Abstract
We present a genome assembly from a male specimen of Ancylis achatana (Triangle-marked Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 547.27 megabases. Most of the assembly (99.25%) is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.0 kilobases.
Keywords: Ancylis achatana, Triangle-marked Roller, genome sequence, chromosomal, Lepidoptera
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Apoditrysia; Tortricoidea; Tortricidae; Olethreutinae; Enarmoniini; Ancylis; Ancylis achatana (Denis & Schiffermüller), 1775 (NCBI:txid1869464)
Background
Ancylis achatana (common name Triangle-marked Roller or Hedge Hook-wing) is a micro-moth in the family Tortricidae. It is common in England and Wales and local in Ireland. It is found eastwards across Europe to Russia ( GBIF Secretariat, 2025 ).
The small moth (forewing length 6–9 mm) is mottled brown and grey with a distinctive pre-tornal triangular rich brown patch in the middle of the trailing edge of the forewings. Although the colouration is variable, the markings are consistent. The moth is on the wing between May and August and comes to light ( Sterling et al., 2023).
Ancylis achatana lays its eggs on hawthorn, blackthorn or occasionally Cotoneaster spp., and the larva spins a tubular shelter from leaves attached to a twig, and then feeds close by ( Hancock et al., 2015). It pupates in the leaf spinnings during May ( Langmaid et al., 2018).
We present a chromosome-level genome sequence for Ancylis achatana based on one male specimen from Wytham Woods, Oxfordshire, UK. The genome 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.
Genome sequence report
Sequencing data
The genome of a specimen of Ancylis achatana ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating 59.18 Gb (gigabases) from 5.55 million reads. GenomeScope analysis of the PacBio HiFi data estimated the haploid genome size at 575.95 Mb, with a heterozygosity of 0.29% and repeat content of 38.29%. These values provide an initial assessment of genome complexity and the challenges anticipated during assembly. Based on this estimated genome size, the sequencing data provided approximately 100.0x coverage of the genome. Chromosome conformation Hi-C sequencing produced 106.37 Gb from 704.46 million reads. Table 1 summarises the specimen and sequencing information.
Figure 1. Photograph of the Ancylis achatana (ilAncAcha1) specimen used for genome sequencing.
Table 1. Specimen and sequencing data for Ancylis achatana.
| Project information | |||
|---|---|---|---|
| Study title | Ancylis achatana (triangle-marked roller) | ||
| Umbrella BioProject | PRJEB78334 | ||
| Species | Ancylis achatana | ||
| BioSpecimen | SAMEA7520689 | ||
| NCBI taxonomy ID | 1869464 | ||
| Specimen information | |||
| Technology | ToLID | BioSample accession | Organism part |
| PacBio long read sequencing | ilAncAcha1 | SAMEA7520779 | whole organism |
| Hi-C sequencing | ilAncAcha2 | SAMEA114806094 | whole organism |
| Sequencing information | |||
| Platform | Run accession | Read count | Base count (Gb) |
| Hi-C Illumina NovaSeq X | ERR13389762 | 7.04e+08 | 106.37 |
| PacBio Revio | ERR13420778 | 5.55e+06 | 59.18 |
Assembly statistics
The primary haplotype was assembled, and contigs corresponding to an alternate haplotype were also deposited in INSDC databases. The assembly was improved by manual curation, which corrected 55 misjoins or missing joins. These interventions decreased the scaffold count by 5.88%. The final assembly has a total length of 547.27 Mb in 111 scaffolds, with 67 gaps, and a scaffold N50 of 20.35 Mb ( Table 2).
Table 2. Genome assembly data for Ancylis achatana.
| Genome assembly | ||
|---|---|---|
| Assembly name | ilAncAcha1.1 | |
| Assembly accession | GCA_964214005.1 | |
| Alternate haplotype accession | GCA_964214015.1 | |
| Assembly level for primary
assembly |
chromosome | |
| Span (Mb) | 547.27 | |
| Number of contigs | 178 | |
| Number of scaffolds | 111 | |
| Longest scaffold (Mb) | 42.27 | |
| Assembly metric | Measure | Benchmark |
| Contig N50 length | 9.22 Mb | ≥ 1 Mb |
| Scaffold N50 length | 20.35 Mb | = chromosome N50 |
| Consensus quality (QV) | Primary: 63.0; alternate: 61.1;
combined 61.9 |
≥ 40 |
| k-mer completeness | Primary: 91.92%; alternate:
90.69%; combined: 99.17% |
≥ 95% |
| BUSCO * | C:98.4%[S:98.0%,D:0.5%],
F:0.2%,M:1.3%,n:5,286 |
S > 90%; D < 5% |
| Percentage of assembly
mapped to chromosomes |
99.26% | ≥ 90% |
| Sex chromosomes | Z |
localised
homologous pairs |
| Organelles | Mitochondrial genome: 16.0 kb |
complete single
alleles |
* BUSCO scores based on the lepidoptera_odb10 BUSCO set using version 5.5.0. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison.
