Abstract
We present a genome assembly from a female specimen of Tinagma dryadis (Arthropoda; Insecta; Lepidoptera; Douglasiidae). The assembly contains two haplotypes with total lengths of 813.92 megabases and 692.99 megabases. Most of the haplotype 1 assembly (99.95%) was scaffolded into 22 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.42 kilobases. This work is part of Project Psyche, a collaborative programme generating genomes for European butterflies and moths.
Keywords: Tinagma dryadis, Douglasiidae, genome sequence, chromosomal, Lepidoptera
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Altocrustacea; Allotriocarida; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Eumetabola; Endopterygota; Aparaglossata; Panorpida; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Tineoidea; Douglasiidae; Tinagma; Tinagma dryadis Staudinger, 1872 (NCBI:txid1195453)
Taxonomic note. The taxonomy above follows NCBI Taxonomy, which currently places Douglasiidae in Tineoidea. Molecular phylogenetic analyses instead support the placement of Douglasiidae in Douglasioidea ( Kawahara et al., 2011; Mitter et al., 2017; Mutanen et al., 2010; Regier et al., 2013; Sohn et al., 2013).
Background
Tinagma dryadis Staudinger, 1872, is a species of micromoth in the family Douglasiidae. The family contains only 16 species in Europe, divided among three genera ( Lepiforum e.V., 2025). With 12 European species, Tinagma Zeller, 1839 is the largest genus. The family Douglasiidae was once placed in the superfamily Gracillarioidea, but molecular phylogenies have indicated that this placement is likely to be incorrect ( Kawahara et al., 2011; Mitter et al., 2017; Mutanen et al., 2010; Regier et al., 2013; Sohn et al., 2013). It is therefore now assigned to the superfamily Douglasioidea. Douglasiidae is an enigmatic family that seems to represent non-obtectomeran Apoditrysia, but its phylogenetic affinities are otherwise poorly resolved; it behaves as a “rogue” taxon in molecular phylogenies.
With a wingspan of only about 6–8 mm, Tinagma dryadis (Figure 1) is a very small species. Its wings show mostly grey, brown and black tones. The forewings appear coarse and mottled, with a pale band in the middle bordered by darker bands. A black apical spot is also present. The fringe line is prominent, and the head is pale grey. The sexes differ slightly, with males being larger, browner, and less contrasted than females.
Figure 1. Voucher photograph of the Tinagma dryadis (ilTinDrya1) specimen used for genome sequencing.
The species is widely distributed but extremely local everywhere. It occurs in several European mountain systems (Scandinavia, the Alps and the Urals) as well as in northern North America, giving the species a Holarctic distribution. In northern Europe, and across most of its range, it is restricted to alpine habitats. In Fennoscandia, it is found on calcareous rocky slopes in the alpine zone. Although the larval food plants are known to be Dryas spp. ( Dryas octopetala in northern Europe), its life history remains unresolved ( Lepiforum e.V., 2025). In its habitats, it can be extremely numerous and, as the adults rest and feed on the flowers of Dryas, it is easily observed despite its small size and rather cryptic appearance. Several dozen individuals can be found resting on the same Dryas flower. The larvae are likely stalk borers. The adults are diurnal and jump or, more rarely, fly low above the patches of Dryas. The adults fly during the short Arctic summer, in Finland typically from midsummer to mid-July. A peculiar and only recently noticed feature is that adults occur only every second year (all Finnish records are from even years). This demonstrates that the life history takes two years, a common feature in Arctic-alpine Lepidoptera. Because of the very few known locations in Finland, the species is regarded as being vulnerable (VU) there.
The genome sequence of Tinagma dryadis will help to improve our understanding of the phylogenetic relationships of this enigmatic group of moths. It might also help to identify the genetic mechanisms behind the periodic occurrence of many species of Lepidoptera adapted to Arctic conditions.
