The genome sequence of the sycamore, Acronicta aceris (Linnaeus, 1758)

We present a genome assembly from an individual female Acronicta aceris (the sycamore; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 466 megabases in span. The complete assembly is scaffolded into 32 chromosomal pseudomolecules, with the W and Z sex chromosome assembled.


Background
Acronicta aceris (sycamore moth) is a widely distributed noctuid moth found in Europe, Morocco and western regions of Asia. In the UK it is locally common in southeast and central England, with a flight season from June to August. Forewing colouration of the moth varies from silvery to dark grey, with variation in ground colour likely controlled by alleles at a single locus (Majerus, 1986). The larvae of A. aceris are amongst the most colourful and flamboyant of all Lepidoptera caterpillars, bearing yellow and orange hairs arranged in striking 'punk' tufts along the body. As the common name suggests, the larvae feed on the leaves of sycamore (Acer pseudoplatanus), other maples (Acer sp.) and, particularly in urban and suburban areas, horse chestnut (Aesculus hippocastanum). Larvae are active from July to September and overwintering occurs as a pupa in a double-layered cocoon in bark crevices or leaf litter. It is known to occasionally overwinter as a pupa through two winters before eclosing as an imago (Waring et al., 2003).

Genome sequence report
The genome was sequenced from one female A. berbera ( Figure 1) collected from Wytham Woods, Oxfordshire (biological vice-county: Berkshire), UK (latitude 51.772, longitude -1.338). A total of 39-fold coverage in Pacific Biosciences singlemolecule long reads and 99-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 14 missing/misjoins, reducing the scaffold number by 20.00% and increasing the scaffold N50 by 4.33%.
The final assembly has a total length of 466 Mb in 32 sequence scaffolds with a scaffold N50 of 16.1 Mb (Table 1). The complete assembly sequence was assigned to 32 chromosomal-level scaffolds, representing 30 autosomes (numbered by sequence length), and the W and 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 98.5%, 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.

Methods
Sample acquisition and DNA extraction A single female A. aceris (ilAcrAcer1) 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. 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 ilAcrAcer1 sample was weighed and dissected on dry ice with 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.

Sequencing
Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers' instructions. Sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II and Illumina HiSeq X instruments. Hi-C data were generated from abdomen tissue using the Arima v2 Hi-C kit and sequenced on an Illumina NovaSeq 6000 X instrument.       after polishing. This will further add knowledge to the quality of the long-reads and to the overall assembly quality.
I think it would be useful to the readers if the authors add an estimate of the base-level accuracy (QV) for the assembly. QV values are useful for downstream applications like population or functional genetics. This stat could be easily calculated using Merqury (Rhie et al. Genome Biol 21, 245 (2020 1 )) 3.