The snail plot in Figure 2 provides a summary of the assembly statistics, indicating the distribution of scaffold lengths and other assembly metrics. Figure 3 shows the distribution of scaffolds by GC proportion and coverage. Figure 4 presents a cumulative assembly plot, with separate curves representing different scaffold subsets assigned to various phyla, illustrating the completeness of the assembly.
Figure 2. Genome assembly of Ancylis achatana, ilAncAcha1.1: metrics.
The BlobToolKit snail plot provides an overview of assembly metrics and BUSCO gene completeness. The circumference represents the length of the whole genome sequence, 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. The longest scaffold is indicated by the red arc, and the deeper orange and pale orange arcs represent the N50 and N90 lengths. A 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. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_964214005.1/dataset/GCA_964214005.1/snail.
Figure 3. Genome assembly of Ancylis achatana, ilAncAcha1.1: BlobToolKit GC-coverage plot.
Blob plot showing sequence coverage (vertical axis) and GC content (horizontal axis). The circles represent scaffolds, with the size proportional to scaffold length and the colour representing phylum membership. The histograms along the axes display the total length of sequences distributed across different levels of coverage and GC content. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_964214005.1/blob.
Figure 4. Genome assembly of Ancylis achatana, ilAncAcha1.1: 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/GCA_964214005.1/dataset/GCA_964214005.1/cumulative.
Most of the assembly sequence (99.26%) was assigned to 28 chromosomal-level scaffolds, representing 27 autosomes and the Z sex chromosome. These chromosome-level scaffolds, confirmed by Hi-C data, are named according to size ( Figure 5; Table 3). During curation, chromosome Z was assigned by synteny to Archips crataeganus (GCA_947859365.1) ( Boyes et al., 2024).
Figure 5. Genome assembly of Ancylis achatana: Hi-C contact map of the ilAncAcha1.1 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=fNieo9pLR92pE1Di_iUfgA.
Table 3. Chromosomal pseudomolecules in the genome assembly of Ancylis achatana, ilAncAcha1.
| INSDC accession | Name | Length (Mb) | GC% |
|---|---|---|---|
| OZ172862.1 | 1 | 32.02 | 38 |
| OZ172863.1 | 2 | 29.49 | 37.5 |
| OZ172864.1 | 3 | 22.82 | 38.5 |
| OZ172865.1 | 4 | 22.72 | 38.5 |
| OZ172866.1 | 5 | 21.89 | 38 |
| OZ172867.1 | 6 | 21.81 | 38.5 |
| OZ172868.1 | 7 | 21.7 | 38 |
| OZ172869.1 | 8 | 21.61 | 38 |
| OZ172870.1 | 9 | 20.52 | 38 |
| OZ172871.1 | 10 | 20.35 | 38.5 |
| OZ172872.1 | 11 | 20.04 | 38.5 |
| OZ172873.1 | 12 | 19.98 | 39 |
| OZ172874.1 | 13 | 19.72 | 38.5 |
| OZ172875.1 | 14 | 19.48 | 38.5 |
| OZ172876.1 | 15 | 19.42 | 38.5 |
| OZ172877.1 | 16 | 18.85 | 38.5 |
| OZ172878.1 | 17 | 17.99 | 39 |
| OZ172879.1 | 18 | 17.9 | 39 |
| OZ172880.1 | 19 | 16.71 | 39 |
| OZ172881.1 | 20 | 14.5 | 38.5 |
| OZ172882.1 | 21 | 13.21 | 39.5 |
| OZ172883.1 | 22 | 13.01 | 39 |
| OZ172884.1 | 23 | 12.66 | 41 |
| OZ172885.1 | 24 | 11.92 | 39 |
| OZ172886.1 | 25 | 10.76 | 39.5 |
| OZ172887.1 | 26 | 9.98 | 39 |
| OZ172888.1 | 27 | 9.87 | 40.5 |
| OZ172861.1 | Z | 42.27 | 38 |
| OZ172889.1 | MT | 0.02 | 19 |
The mitochondrial genome was also assembled. This sequence is included as a contig in the multifasta file of the genome submission and as a standalone record.
