The genome sequence of the Dotted Grey Groundling, Athrips mouffetella (Linnaeus, 1758)

We present a genome assembly from an individual female Athrips mouffetella (the Dotted Grey Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 869.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,889 protein coding genes.


Background
Athrips mouffetella, the Dotted Grey Groundling, is a micromoth in the family Gelechiidae.This small moth (forewing length 7-8.5mm) is silvery grey, with a number of black elongated spots running along the forewings.It is single brooded, flying between June and early September, and readily comes to light (Sterling et al., 2012).
The moth is common but local in England and Wales and there is a lone record from Scotland (Palmer & Palmer, 2023).It is widespread throughout Europe, excluding the Iberian Peninsula and there are isolated records to the far east of Asia (GBIF Secretariat, 2023).It has been accidentally introduced to North America (Emmet & Langmaid, 2002).
The larvae feed on the terminal leaves of honeysuckle and snowberry, spinning a silken web.They can be distinguished by their colouration from other web-spinning moth larvae which share these food plants.A mouffetella larvae are dark purplish-black or grey with white spots behind the head, and along the side of the body.These spots are brighter on the thorax but more faded on subsequent segments (Emmet & Langmaid, 2002).
The genome of A. mouffetella 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 Athrips mouffetella based on one female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report
The genome was sequenced from one female Athrips mouffetella (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 33-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 51 missing joins or mis-joins and removed 11 haplotypic duplications, reducing the assembly length by 0.51% and the scaffold number by 10.56%, and decreasing the scaffold N50 by 1.32%. The final assembly has a total length of 869.7 Mb in 126 sequence scaffolds with a scaffold N50 of 29.8 Mb (Table 1).The snailplot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3.The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla.Most (99.2%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 29 autosomes and the Z and W sex chromosomes.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (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 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
A female Athrips mouffetella (specimen ID Ox000593, ToLID ilAthMouf1) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2020-07-05.The specimen used for Hi-C sequencing (specimen ID Ox001679, ToLID ilAthMouf2) was collected from the same location on 2021-07-17.Both     SEQUEL II (HiFi) instrument.Hi-C data were also generated from whole organism tissue of ilAthMouf2 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 purge_dups (Guan et al., 2020).The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023).The assembly was checked for contamination and corrected as described previously (Howe et al., 2021).Manual curation was performed using 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.
Table 3 contains a list of relevant software tool versions and sources.

Genome annotation
The BRAKER2 pipeline (Brůna et al., 2021) was used in the default protein mode to generate annotation for the Athrips mouffetella assembly (GCA_947532105.1) in Ensembl Rapid Release.

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 In this manuscript, the authors sequenced and annotated the genome of Dotted Grey Groundling, from UK part of the part of the Darwin Tree of Life Project focused on sequencing all named eukaryotic species in Britain and Ireland.The authors employed standard/established procedures and protocols in this excise.The findings/conclusions are acceptable and supported by the data.It appears that the focus of the project, at this point on generating generic/automatic annotations that can be refined later thorough community annotations, probably by end users.This might account for absence of in-depth information on the annotations, such as gene families identified, which should have come out clearly.That being the case, I have the following minor concerns.
The authors should provide more information on the Darwin Tree of Life Project and probably what informed the choice of this species for preferential sequencing/annotations beyond the goal of the project and feeding on honeysuckle and snowberry. 1.
Better description of identification/validation of the specimen e.g.taxonomic key other that who and where this was done [identified by Douglas Boyes (University of Oxford)] to facilitate reproducibility.

Is the rationale for creating the dataset(s) clearly described? Partly
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

Melody Clark
Natural Environment Research Council, Cambridge, UK This article describes the genome sequencing of the Dotted Grey Groundling, a moth common to the southern two thirds of England.The sequenced specimen was sourced from Wytham Woods.This is one of the most researched areas of woodland in the world and includes a Wytham Genome Project which aims to sequence all species in this wood.The Wytham Genome Project is a key site for the Darwin Tree of Life Project.The protocols underpinning the genome sequencing and assembly are fully described and referenced.The bioinformatic tools used to assemble, curate and annotate this genome are all freely available.The genome assembly is of very high quality with most data scaffolded to 31 chromosomal pseudomolecules, including the sex chromosomes.These data are freely available for reuse.
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, transcriptomics, organisms responses to change 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.

Figure 2 .
Figure 2. Genome assembly of Athrips mouffetella, ilAthMouf1.1: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 869,731,197 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 (57,334,238 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (29,779,897 and 18,863,855 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/CANNWQ01/dataset/CANNWQ01/snail.

Figure 3 .
Figure 3. Genome assembly of Athrips mouffetella, ilAthMouf1.1:BlobToolKit GC-coverage plot.Scaffolds are coloured by phylum.Circles are sized in proportion to scaffold length.Histograms show the distribution of scaffold length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CANNWQ01/dataset/CANNWQ01/blob.

Figure 4 .
Figure 4. Genome assembly of Athrips mouffetella, ilAthMouf1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all scaffolds.Coloured lines show cumulative lengths of scaffolds assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CANNWQ01/dataset/CANNWQ01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Athrips mouffetella, ilAthMouf1.1:Hi-C contact map of the ilAthMouf1.1 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=Pk3PR6WiSgCVbfOA0levGg.