The genome sequence of the Water Carpet, Lampropteryx suffumata (Denis & Schiffermiiller, 1775) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual male Lampropteryx suffumata (the Water Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 581.6 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 16.48 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,663 protein coding genes.


Background
Many species of insect are found widely across the Palaearctic realm from Europe to Asia, but relatively few have distributions that also extend to North America. Some exceptions include highly migratory species and those transported by human activity. A land connection existed until around five million years ago, the Bering land bridge, and until the land connection was lost there was some dispersal of species in each direction (Gladenkov et al., 2002;Jiang et al., 2019). The Water Carpet Lampropteryx suffumata is a moth in the family Geometridae now known to exist on both sides of the Bering Strait. In Eurasia, the species is found commonly in northern and central Europe with the largest numbers of records from Britain, Scandinavia and Austria; there are scattered records ranging from Ireland and France in the west across to the far east of Russia, including Khabarovsk Krai and the Kamchatka peninsula, and on the Japanese island of Hokkaido (Beljaev & Vasilenko, 2002;Beljaev et al., 2022). In 2000 eight specimens of L. suffumata were recorded from Alaska, and in 2008 several Canadian specimens in museum collections were retrospectively identified as L. suffumata by DNA barcoding, including a historical specimen dating from 1919 (Choi, 2000;Dewaard et al., 2008). There is no suggestion that these North American individuals were accidentally introduced. Hence, the longitudinal range of L. suffumata extends from the Dingle Peninsula, Ireland, eastward across Eurasia and the Bering Strait to reach Alberta, Canada.
Like most 'carpet' moths, named for their resemblance to the intricate patterns on woven carpets, the Water Carpet rests with its wings flat against the surface in a delta shape. The forewings are silvery-grey with a deeply indented brown cross-band outlined in white. In Britain and Ireland, the moth is on the wing from March to May, with the emergence time having moved earlier in the year since the 1970s (Randle et al., 2019). The species is most commonly encountered in damp woodland, moorland and fens, where the larvae feed on cleavers (Galium aparine) and other Galium species; the pupal stage overwinters (South, 1961;Waring et al., 2017).
The complete genome sequence of Lampropteryx suffumata was determined as part of the Darwin Tree of Life project. The assembled genome will facilitate studies into the biogeography and population genetics of this widespread species and contribute to the growing set of resources for studying insect ecology and evolution.

Genome sequence report
The genome was sequenced from one male Lampropteryx suffumata ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, -1.34). A total of 39-fold coverage in Pacific Biosciences single-molecule HiFi long was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 31 missing joins or mis-joins and removed 16 haplotypic duplications, reducing the assembly length by 1.99 % and the scaffold number by 11.86%, and increasing the scaffold N50 by 1.22%.
The final assembly has a total length of 581.6 Mb in 51 sequence scaffolds with a scaffold N50 of 20.0 Mb (Table 1). Most (99.81%) 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 Z chromosome was identified based on synteny with Eulithis prunata (GCA_918843925.1) (Boyes & Holland, 2023). 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/934945.

Sample acquisition and nucleic acid extraction
The specimen used for genome sequencing was a male Lampropteryx suffumata (specimen ID Ox001102, ilLamSuff1) 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   Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from head tissue of ilLamSuff1 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 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.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021)  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