The genome sequence of the lime hawk-moth, Mimas tiliae (Linnaeus, 1758)

We present a genome assembly from an individual male Mimas tiliae (the lime hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 478 megabases in span. The complete assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled.


Background
Mimas tiliae (lime hawk-moth) is characterised by scalloped edges to the forewing, along with bold green and buff markings, which are thought to disrupt object perception by predators through 'disruptive coloration' (Stevens et al., 2006). The wing markings also show 'edge enhanced colouration' which may also slow object recognition by a predator (Sharman et al., 2018). Mimas tiliae is common throughout southern England, particularly London, and has spread further north in recent years, with one record of breeding as far north as Glasgow, Scotland (Payne, 2020). The species can be found in woodland and in suburban habitats, and flies in May and June. The genome of M. tiliae 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 M. tiliae, based on one male specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from a single male M. tiliae ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (latitude 51.768, longitude -1.337). A total of 37-fold coverage in Pacific Biosciences single-molecule long reads and 80-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 10 missing/misjoins and removed 2 haplotypic duplications, reducing the assembly length by 0.05% and the scaffold number by 21.62%.
The final assembly has a total length of 478 Mb in 29 sequence scaffolds with a scaffold N50 of 18 Mb (Table 1). Of the assembly sequence, 100% was assigned to 29 chromosomal-level scaffolds, representing 28 autosomes (numbered by sequence length), and the Z sex chromosome (Figure 2- Figure 5; Table 2). The assembly has a BUSCO v5.1.2 (Simão et al., 2015) completeness of 98.8% (single 98.5%, duplicated 0.3%) 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.  by Douglas Boyes, UKCEH, using a light trap. The specimen was identified by the same individual and preserved on dry ice.

Sample acquisition and DNA extraction
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute. The ilMimTili1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.
Abdomen tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle. 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 sequencing libraries were constructed according to the manufacturers' instructions. Sequencing was performed by the Scientific Operations core at the Wellcome Sanger Institute on Pacific Biosciences SEQUEL II and Illumina HiSeq X instruments. Hi-C data were generated from head/thorax tissue using the Arima Hi-C+ kit and sequenced on HiSeq X.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound? Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format? Yes