The genome sequence of the poplar hawk-moth, Laothoe populi (Linnaeus, 1758) [version 1; peer review: 1 approved]

We present a genome assembly from an individual female Laothoe populi (the poplar hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 576 megabases in span. The majority of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.


Introduction
Laothoe populi (Poplar hawk-moth) is one of the largest native Lepidoptera species in the UK; larval colouration varies and relates to differences in sequestration and transport of carotenoids derived from foodplants, poplar (Populus sp.) and willow (Salix sp.) (Grayson et al., 1991). The genome of L. populi was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all of the named eukaryotic species in the Atlantic Archipelago of Britain and Ireland. Here we present a chromosomally complete genome sequence for L. populi, based on one female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from a single female L. populi collected from Wytham Woods, Oxfordshire, UK (latitude 51.768, longitude -1.337). A total of 28-fold coverage in Pacific Biosciences single-molecule long reads and 68-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 103 missing/ misjoins and removed 20 haplotypic duplications, reducing the assembly length by 1.19% and the scaffold number by 61.45%, and increasing the scaffold N50 by 12.08%. The final assembly has a total length of 576 Mb in 33 sequence scaffolds with a scaffold N50 of 21 Mb (Table 1). Of the assembly sequence, >99.9% was assigned to 29 chromosomal-level scaffolds, representing 27 autosomes (numbered by sequence length), and the W and Z sex chromosome (Figure 1-Figure 4; Table 2). The assembly has a BUSCO (Simão et al., 2015) completeness of 98.8% 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 female L. populi was collected from Wytham Woods, Oxfordshire, UK (latitude 51.768, longitude -1.337) by Douglas Boyes, University of Oxford using a light trap. The specimens were snap-frozen in dry ice using a CoolRack before transferring to the Wellcome Sanger Institute (WSI).
DNA was extracted at the Tree of Life laboratory, WSI. The ilLaoPopu1 sample was weighed and dissected on dry ice with head/thorax tissue set aside for Hi-C sequencing. Abdomen 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. HiSeq X instruments. HiC data were generated from head/thorax tissue using the Arima v2.0 kit and sequenced on HiSeq X.
Assembly was carried out with Hifiasm (Cheng et al., 2021); haplotypic duplication was identified and removed with purge_dups ( Guan et al., 2020). The assembly was polished with the 10X Genomics Illumina data by aligning to the assembly with longranger align, calling variants with freebayes (Garrison & Marth 2012). One round of the Illumina polishing was applied. Scaffolding with Hi-C data (Rao et al., 2014) was carried out with 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 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.
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, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired

Data availability
European Nucleotide Archive: Laothoe populi (poplar hawk-moth). Accession number PRJEB42952: https://identifiers. org/ena.embl:PRJEB42952 The genome sequence is released openly for reuse. The L. populi 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. Raw data and assembly accession identifiers are reported in Table 1.