Methods
Sample acquisition
The specimen used for genome sequencing was an adult female Tinagma dryadis (specimen ID OULUPSY000392, ToLID ilTinDrya1; Figure 1), collected from Saana, Kilpisjärvi, Finland (latitude 69.0318, longitude 20.8467) on 2024-07-07. The specimen was collected and identified by Marko Mutanen and Niina Kiljunen (University of Oulu).
Nucleic acid extraction
Protocols for high molecular weight (HMW) DNA extraction developed at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory are available on protocols.io ( Howard et al., 2025). For HMW DNA extraction, tissue from the whole organism of ilTinDrya1 was homogenised by powermashing using a PowerMasher II tissue disruptor.
HMW DNA was extracted in the WSI Scientific Operations core using the Automated MagAttract v2 protocol. DNA was sheared into an average fragment size of 12–20 kb following the Megaruptor®3 for LI PacBio protocol. Sheared DNA was purified by automated SPRI (solid-phase reversible immobilisation). The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the Femto Pulse system. For this sample, the final post-shearing DNA had a Qubit concentration of 3.92 ng/μL and a yield of 184.24 ng, with a fragment size of 15.0 kb. The Genomic Quality Number (GQN) was 7.6.
PacBio HiFi library preparation and sequencing
Library preparation and sequencing took place in the WSI Scientific Operations core. Library PSYCHE15639121 was prepared with the SMRTbell Prep Kit 3.0 (Pacific Biosciences) according to the manufacturer’s instructions. The kit includes reagents for end repair/A-tailing, adapter ligation, post-ligation SMRTbell bead clean-up, and nuclease treatment. Size selection and clean-up were performed using diluted AMPure PB beads (Pacific Biosciences). DNA concentration was quantified with a Qubit Fluorometer v4.0 (Thermo Fisher Scientific) and the Qubit 1X dsDNA HS assay kit. Final library fragment size was assessed with the Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies) using the gDNA 55 kb BAC analysis kit.
The library was sequenced on a Revio instrument (Pacific Biosciences, California, USA). The prepared libraries selected for multiplexing were pooled based on genome size, library molarity and the intended plex level. Primers were annealed and polymerases were bound to generate circularised complexes following the manufacturer’s instructions. Complexes were purified using SMRTbell beads, diluted to the Revio loading concentration, and spiked with a Revio sequencing internal control. The pooled libraries were sequenced on a Revio 25M Plex SMRT cell in a 2-plex run. SMRT Link software (Pacific Biosciences) was used to configure and monitor the run and to perform primary and secondary data analysis.
Hi-C
Sample preparation and crosslinking
Hi-C data were generated from the ilTinDrya1 whole organism sample using the Arima-HiC v2 kit (Arima Genomics). Following the manufacturer’s instructions, tissue was fixed and DNA crosslinked using TC buffer to a final formaldehyde concentration of 2%. The tissue was homogenised using the Diagnocine Power Masher-II. Crosslinked DNA was digested with a restriction enzyme master mix, biotinylated, and ligated. Clean-up was performed with SPRISelect beads before library preparation. DNA concentration was measured with the Qubit Fluorometer (Thermo Fisher Scientific) and Qubit HS Assay Kit. The biotinylation percentage was estimated using the Arima-HiC v2 QC beads.
Hi-C library preparation and sequencing
Biotinylated DNA constructs were fragmented using a Covaris E220 sonicator and size-selected to 400–600 bp using SPRISelect beads. DNA was enriched with Arima-HiC v2 kit Enrichment beads. End repair, A-tailing, and adapter ligation were carried out with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs), following a modified protocol where library preparation occurs while DNA remains bound to the Enrichment beads. Libraries were amplified with KAPA HiFi HotStart mix and a custom Unique Dual Index (UDI) barcode set (Integrated DNA Technologies). Depending on sample concentration and biotinylation percentage determined at the crosslinking stage, libraries were amplified with 10–16 PCR cycles. Post-PCR clean-up was performed with SPRISelect beads. Libraries were quantified using the AccuClear Ultra High Sensitivity dsDNA Standards Assay Kit (Biotium) and a FLUOstar Omega plate reader (BMG Labtech).