Assembly quality metrics
The estimated Quality Value (QV) and k-mer completeness metrics, along with BUSCO completeness scores, were calculated for each haplotype and the combined assembly. The QV reflects the base-level accuracy of the assembly, while k-mer completeness indicates the proportion of expected k-mers identified in the assembly. BUSCO scores provide a measure of completeness based on benchmarking universal single-copy orthologues.
The combined primary and alternate assemblies achieve an estimated QV of 61.9. The k-mer recovery for the primary haplotype is 91.92%, and for the alternate haplotype 90.69%; the combined primary and alternate assemblies have a k-mer recovery of 99.17%. BUSCO analysis using the lepidoptera_odb10 reference set ( n = 5,286) identified 98.4% of the expected gene set (single = 98.0%, duplicated = 0.5%).
Table 2 provides assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project (EBP) Report on Assembly Standards September 2024. The assembly achieves the EBP reference standard of 6.C.Q61.
Methods
Sample acquisition and DNA barcoding
An adult male Ancylis achatana (specimen ID Ox000473, ToLID ilAncAcha1) was collected from Wytham Woods, Oxfordshire, United Kingdom (latitude 51.77, longitude –1.34) on 2020-06-13 by light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.
The specimen used for Hi-C sequencing (specimen ID NHMUK014584877, ToLID ilAncAcha2) was collected from Bure Marshes Stables, England, United Kingdom (latitude 52.69, longitude 1.45) on 2022-06-29. The specimen was collected by David Lees (Natural History Museum) and identified by Mark Sterling (Natural History Museum) and preserved by dry freezing (–80 °C).
The initial identification was verified by an additional DNA barcoding process according to the framework developed by Twyford et al. (2024). A small sample was dissected from the specimen and stored in ethanol, while the remaining parts were shipped on dry ice to the Wellcome Sanger Institute (WSI) ( Pereira et al., 2022). The tissue was lysed, the COI marker region was amplified by PCR, and amplicons were sequenced and compared to the BOLD database, confirming the species identification ( Crowley et al., 2023). Following whole genome sequence generation, the relevant DNA barcode region was also used alongside the initial barcoding data for sample tracking at the WSI ( Twyford et al., 2024). The standard operating procedures for Darwin Tree of Life barcoding have been deposited on protocols.io ( Beasley et al., 2023).
Metadata collection for samples adhered to the Darwin Tree of Life project standards described by Lawniczak et al. (2022).
Nucleic acid extraction
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of procedures: sample preparation and homogenisation, DNA extraction, fragmentation and purification. Detailed protocols are available on protocols.io ( Denton et al., 2023b). The ilAncAcha1 sample was prepared for DNA extraction by weighing and dissecting it on dry ice ( Jay et al., 2023). Tissue from the whole organism was homogenised using a PowerMasher II tissue disruptor ( Denton et al., 2023a).
HMW DNA was extracted using the Automated MagAttract v2 protocol ( Oatley et al., 2023a). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation, using AMPure PB beads to eliminate shorter fragments and concentrate the DNA ( Oatley et al., 2023b). 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 FemtoPulse system.
Hi-C sample preparation
Tissue from the whole organism of the ilAncAcha2 sample was processed for Hi-C sequencing at the WSI Scientific Operations core, using the Arima-HiC v2 kit. In brief, 20–50 mg of frozen tissue (stored at –80 °C) was fixed, and the DNA crosslinked using a TC buffer with 22% formaldehyde concentration. After crosslinking, the tissue was homogenised using the Diagnocine Power Masher-II and BioMasher-II tubes and pestles. Following the Arima-HiC v2 kit manufacturer's instructions, crosslinked DNA was digested using a restriction enzyme master mix. The 5’-overhangs were filled in and labelled with biotinylated nucleotides and proximally ligated. An overnight incubation was carried out for enzymes to digest remaining proteins and for crosslinks to reverse. A clean up was performed with SPRIselect beads prior to library preparation. Additionally, the biotinylation percentage was estimated using the Qubit Fluorometer v4.0 (Thermo Fisher Scientific) and Qubit HS Assay Kit and Arima-HiC v2 QC beads.
