The genome sequence of the Dingy Dowd, Blastobasis adustella (Walsingham, 1894) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual female Blastobasis adustella (the Dingy Dowd; Arthropoda; Insecta; Lepidoptera; Blastobasidae). The genome sequence is 557.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 9,783 protein coding genes


Background
Five species of Blastobasis Zeller, 1855 have been recorded in the British Isles, all of which have been introduced here.The members of this genus have a characteristic resting posture, with their wings held overlapping and wrapped around the abdomen (Sterling et al., 2012).Blastobasis adustella is thought to originate from Madeira (De Prins et al., 2009), and is one of the two Blastobasis species that have spread the fastest here, now occurring across most of Britain and Ireland, although in Ireland it is recorded mainly in coastal regions.
It can be separated from most of the other British species by its dark ground colour and presence of an oblique white streak across each forewing at about one quarter of the wing length, forming an 'inverted V' shape.However, the rarer B. vittata Wollaston, 1858 is very similar, and examination of the genitalia may be required to separate some individuals, although the latter species is generally smaller, slimmer and more warmly coloured.Similarly, B. maroccanella Amsel, 1952 may appear very similar to both species, but is no longer considered to be a part of the UK fauna after British specimens were re-identified as vittata (Dickson et al., 2022).Records of B. adustella in the UK were initially referred to as B. lignea Walsingham, 1894 but were misidentifications, as B. lignea is now understood to be a junior synonym of B. vittata.B. adustella is highly polyphagous, with the larvae feeding in spinnings on a wide range of plants and plant material, but seeming to show a preference for the leaves of yew (Taxus baccata).The purplish larvae occur from September to June and are very similar to those of B. lacticolella Rebel, 1940, but can be separated from that species by the prothoracic plate being much darker than the head (Smart, 2021).They pupate in June in a silken cocoon amongst leaf litter or on the foodplant.The single-brooded adults are readily attracted to light and are on the wing from mid-May to December, peaking in June and again in September (Dickson, 2018).
We present a chromosomally complete genome sequence for Blastobasis adustella, based on one female specimen from Wytham Woods, Oxfordshire, as part of the Darwin Tree of Life Project.This project is a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland, with a view to further understanding of their evolutionary relationships and biodiversity.

Genome sequence report
The genome was sequenced from one female Blastobasis adustella (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 50-fold coverage in Pacific Biosciences single-molecule HiFi long reads and 73-fold coverage in 10X Genomics read clouds were generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 9 missing joins or misjoins and removed 3 haplotypic duplications, reducing the scaffold number by 13.33%, and increasing the scaffold N50 by 5.97%. The final assembly has a total length of 557.4 Mb in 39 sequence scaffolds with a scaffold N50 of 19.4 Mb (Table 1).Most (98.67%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes and the Z sex chromosome.It is assumed that the karyotype for this sample is ZO as no evidence was found to support the existence of a W chromosome in the assembly.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-Figure 5; Table 2).Several scaffolds consisting largely of centromeric repeats that, by Hi-C data, associate with Chromosome 1, but cannot be accurately placed.These were submitted as unlocalised.While not fully phased, the assembly deposited is of one haplotype.Contigs corresponding to the second haplotype have also been deposited.The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Sample acquisition and nucleic acid extraction
The Blastobasis adustella specimen used for DNA sequencing was specimen ID Ox000209, ToLID ilBlaAdus2, while the specimen used for Hi-C data was specimen ID Ox000210, ToLID ilBlaAdus1.Both specimens were collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2019-08-24 using a light trap.The specimens were collected and identified by Douglas Boyes (University of Oxford).They were preserved on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The ilBlaAdus2 sample was weighed and dissected on dry ice.Tissue from the whole organism was disrupted using a Nippi Powermasher fitted with a BioMasher pestle.High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit.Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 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 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 Pacific Biosciences SEQUEL II (HiFi) and HiSeq X Ten (10X) instruments.Hi-C data were also generated from whole organism tissue of ilBlaAdus2 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
Assembly was carried out with Hifiasm (Cheng et al., 2021) and haplotypic duplication was identified and removed with   Table 3. Software tools: versions and sources.

Software tool Version
purge_dups (Guan et al., 2020).One round of polishing was performed by aligning 10X Genomics read data to the assembly with Long Ranger 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 was performed using gEVAL, HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022).The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2023), which runs MitoFinder (Allio et al., 2020) or MITOS (Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020).To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury (Rhie et al., 2020).This work was done using Nextflow (Di Tommaso et al

Genome annotation
The Ensembl Genebuild annotation system (Aken et al., 2016) was used to generate annotation for the Blastobasis adustella assembly (GCA_907269095.1).Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt (UniProt Consortium, 2019).

Wellcome Sanger Institute -Legal and Governance
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', which can be found in full on the Darwin Tree of Life website here.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 for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use.
The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.The overarching areas of consideration are: • Ethical review of provenance and sourcing of the material

Figure 2 .
Figure 2. Genome assembly of Blastobasis adustella, ilBlaAdus2.1:metrics.The BlobToolKit Snailplot shows N50 metrics and BUSCO gene completeness.The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 557,440,016 bp assembly.The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (33,699,264 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (19,379,192 and 13,890,508 bp), respectively.The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude.The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot.A summary of complete, fragmented, duplicated and missing BUSCO genes in the lepidoptera_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/ilBlaAdus2.1/dataset/CAJSME01.1/snail.

Figure 5 .
Figure 5. Genome assembly of Blastobasis adustella, ilBlaAdus2.1:Hi-C contact map of the ilBlaAdus2.1 assembly, visualised using HiGlass.Chromosomes are shown in order of size from left to right and top to bottom.An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=cg4RwO9BSmyF6YJgJPikLg.

Table 3
contains a list of relevant software tool versions and sources.
• Legality of collection, transfer and use (national and international) Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.