Prior to sequencing, libraries were normalised to 10 ng/μL. Normalised libraries were quantified again to create equimolar and/or weighted 2.8 nM pools. Pool concentrations were checked using the Agilent 4200 TapeStation (Agilent) with High Sensitivity D500 reagents before sequencing. Libraries were sequenced on the Illumina NovaSeq X, generating paired-end 150-bp reads.
Genome assembly
Prior to assembly of the PacBio HiFi reads, a database of k-mer counts ( k = 31) was generated from the filtered reads using FastK. The k-mer frequency distribution was analysed with GenomeScope (version 2.1.0) ( Ranallo-Benavidez et al., 2020), providing fitted point estimates of genome size, heterozygosity and repeat content.
The HiFi reads were assembled using Hifiasm in Hi-C phasing mode ( Cheng et al., 2021, 2022), producing two haplotypes. Hi-C reads ( Rao et al. , 2014) were mapped to contigs using bwa-mem2 ( Vasimuddin et al., 2019). Contigs were further scaffolded with Hi-C data in YaHS ( Zhou et al., 2023), using the --break option for handling potential misassemblies. The scaffolded assemblies were evaluated using Gfastats ( Formenti et al. , 2022), BUSCO ( Manni et al., 2021) and MerquryFK ( Rhie et al., 2020).
The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al. , 2023), which runs MitoFinder ( Allio et al., 2020) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Assembly curation
The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants ( ASCC) pipeline. The flat files and maps for curation were generated with TreeVal. Manual curation was conducted primarily in PretextView and HiGlass ( Kerpedjiev et al. , 2018). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). The two haplotype assemblies were combined for curation. Manual corrections included 15 breaks and 178 joins. This reduced the scaffold count by 67.4%, increased the scaffold N50 by 1.1%, and increased the total assembly length by 4.5%. The curation process is described at sanger-tol/curation-resources. A Hi-C contact map of the haplotype 1 assembly was generated with PretextSnapshot.
Assembly quality assessment
The MerquryFK tool ( Rhie et al., 2020), run in a Singularity container ( Kurtzer et al., 2017), was used to evaluate k-mer completeness and assembly quality for both haplotypes using the k-mer databases ( k = 31) computed prior to genome assembly. The analysis outputs included assembly QV scores and completeness statistics.
The haplotype 1 assembly was assessed using BlobToolKit ( Challis et al., 2020). PacBio reads were mapped to the haplotype 1 assembly to derive sequence coverage, and BUSCO ( Manni et al., 2021) was used to assess gene-set completeness. DIAMOND BLASTp searches of extracted BUSCO proteins and DIAMOND BLASTx searches of assembly sequences against UniProt Reference Proteomes ( Buchfink et al., 2021), followed by BLASTn searches of sequences without DIAMOND BLASTx hits against the NCBI nt database ( Altschul et al., 1990), supported taxonomic assignment. Coverage, sequence composition, taxonomic assignment and BUSCO results were integrated into a BlobDir for interactive inspection and visualisation. The snail and blob plots were rendered locally from this hosted BlobDir using BlobTk v0.8.3. The scaffold-length radial scale function for the snail plot was set to linear ( Challis & Blaxter, 2026). The blob plot used circular markers with area proportional to scaffold length ( Challis et al., 2020).
We used busco-alg-painter v0.1.0, a Python reimplementation and extension of lep_busco_painter, to paint Merian elements along chromosomes. Merian elements represent the 32 ancestral linkage groups reconstructed for Lepidoptera ( Wright et al., 2024). The BUSCO-to-Merian reference assignments were derived from lep_busco_painter. Complete single-copy and duplicated BUSCO genes from the lepidoptera_odb10 results were assigned to Merian elements. Chromosome identifiers and lengths were obtained from NCBI Datasets, and BUSCO positions were plotted on chromosomes drawn to scale.
