The genome sequence of the pebble prominent, Notodonta ziczac (Linnaeus, 1758)

We present a genome assembly from an individual male Notodonta ziczac (the pebble prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 352 megabases in span. The majority of the assembly (99.66%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assembled, and is 18.3 kilobases in length.


Background
The pebble prominent (Notodonta ziczac) is a moth of the family Notodontidae. A typical specimen's wingspan is 42 to 52 mm; its forewings are primarily ochreous brown, with the apical area carrying a grey, pebble-shaped marking from which its common name is drawn (Skinner & Wilson, 2009). Its species name ziczac, from the German zickzack, meaning zigzag, comes from the humps on its caterpillars' sixth, seventh and twelfth segments and the posture it assumes at rest, which creates a zigzag-like pattern (Emmet, 1991;Newman, 1869).
It can be found across the Palearctic region, from North Africa to China, within which the species is sometimes divided into three subspecies (Schintlmeister, 2008). It is widely distributed throughout Britain and Ireland, with observations most frequent in southern England and Wales (Randle et al., 2019). Double-brooded in the south and single-brooded in the north, it usually feeds on willow (Salix spp.), and is less commonly observed on poplar (Populus spp.) (Skinner & Wilson, 2009). It can be found in almost any kind of habitat containing its host plants, including in urban environments (Schintlmeister, 2008). After overwintering as a pupa, the emergence of its first generation currently peaks in May in the UK; this is a notable advancement of several weeks since observations of the 1970s (Randle et al., 2019;South, 1977). Its abundance in the UK declined sharply from 1970 to 2016, and shows a consistent downward trend (Randle et al., 2019).

Genome sequence report
The genome was sequenced from one male N. ziczac ( Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.772, longitude -1.338). A total of 38-fold coverage in Pacific Biosciences single-molecule long reads and 127-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 3 missing/misjoins.
The final assembly has a total length of 352 Mb in 31 sequence scaffolds with a scaffold N50 of 12.7 Mb ( Table 1). The majority of the assembly sequence (99.99%) was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes (numbered by sequence length), and the Z sex chromosome (Figure 2- Figure 5; Table 2). The assembly has a BUSCO v5.2.2 (Manni et al., 2021) completeness of 98.9% (single 98.4%, duplicated 0.5%) 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.

Sample acquisition and DNA extraction
A single male N. ziczac (ilNotZicz1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.772, longitude -1.338) by Douglas Boyes, UKCEH, using a light trap in woodland. The sample was identified by the same individual and preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute. The ilNotZicz1 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. Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. Low molecular weight DNA was removed from a 200-ng aliquot of extracted DNA using 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing. HMW DNA was sheared into an average fragment size between 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

Genome assembly
Assembly was carried out with Hifiasm (Cheng et al., 2021); haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020). One round of polishing was performed by aligning 10X Genomics read data to the assembly with longranger align, calling variants with freebayes   described previously (Howe et al., 2021). Manual curation (Howe et al., 2021) was performed using HiGlass (Kerpedjiev et al., 2018) and Pretext. The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2021), which performs annotation using MitoFinder (Allio et al., 2020). The genome was analysed and BUSCO scores generated within the BlobToolKit environment (Challis et al., 2020). Table 3 contains a list of all software tool versions used, where appropriate.   The genome sequence is released openly for reuse. The N. ziczac 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 and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1.