The genome sequence of the Crescent Groundling, Teleiodes luculella (Hübner, 1813)

We present a genome assembly from an individual male Teleiodes luculella (the Crescent Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 454.5 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 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,943 protein coding genes.


Background
Teleiodes luculella (Crescent Groundling) is a micro-moth in the family Gelechiidae, and is found throughout Europe (GBIF Secretariat, 2024).In the UK it is fairly common in oak woods in England and Wales.The moth is small with a forewing length of 5-6 mm.The forewing is dark grey with a semi-circular white costal blotch, often with an orangeyyellow mark, and smaller white costal spots about two-thirds of the way along the wing (Emmet & Langmaid, 2002).
The moth is thought to be single-brooded, flying between May and August Click or tap here to enter text.(Sterling et al., 2012).However, there is some suggestion that the moth may be double-brooded in southern parts of its European range (Palmer & Palmer, 2023).The larvae feed on oak in spun leaves and pupate in leaf litter on the ground (Emmet & Langmaid, 2002).
The genome of T. luculella was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in Britain and Ireland.

Genome sequence report
The genome was sequenced from one male Teleiodes luculella (Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77,.A total of 35-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 324 missing joins or mis-joins and removed 19 haplotypic duplications, reducing the assembly length by 0.59% and the scaffold number by 7.53%, and decreasing the scaffold N50 by 0.78%. The final assembly has a total length of 454.5 Mb in 527 sequence scaffolds with a scaffold N50 of 15.3 Mb (Table 1).The snail plot 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 (95.93%) of the assembly sequence was assigned to 30 chromosomal-level scaffolds, representing 29 autosomes and the Z sex chromosome.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
Teleiodes luculella specimens were collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.77, longitude -1.34) on 2021-06-16 using a light trap.The specimens were collected and identified by Douglas Boyes (University of Oxford).The specimens were snap-frozen on dry ice.One specimen was used for DNA sequencing (specimen ID Ox001931, ToLID ilTelLucu1) and a second for Hi-C sequencing (specimen ID Ox001932, ToLID ilTelLucu2).
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up.In sample preparation, the ilTelLucu1 sample was weighed and dissected on dry ice (Jay et al., 2023).Tissue of the whole organism was homogenised using a PowerMasher II tissue disruptor (Denton et al., 2023a).
HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol

Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers'  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 Teleiodes luculella assembly (GCA_948473455.1) in Ensembl Rapid Release at the EBI.

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

Software tool Version
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

Axel Künstner
University of Lübeck, Lübeck, Germany The manuscript presents the genome assembly of the Crescent Groundling, Teleiodes luculella.The manuscript exhibits clear writing and sound methodologies.The raw data for this study was submitted to ENA.
Besides one minor comment (see below), I have no further complaints.

Minor comment:
In the Background section, there is the following unassociated sentence: 'Click or tap here to enter text'.
Is the rationale for creating the dataset(s) clearly described?

Wai Lok So
School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong The authors sequenced the Crescent Groundling, Teleiodes luculella, yielding a high-quality chromosomal-level genome, together with the sex-chromosome and the mitochondrial genome.
The methods are standard, sound, and logical.Sufficient details have been given regarding sample preparation, genome sequencing, and assembly.The genome and other associated materials have been properly deposited, which is accessible and reusable for future users.
Though the genome sequencing part is well done, I would like to see a bit more background on this moth species, especially its special biology or ecological significance.The inclusion of additional biological details of this species in the "Background" would be greatly appreciated.

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: myriapod biology, invertebrate biology, evolution, genomics, molecular biology, soil biodiversity, invertebrate endocrinology 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 Teleiodes luculella, ilTelLucu1.1:metrics.The BlobToolKit snail plot 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 454,474,787 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 (30,471,558 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (15,281,747 and 8,929,433 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/CAOKYR01/dataset/CAOKYR01/snail.

Figure 3 .
Figure 3. Genome assembly of Teleiodes luculella, ilTelLucu1.1:BlobToolKit GC-coverage plot.Sequences are coloured by phylum.Circles are sized in proportion to sequence length.Histograms show the distribution of sequence length sum along each axis.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAOKYR01/dataset/CAOKYR01/blob.

Figure 4 .
Figure 4. Genome assembly of Teleiodes luculella, ilTelLucu1.1:BlobToolKit cumulative sequence plot.The grey line shows cumulative length for all sequences.Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAOKYR01/dataset/CAOKYR01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Teleiodes luculella, ilTelLucu1.1:Hi-C contact map of the ilTelLucu1.1 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=ZLnB8ozxSOygY9xC6AzPNg.

Table 1 . Genome data for Teleiodes luculella, ilTelLucu1.1. Project accession data
(Denton et al., 2023b)23)rks are adapted from column VGP-2020 of "Table1: Proposed standards and metrics for defining genome assembly quality" from Rhie et al.(2021).**BUSCOscoresbased on the lepidoptera_odb10 BUSCO set using version 5.3.2.C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison.A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/CAOKYR01/dataset/CAOKYR01/busco.solid-phasereversibleimmobilisation(Stricklandetal., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA.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.Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io(Dentonetal., 2023b).

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
Reviewer Expertise: Bioinformatics, Cancer research, Microbiome 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.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.