The genome sequence of the spectacle, Abrostola tripartita Hufnagel, 1766

We present a genome assembly from an individual male Abrostola tripartita (the spectacle; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 381 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.


Background
Abrostola tripartita (the spectacle) is a grey and white noctuid moth recorded from across the Palaearctic region. It is found commonly across the UK where it has increased significantly in abundance in recent decades (Sterling & Henwood, 2020). The common name derives from two rings of grey hairs on the thorax with the appearance of a pair of goggles, visible when the moth is viewed from anterior; these hairs are on the thorax and are not associated with the head or eyes. The larvae feed on nettle (Urtica dioica) and may be found across any habitat where the food plant is in abundance. Adults often feed at flowers including red valerian (Centranthus ruber) and sage (Salvia). In the UK the adult flight period occurs as a single generation in the north (May to July) and as two generations in the south (May-July and July-September) (Waring et al., 2003). Overwintering occurs as a pupa among plant litter on the ground or under bark.

Genome sequence report
The genome was sequenced from one male A. tripartita ( Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.769, longitude -1.339). A total of 54-fold coverage in Pacific Biosciences single-molecule long reads and 102-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 30 missing/misjoins and removed 3 haplotypic duplications, reducing the assembly size by 0.44% and the scaffold number by 20.00%.
The final assembly has a total length of 381 Mb in 32 sequence scaffolds with a scaffold N50 of 13.6 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 v5.1.2 (Manni et al., 2021) completeness of 99.0% (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.

Methods
A single male A. tripartita (ilAbrTrip1) was collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.769, longitude -1.339) by Douglas Boyes, UKCEH, using a light trap. 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 ilAbrTrip1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C and RNA 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 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.
RNA was extracted from abdomen tissue in the Tree of Life Laboratory at the WSI using TRIzol (Invitrogen), according to the manufacturer's instructions. RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit. Analysis of the  Hi-C data were generated from head tissue using the Arima Hi-C+ kit and sequenced on HiSeq X.

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 (Garrison & Marth, 2012). The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using SALSA2 (Ghurye et al., 2019). The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021). Manual curation (Howe et al., 2021) was performed using gEVAL, HiGlass  (Kerpedjiev et al., 2018) and Pretext. The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2021). 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.

Ethics/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,