Genome sequence report
Sequence data
PacBio sequencing of the T. dryadis specimen generated 43.83 Gb (gigabases) from 4.28 million reads. We assembled the genome from these reads. GenomeScope analysis using a p = 2 model gave a k-mer-based haploid genome size estimate of 740.10 Mb, with heterozygosity of 0.87% and repeat content of 37.51%; the full-model fit was 97.90% (Figure 2). The GenomeScope estimates guided expectations for the assembly. The sequencing data provided approximately 58× coverage of the haplotype 1 assembly. Hi-C sequencing produced 107.45 Gb from 355.80 million reads, which were used to scaffold the haplotype 1 assembly. Table 1 summarises the specimen and sequencing details.
Figure 2. GenomeScope model fitted to the k-mer frequency distribution.
The plot shows the observed and modelled k-mer spectra used to estimate genome size, heterozygosity and repeat content from unassembled sequencing reads.
Table 1. Specimen and sequencing data for T. dryadis (BioProject PRJEB97050).
| Platform | PacBio HiFi | Hi-C |
|---|---|---|
| ToLID | ilTinDrya1 | ilTinDrya1 |
| Specimen ID | OULUPSY000392 | OULUPSY000392 |
| BioSample (source individual) | SAMEA117574380 | SAMEA117574380 |
| BioSample (tissue) | SAMEA117574434 | SAMEA117574434 |
| Tissue | whole organism | whole organism |
| Instrument | Revio (1 run) | Illumina NovaSeq X |
| Library ID & run accession(s) | PSYCHE15639121: ERR15532278 | ERR15551580 |
| Read count total | 4.28 million reads | 355.80 million read pairs |
| Base count total | 43.83 Gb | 107.45 Gb |
Assembly statistics
The genome was assembled into two haplotypes using Hi-C phasing. The haplotype 1 assembly was curated to chromosome level, while haplotype 2 was assembled to scaffold level. The haplotype 1 assembly, which is proposed as the reference assembly for this species, has a total length of 813.92 Mb in 41 scaffolds (excluding organelle sequences), with 192 gaps, and a scaffold N50 of 36.4 Mb (Table 2). The haplotype 1 assembly has a scaffold auN of 41.5 Mb.
Table 2. Genome assembly statistics for T. dryadis .
| Genome assembly | Haplotype 1 | Haplotype 2 |
|---|---|---|
| Assembly name | ilTinDrya1.hap1.1 | ilTinDrya1.hap2.1 |
| Assembly accession | GCA_977019765.1 | GCA_977019915.1 |
| Assembly level | chromosome | scaffold |
| Span (Mb) | 813.92 | 692.99 |
| Number of chromosomes | 22 | - |
| Number of contigs | 233 | 68 |
| Contig N50 (Mb) | 24.99 | 25.41 |
| Number of scaffolds (excluding organelle sequences) | 41 | 38 |
| Scaffold N50 (Mb) | 36.4 | 31.44 |
| Scaffold auN (Mb) | 41.5 | 38.2 |
| Longest scaffold length (Mb) | 62.49 | 59.31 |
| Sex chromosomes | W and Z | - |
| Organelles | Mitochondrial genome: 15.42 kb | - |
Most of the haplotype 1 assembly sequence (99.95%) was assigned to 22 chromosome-level scaffolds, representing 20 autosomes and the W and Z sex chromosomes. These chromosome-level scaffolds, confirmed by Hi-C data, are named according to size (Figure 3; Table 3). Chromosome painting of the haplotype 1 assembly with Merian elements illustrates the distribution of orthologues along chromosomes and highlights patterns of chromosomal evolution relative to Lepidopteran ancestral linkage groups (Figure 4). The Z chromosome of the haplotype 1 assembly was assigned based on the presence of the ancestral Merian element MZ ( Wright et al., 2024). The Z and W chromosomes were assigned based on their single-copy status within the diploid assembly. The exact order and orientation of the contigs on the W chromosome are unknown.