Library preparation and sequencing
Library preparation and sequencing were performed at the WSI Scientific Operations core.
PacBio HiFi
At a minimum, samples were required to have an average fragment size exceeding 8 kb and a total mass over 400 ng to proceed to the low input SMRTbell Prep Kit 3.0 protocol (Pacific Biosciences, California, USA), depending on genome size and sequencing depth required. Libraries were prepared using the SMRTbell Prep Kit 3.0 (Pacific Biosciences, California, USA) as per the manufacturer's instructions. The kit includes the reagents required for end repair/A-tailing, adapter ligation, post-ligation SMRTbell bead cleanup, and nuclease treatment. Following the manufacturer’s instructions, size selection and clean up was carried out using diluted AMPure PB beads (Pacific Biosciences, California, USA). DNA concentration was quantified using the Qubit Fluorometer v4.0 (Thermo Fisher Scientific) with Qubit 1X dsDNA HS assay kit and the final library fragment size analysis was carried out using the Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies) and gDNA 55kb BAC analysis kit.
Samples were sequenced on a Revio instrument (Pacific Biosciences, California, USA). Prepared libraries were normalised to 2 nM, and 15 μL was used for making complexes. Primers were annealed and polymerases were hybridised to create circularised complexes according to manufacturer’s instructions. The complexes were purified with the 1.2X clean up with SMRTbell beads. The purified complexes were then diluted to the Revio loading concentration (in the range 200–300 pM), and spiked with a Revio sequencing internal control. Samples were sequenced on Revio 25M SMRT cells (Pacific Biosciences, California, USA). The SMRT link software, a PacBio web-based end-to-end workflow manager, was used to set-up and monitor the run, as well as perform primary and secondary analysis of the data upon completion.
Hi-C
For Hi-C library preparation, DNA was fragmented using the Covaris E220 sonicator (Covaris) and size selected using SPRISelect beads to 400 to 600 bp. The DNA was then enriched using the Arima-HiC v2 kit Enrichment beads. Using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) for end repair, a-tailing, and adapter ligation. This uses a custom protocol which resembles the standard NEBNext Ultra II DNA Library Prep protocol but where library preparation occurs while DNA is bound to the Enrichment beads. For library amplification, 10 to 16 PCR cycles were required, determined by the sample biotinylation percentage. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp on an Illumina NovaSeq X instrument.
Genome assembly, curation and evaluation
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. GenomeScope2 ( Ranallo-Benavidez et al., 2020) was used to analyse the k-mer frequency distributions, providing estimates of genome size, heterozygosity, and repeat content.
The HiFi reads were first assembled using Hifiasm ( Cheng et al., 2021) with the --primary option. Haplotypic duplications were identified and removed using purge_dups ( Guan et al., 2020). The Hi-C reads were mapped to the primary contigs using bwa-mem2 ( Vasimuddin et al., 2019). The contigs were further scaffolded using the provided Hi-C data ( Rao et al., 2014) 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 MERQURY.FK ( 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. Flat files and maps used in curation were generated via the TreeVal pipeline ( Pointon et al., 2023). Manual curation was conducted primarily in PretextView ( Harry, 2022) and HiGlass ( Kerpedjiev et al., 2018), with additional insights provided by JBrowse2 ( Diesh et al., 2023). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). Any identified contamination, missed joins, and mis-joins were amended, and duplicate sequences were tagged and removed. Sex chromosomes were identified by synteny analysis. The curation process is documented at https://gitlab.com/wtsi-grit/rapid-curation.
Assembly quality assessment
The Merqury.FK 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 the primary and alternate haplotypes using the k-mer databases ( k = 31) that were computed prior to genome assembly. The analysis outputs included assembly QV scores and completeness statistics.
A Hi-C contact map was produced for the final version of the assembly. The Hi-C reads were aligned using bwa-mem2 ( Vasimuddin et al., 2019) and the alignment files were combined using SAMtools ( Danecek et al., 2021). The Hi-C alignments were converted into a contact map using BEDTools ( Quinlan & Hall, 2010) and the Cooler tool suite ( Abdennur & Mirny, 2020). The contact map was visualised in HiGlass ( Kerpedjiev et al., 2018).
