). Unlike some Oak-(Quercus) feeding specialists, the tannin Vescalagin has a severe impact on the growth of A. psi larvae. This genome adds to a rapidly increasing number of genomes for Lepidoptera and should be very useful to researchers interested in the hugely significant radiation of the family Noctuidae.

Genome sequence report
The genome was sequenced from one male Acronicta psi ( Figure 1) collected from a garden in Tonbridge, UK (51.19,0.29). A total of 45-fold coverage in Pacific Biosciences singlemolecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation  Hi-C data. Manual assembly curation corrected one missing join, reducing the scaffold number by 3.03%. The final assembly has a total length of 404.7 Mb in 32 sequence scaffolds with a scaffold N50 of 14.2 Mb (Table 1). The whole assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes, and the Z sex chromosome (Figure 2- Figure 5; Table 2). Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size. The genome assembly for Acronicta aceris (GCA_910591435) (Boyes et al., 2021) was used to identify the sex chromosome. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 98.6% (single 98.6%, duplicated 0.3%) using the lepidoptera_odb10 reference set.

Sample acquisition and nucleic acid extraction
A male Acronicta psi specimen (ilAcrPsix1) was collected from a garden in Tonbridge, Kent, UK (latitude 51.19, longitude 0.29), using a light trap and then snap-frozen at -80°C. The specimen was collected and identified by Gavin Broad (Natural History Museum).
DNA was extracted from thorax tissue of ilAcrPsix1 at the Wellcome Sanger Institute (WSI) Scientific Operations core from the whole organism using the Qiagen MagAttract HMW DNA kit, according to the manufacturer's instructions.

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 Pacific Biosciences SEQUEL II (HiFi) instrument. Hi-C data were also generated from head tissue of ilAcrPsix1 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., 2022). 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., 2021), which performed annotation using MitoFinder (Allio et al., 2020). The genome was analysed and BUSCO scores were generated within the Blob-ToolKit environment (Challis et al., 2020). Table 3    The genome sequence is released openly for reuse. The Acronicta psi 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. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1.

Open Peer Review
Reviewer Expertise: Analyzing the phylogenetic relationships 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.