The genome sequence of the Streamer, Anticlea derivata (Denis & Schiffermüller, 1775) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual female Anticlea derivata (the Streamer; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 355.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.39 kilobases in length.


Background
Anticlea derivata, the Streamer, is an elegant and distinctive moth in the family Geometridae. The forewings are light silvery brown, suffused with violet in fresh specimens. This ground colour is overlain by a series of dark bands, the most distal of which has a sinuous river-like shape that gives the moth its common name. A. derivata has been recorded widely across Europe and east through Russia (GBIF Secretariat, 2022). In Britain, the species can be found throughout England, Scotland, Northern Ireland and Wales, although it is commoner in the south (NBN Atlas Partnership, 2021). In Ireland, A. derivata has been recorded in the west and south of the country (MothsIreland, 2023). The moth is found predominantly around woodland edges and on well-drained hillsides with abundant shrubs and bushes (Wagner, 2023).
In southern Britain and central Europe, the adult moth is on the wing in April and May, with larvae feeding from May to June or July on leaves of dog-rose Rosa canina. The larvae are green with a series of pale yellow hoops encircling the body, and brown diamond-shaped patches along the dorsal midline. The pupae overwinter (Wagner, 2023).
We present a complete genome sequence for Anticlea derivata, determined as part of the Darwin Tree of Life project. The assembled genome sequence will facilitate research into host plant adaptations in Lepidoptera and contribute to the growing set of resources for understanding molecular evolution in insects.

Genome sequence report
The genome was sequenced from one female Anticlea derivata ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.34). A total of 67-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 5 missing joins or mis-joins, reducing the scaffold number by 4.76%.
The final assembly has a total length of 355.8 Mb in 39 sequence scaffolds with a scaffold N50 of 12.7 Mb (Table 1). Most (99.99%) of the assembly sequence was assigned to 32 chromosomal-level scaffolds, representing 30 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). 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/934824.

Sample acquisition and nucleic acid extraction
A female Anticlea derivata (ilAntDeri1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2021-03-31, using a light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford) and was snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The ilAntDeri1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Head and 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. 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 Pacific Biosciences SEQUEL II (HiFi) instrument. Hi-C data were also generated from head and thorax tissue of ilAntDeri1 that had been set aside, using the Arimav2 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 purge_dups (Guan et al., 2020). The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou 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., 2022), 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.
A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020). To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury (Rhie et al., 2020). This work was done using Nextflow (Di Tommaso et al., 2017) DSL2 pipelines "sanger-tol/readmapping" (Surana et al., 2023a) and "sanger-tol/genomenote" (Surana et al., 2023b). The genome was analysed within the BlobToolKit environment (Challis et al., 2020) and BUSCO scores (Manni et al., 2021;Simão et al., 2015) were calculated.  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   The genome sequence is released openly for reuse. The Anticlea derivata 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.