Figure 3. Hi-C contact map of the T. dryadis haplotype 1 assembly.
Assembled chromosomes are shown in order of size and labelled along the axes. The plot was generated using PretextSnapshot.
Figure 4. Merian elements painted across chromosomes in the ilTinDrya1.hap1.1 haplotype 1 assembly of T. dryadis.
Chromosomes are drawn to scale, with the positions of orthologues shown as coloured bars. Each orthologue is coloured by the Merian element that it belongs to. All orthologues which could be assigned to Merian elements are shown.
The mitochondrial genome was also assembled (length 15.42 kb, OZ363802.1). This sequence is included as a contig in the multifasta file of the haplotype 1 genome submission and as a standalone record.
Table 3. Chromosomal pseudomolecules in the haplotype 1 genome assembly of T. dryadis ilTinDrya1.
| INSDC accession | Molecule | Length (Mb) | GC% | Assigned Merian elements |
|---|---|---|---|---|
| OZ363780.1 | 1 | 58.72 | 36.50 | M16; M17; M20; M21; M22; M28; M5; M6; M8; M9 |
| OZ363781.1 | 2 | 53.11 | 36.50 | M12; M23; M27; M7; M8; M9 |
| OZ363782.1 | 3 | 51.65 | 36.50 | M10; M12; M25; M26; M4; M6; M9 |
| OZ363783.1 | 4 | 51.16 | 36.50 | M11; M28; M3; M30; M5 |
| OZ363784.1 | 5 | 47.40 | 36.50 | M1; M12; M15; M22; M27; M7; M9 |
| OZ363785.1 | 6 | 36.40 | 37 | M28; M4; M5; M7; M8 |
| OZ363786.1 | 7 | 36.01 | 36.50 | M1; M18; M29; M9 |
| OZ363787.1 | 8 | 31.64 | 36.50 | M11; M14; M26; M4 |
| OZ363788.1 | 9 | 30.74 | 37 | M16; M18; M21; M22; M8 |
| OZ363789.1 | 10 | 30.71 | 37 | M1; M10; M13; M31 |
| OZ363790.1 | 11 | 30.65 | 36.50 | M11; M17; M21; M3; M9 |
| OZ363791.1 | 12 | 29.95 | 36.50 | M13; M24; M26 |
| OZ363792.1 | 13 | 29.14 | 36.50 | M1; M12; M16; M18; M5 |
| OZ363793.1 | 14 | 27.90 | 37 | M1; M11; M12; M21; M30 |
| OZ363794.1 | 15 | 27.47 | 36.50 | M1; M3; M5; M8 |
| OZ363795.1 | 16 | 26.04 | 37 | M20; M24 |
| OZ363796.1 | 17 | 26.03 | 37 | M19; M3; M6 |
| OZ363797.1 | 18 | 25.56 | 36.50 | M10; M16; M27; M7; M9 |
| OZ363798.1 | 19 | 24.64 | 37 | M1; M14; M7 |
| OZ363799.1 | 20 | 17.21 | 38 | M6 |
| OZ363800.1 | W | 62.49 | 38 | - |
| OZ363801.1 | Z | 58.86 | 36.50 | M2; MZ |
Assembly quality metrics
For the haplotype 1 assembly, the estimated QV is 69.7, and for the haplotype 2 assembly, 69.8. When the two haplotypes are combined, the assembly achieves an estimated QV of 69.7. The k-mer completeness is 84.54% for the haplotype 1 assembly, 77.65% for the haplotype 2 assembly, and 99.56% for the combined haplotypes (Figure 5).
Figure 5. Evaluation of k-mer completeness using MerquryFK.
