The genome sequence of the White-barred Gold, Micropterix aruncella (Scopoli, 1763)

We present a genome assembly from an individual female Micropterix aruncella (the White-barred Gold; Arthropoda, Insecta, Lepidoptera; Micropterigidae). The genome sequence is 1,079 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.0 kilobases in length.


Background
The phylogenetic relationships between families of Lepidoptera have been the subject of debate and discussion for decades, with much uncertainty. One point of almost total agreement, from the earliest morphological analyses to the latest molecular trees, is that the family Micropterygidae is the extant sister group to all other Lepidoptera (with the rare family Agathiphagidae sometimes placed sister to Micropterygidae (Regier et al., 2013;Regier et al., 2015). Therefore, the most ancient node in lepidopteran phylogeny separates Micropterygidae from all other moths and butterflies. In order to catalogue and understand the molecular innovations that characterise all Lepidoptera, it is essential to include genomic data from moths in this family. Li et al. (2021) previously reported the genome of Neomicropteryx cornuta, but there is a need for additional genome sequence data from the Micropterygidae.
Micropterix aruncella (White-barred Gold) is a small dayflying moth in the family Micropterygidae, with a scattered distribution across the UK, Europe and Russia (National Biodiversity Atlas, no date; GBIF Secretariat, 2021). Adults have a wingspan of only 6-7 mm. Males are recognisable by their bright golden colouration crossed by two silver stripes, while females lack the stripes and can be difficult to distinguish from some other Micropterix species. Sex determination in the genus Micropterix is reported to involve a Z/ZZ chromosome system (Traut & Marec, 1997). Like other members of the family, adult M. aruncella lack a proboscis: adults feed on pollen using chewing mouthparts, often from buttercup flowers in sunny woodland glades. Larvae are thought to feed at the base of herbaceous plants, but much remains to be learnt about their habits. The anatomy of the larva has been described in detail by (Klausnitzer et al., 2002).
The genome of M. aruncella was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland. Here we present a chromosomally complete genome sequence for M. aruncella, based on the ilMicArun2 specimen from Bagley Wood, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from a female M. aruncella specimen ( Figure 1) collected from Bagley Wood, Berkshire, UK (51.72, -1.27). A total of 18-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 462 missing or mis-joins and removed 75 haplotypic duplications, reducing the assembly length by 0.8% and the scaffold number by 15.8%, and increasing the scaffold N50 by 5.29%.
The final assembly has a total length of 1,079.2 Mb in 826 sequence scaffolds with a scaffold N50 of 35.3 Mb (Table 1). Most (95.96%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 autosomes and the Z sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2- Figure 5; Table 2). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.
The assembly has a BUSCO v5.3.2 (Manni et al., 2021) completeness of 75.8% (single 74.4%, duplicated 1.5%), using the OrthoDB version 10 lepidoptera reference set This test may not be optimal for M. aruncella as the Micropterygidae are an outgroup to the set of species used to generate the Lepidoptera reference set. Using the Insecta reference set, the BUSCO completeness is 97.7% (single 96.0%, duplicated 1.7%). Evaluation of the assembly shows a consensus quality value (QV) of 53.9 and k-mer completeness of 99.98%. Specimens were identified by James Hammond and snapfrozen at -80°C by Peter Holland. Specimen ilMicArun2 (female) was used for acquisition of the genome sequence; specimen ilMicArun4 (male) was used for Hi-C scaffolding.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute. The ilMicArun2 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Whole body tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. HMW DNA was sheared into an average fragment size of 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. DNA sequencing was performed by the Scientific Operations core at the WSI on the Pacific Biosciences SEQUEL II (HiFi) instruments. Hi-C data were also generated from whole body tissue of ilMicArun4 using the Arima v2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

University of Copenhaguen, Copenhaguen, Denmark
The authors describe the genome assembly of Micropterix aruncella in the submitted data note, which is a high quality phased genome assembled at the chromosome level. This genome is a valuable resource for phylogenomic and comparative genomics analyses as an outgroup of Lepidoptera.
The methods are robust, and I would recommend this manuscript to be accepted although I have some suggestions that could improve the manuscript: Table 1: The BUSCO score calls the attention as it is very low for a high quality genome, so I would recommend to add another row with the Insecta BUSCO dataset so the reader can see that it might just be an artifact of the Lepidopera dataset. The authors discuss it in the text, but I would add it in the table. In addition, they could add a more general BUSCO dataset, such as Eukaryota to validate the gene completeness.
○ I see in the dTol webpage that this genome is already annotated and the annotations are publicly available. The authors need to update this information in the text, and I would encourage to include the statistics from gene annotation in the manuscript.

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 Competing Interests: No competing interests were disclosed.

Reviewer Expertise: Genomics
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.