This plot illustrates the recovery of k‐mers from the original read data in the haplotype 1 assembly, the haplotype 2 assembly and the combined haplotypes. The horizontal axis represents k‐mer multiplicity, and the vertical axis shows the number of k‐mers. The black curve represents k‐mers that appear in the reads but are not assembled. The green curve corresponds to k‐mers shared by both haplotypes, and the red and blue curves show k‐mers found only in one of the haplotypes.
BUSCO analysis using the lepidoptera_odb10 reference set ( n = 5,286) identified 98.1% of the expected gene set (single = 97.0%, duplicated = 1.1%) in the haplotype 1 assembly. For the haplotype 2 assembly, BUSCO analysis identified 89.2% of the expected gene set (single = 88.5%, duplicated = 0.7%).
The snail plot in Figure 6 provides a summary of assembly contiguity, cumulative scaffold count, sequence composition and BUSCO completeness for the haplotype 1 assembly ( Challis & Blaxter, 2026). The relative sizes of the longest scaffold, scaffold N50 and N90, together with the dark-grey scaffold-length distribution, show how much of the assembly is contained in long scaffolds. The outer composition track shows variation in GC, AT and N content, while the central track shows the cumulative scaffold count and the BUSCO inset summarises gene-set completeness.
Figure 6. Assembly metrics for ilTinDrya1.hap1.1, the haplotype 1 assembly.
The BlobToolKit snail plot provides an overview of assembly metrics and BUSCO gene completeness. The circumference represents the length of the haplotype 1 assembly, and the main plot is divided into 1,000 bins around the circumference. The outermost blue tracks display the distribution of GC, AT, and N percentages across the bins. Scaffolds are arranged clockwise from longest to shortest and are depicted in dark grey. Scaffold length is shown on a linear radial scale, scaled to the longest scaffold. Red shading indicates the longest scaffold, and the deeper orange and pale orange shading represent the N50 and N90 lengths. The summary statistics include scaffold auN, the area under the scaffold Nx curve. The light grey spiral at the centre shows the cumulative scaffold count on a logarithmic scale. A summary of complete, fragmented, duplicated, and missing BUSCO genes in the lepidoptera_odb10 set is presented at the top right. The assembly can be explored interactively in the BlobToolKit viewer.
The blob plot in Figure 7 displays scaffolds from the haplotype 1 assembly by GC proportion and base coverage. Marker area is proportional to scaffold length, and colour indicates taxonomic assignment ( Challis et al., 2020).
Figure 7. BlobToolKit blob plot for ilTinDrya1.hap1.1, the haplotype 1 assembly.
The plot shows base coverage (vertical axis) and GC content (horizontal axis). Circles represent scaffolds; marker area is proportional to scaffold length, and colour indicates taxonomic assignment. The histograms along the axes display the total length of sequences distributed across different levels of coverage and GC content. The assembly can be explored interactively in the BlobToolKit viewer.
Table 4 lists the assembly metric benchmarks adapted from Rhie et al.. (2021) the Earth BioGenome Project (EBP) Report on Assembly Standards. The three-part EBP metric, calculated for the haplotype 1 assembly, is 7.C.Q69.
Table 4. Earth BioGenome Project summary metrics for the T. dryadis assembly.
| Measure | Value | Benchmark |
|---|---|---|
| EBP summary (haplotype 1) | 7.C.Q69 | 6.C.Q40 |
| Contig N50 length | 24.99 Mb | > 1 Mb |
| Scaffold N50 length | 36.40 Mb | = chromosome N50 |
| Consensus quality (QV) | Haplotype 1: 69.7; haplotype 2: 69.8; combined: 69.7 | ≥ 40 |
| k-mer completeness | Haplotype 1: 84.54%; Haplotype 2: 77.65%; combined: 99.56% | > 90% |
| BUSCO | Haplotype 1: C:98.1% [S:97.0%, D:1.1%], F:0.1%, M:1.7%, n:5,286; Haplotype 2: C:89.2% [S:88.5%, D:0.7%], F:0.1%, M:10.7%, n:5,286 | S > 90%; D < 5% |
| Percentage of assembly assigned to chromosomes | 99.95% | ≥ 90% |
Notes: The EBP summary uses log10(Contig N50); chromosome-level (C) or log10(Scaffold N50); Q (Merqury QV). BUSCO v6.0.0 using the lepidoptera_odb10 lineage dataset: C=complete; S=single-copy; D=duplicated; F=fragmented; M=missing; n=orthologues.
Data availability
European Nucleotide Archive: Tinagma dryadis. Accession number: PRJEB97050; URL: https://identifiers.org/ena.embl/PRJEB97050. The genome sequence is released openly for reuse. The T. dryadis genome sequencing initiative is part of the Sanger Institute Tree of Life Programme ( PRJEB43745) and Project Psyche ( PRJEB71705). All raw sequence data and the haplotype assemblies have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through Ensembl at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1 and Table 2.
Pipelines used for genome assembly at the WSI Tree of Life are available at https://pipelines.tol.sanger.ac.uk/pipelines. Table 5 lists software versions used in this study.
Table 5. Software versions and sources used for T. dryadis .
Wellcome Sanger Institute – Legal and Governance
The materials that have contributed to this genome note have been supplied by a Tree of Life collaborator. 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
Legality of collection, transfer and use (national and international).
Each transfer of samples is undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Tree of Life collaborator, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances, other Tree of Life collaborators.
Funding Statement
This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [220540]. The Oulu hub is supported by the Biodiverse Anthropocenes Research Profiling programme funded by the Research Council of Finland (decision #336449) and the University of Oulu.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
[version 1; peer review: 2 approved]
References
- Allio R., Schomaker-Bastos A., Romiguier J., et al. : MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Molecular Ecology Resources ;2020;20(4):892–905. 10.1111/1755-0998.13160 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Altschul S. F., Gish W., Miller W., et al. : Basic Local Alignment Search Tool. Journal of Molecular Biology ;1990;215(3):403–410. 10.1016/S0022-2836(05)80360-2 [DOI] [PubMed] [Google Scholar]
- Buchfink B., Reuter K., Drost H.-G.: Sensitive protein alignments at tree-of-life scale using DIAMOND. Nature Methods ;2021;18(4):366–368. 10.1038/s41592-021-01101-x [DOI] [PMC free article] [PubMed] [Google Scholar]
- Challis R., Richards E., Rajan J., et al. : BlobToolKit – interactive quality assessment of genome assemblies. G3: Genes, Genomes, Genetics ;2020;10(4):1361–1374. 10.1534/g3.119.400908 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Challis Richard, Blaxter Mark: Snail plots are badges of genome assembly quality. G3 Genes|Genomes|Genetics ;2026;16(6):jkag074. 10.1093/g3journal/jkag074 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng H., Jarvis E. D., Fedrigo O., et al. : Haplotype-resolved assembly of diploid genomes without parental data. Nature Biotechnology ;2022;40(9):1332–1335. 10.1038/s41587-022-01261-x [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng H., Concepcion G. T., Feng X., et al. : Haplotype-resolved de novo assembly using phased assembly graphs with Hifiasm. Nature Methods ;2021;18(2):170–175. 10.1038/s41592-020-01056-5 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Formenti G., Abueg L., Brajuka A., et al. : Gfastats: Conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics ;2022;38(17):4214–4216. 10.1093/bioinformatics/btac460 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Howard Caroline, Denton Amy, Jackson Benjamin W., et al. : On the path to reference genomes for all biodiversity: Laboratory protocols and lessons learned from processing over 2,000 species in the Sanger Tree of Life. GigaScience ;2025;14giaf119. Reference Source 10.1093/gigascience/giaf119 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Howe K., Chow W., Collins J., et al. : Significantly improving the quality of genome assemblies through curation. GigaScience ;2021;10(1):giaa153. 10.1093/gigascience/giaa153 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kawahara Akito Y., Ohshima Issei, Kawakita Atsushi, et al. : Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae). BMC Evolutionary Biology ;2011;11:182. 10.1186/1471-2148-11-182 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kerpedjiev P., Abdennur N., Lekschas F., et al. : HiGlass: Web-based visual exploration and analysis of genome interaction maps. Genome Biology ;2018;19(1):125. 10.1186/s13059-018-1486-1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kurtzer G. M., Sochat V., Bauer M. W.: Singularity: Scientific containers for mobility of compute. PLOS ONE ;2017;12(5):e0177459. 10.1371/journal.pone.0177459 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lepiforum e.V. : Lepiforum: Bestimmungshilfe für die in Europa nachgewiesenen Schmetterlingsarten. Lepiforum e.V..2025. Accessed: 2026-01-11. Reference Source [Google Scholar]
- Manni Mosè, Berkeley Matthew R, Seppey Mathieu, et al. : BUSCO update: Novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Molecular Biology and Evolution ;2021;38(10):4647–4654. 10.1093/molbev/msab199 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Mitter Charles, Davis Donald R., Cummings Michael P.: Phylogeny and evolution of Lepidoptera. Annual Review of Entomology ;2017;62:265–283. 10.1146/annurev-ento-031616-035125 [DOI] [PubMed] [Google Scholar]
- Mutanen Marko, Wahlberg Niklas, Kaila Lauri: Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies. Proceedings of the Royal Society B: Biological Sciences ;2010;277(1695):2839–2848. 10.1098/rspb.2010.0392 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ranallo-Benavidez Timothy R., Jaron Kai S., Schatz Michael C.: GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications ;2020;11(1):1432. 10.1038/s41467-020-14998-3 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rao S. S. P., Huntley M. H., Durand N. C., et al. : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell ;2014;159(7):1665–1680. 10.1016/j.cell.2014.11.021 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Regier Jerome C., Mitter Charles, Zwick Andreas, et al. : A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies). PLOS ONE ;2013;8(3):e58568. 10.1371/journal.pone.0058568 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhie A., Walenz B. P., Koren S., et al. : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biology ;2020;21(1):245. 10.1186/s13059-020-02134-9 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhie A., McCarthy S. A., Fedrigo O., et al. : Towards complete and error-free genome assemblies of all vertebrate species. Nature ;2021;592(7856):737–746. 10.1038/s41586-021-03451-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sohn Jae-Cheon, Regier Jerome C., Mitter Charles, et al. : A molecular phylogeny for Yponomeutoidea (Insecta, Lepidoptera, Ditrysia) and its implications for classification, biogeography and the evolution of host plant use. PLOS ONE ;2013;8(1):e55066. 10.1371/journal.pone.0055066 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Uliano-Silva M., Ferreira J. G. R. N., Krasheninnikova K., et al. : MitoHiFi: A Python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics ;2023;24(1):288. 10.1186/s12859-023-05385-y [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vasimuddin Md., Misra S., Li H., et al. : Efficient architecture-aware acceleration of BWA-MEM for multicore systems. 2019 IEEE international parallel and distributed processing symposium (IPDPS) . IEEE.2019.314–324. 10.1109/IPDPS.2019.00041 [DOI] [Google Scholar]
- Wright Charlotte J., Stevens Lewis, Mackintosh Alexander, et al. : Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera. Nature Ecology & Evolution ;2024;8(4):777–790. 10.1038/s41559-024-02329-4 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zhou C., McCarthy S. A., Durbin R.: YaHS: Yet another Hi-C scaffolding tool. Bioinformatics ;2023;39(1):btac808. 10.1093/bioinformatics/btac808 [DOI] [PMC free article] [PubMed] [Google Scholar]