The blobtoolkit pipeline is a Nextflow port of the previous Snakemake Blobtoolkit pipeline ( Challis et al., 2020). It aligns the PacBio reads in SAMtools and minimap2 ( Li, 2018) and generates coverage tracks for regions of fixed size. In parallel, it queries the GoaT database ( Challis et al., 2023) to identify all matching BUSCO lineages to run BUSCO ( Manni et al., 2021). For the three domain-level BUSCO lineages, the pipeline aligns the BUSCO genes to the UniProt Reference Proteomes database ( Bateman et al., 2023) with DIAMOND blastp ( Buchfink et al., 2021). The genome is also divided into chunks according to the density of the BUSCO genes from the closest taxonomic lineage, and each chunk is aligned to the UniProt Reference Proteomes database using DIAMOND blastx. Genome sequences without a hit are chunked using seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). The blobtools suite combines all these outputs into a blobdir for visualisation.
The blobtoolkit pipeline was developed using nf-core tooling ( Ewels et al., 2020) and MultiQC ( Ewels et al., 2016), relying on the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), as well as the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.
Table 4 contains a list of relevant software tool versions and sources.
Table 4. Software tools: versions and sources.
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
• 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.
Funding Statement
This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (220540) and the Darwin Tree of Life Discretionary Award [218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328 </a>].
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
[version 1; peer review: 3 approved, 1 approved with reservations]
Data availability
European Nucleotide Archive: Ancylis achatana (triangle-marked roller). Accession number PRJEB78334; https://identifiers.org/ena.embl/PRJEB78334. The genome sequence is released openly for reuse. The Ancylis achatana genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1 and Table 2.
Author information
Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.12157525.
Members of the Natural History Museum Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.12159242.
Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.12158331.
Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.12162482.
Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.12165051.
Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.12160324.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.12205391.
Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.
References
- Abdennur N, Mirny LA: Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 10.1093/bioinformatics/btz540 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Allio R, Schomaker-Bastos A, Romiguier J, et al. : MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20(4):892–905. 10.1111/1755-0998.13160 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Altschul SF, Gish W, Miller W, et al. : Basic Local Alignment Search Tool. J Mol Biol. 1990;215(3):403–410. 10.1016/S0022-2836(05)80360-2 [DOI] [PubMed] [Google Scholar]
- Bateman A, Martin MJ, Orchard S, et al. : UniProt: the universal protein knowledgebase in 2023. Nucleic Acids Res. 2023;51(D1):D523–D531. 10.1093/nar/gkac1052 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bates A, Clayton-Lucey I, Howard C: Sanger Tree of Life HMW DNA fragmentation: diagenode Megaruptor ®3 for LI PacBio. protocols.io. 2023. 10.17504/protocols.io.81wgbxzq3lpk/v1 [DOI] [Google Scholar]
- Beasley J, Uhl R, Forrest LL, et al. : DNA barcoding SOPs for the Darwin Tree of Life project. protocols.io. 2023; [Accessed 25 June 2024]. 10.17504/protocols.io.261ged91jv47/v1 [DOI] [Google Scholar]
- Boyes D, Gibbs M, University of Oxford and Wytham Woods Genome Acquisition Lab, et al. : The genome sequence of the Brown Oak Tortrix, Archips crataeganus (Hübner, 1796) [version 1; peer review: 3 approved, 1 approved with reservations]. Wellcome Open Res. 2024;9:9. 10.12688/wellcomeopenres.20413.1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Buchfink B, Reuter K, Drost HG: Sensitive protein alignments at Tree-of-Life scale using DIAMOND. Nat Methods. 2021;18(4):366–368. 10.1038/s41592-021-01101-x [DOI] [PMC free article] [PubMed] [Google Scholar]
- Challis R, Kumar S, Sotero-Caio C, et al. : Genomes on a Tree (GoaT): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic Tree of Life [version 1; peer review: 2 approved]. Wellcome Open Res. 2023;8:24. 10.12688/wellcomeopenres.18658.1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Challis R, Richards E, Rajan J, et al. : BlobToolKit – interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g3.119.400908 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng H, Concepcion GT, Feng X, et al. : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18(2):170–175. 10.1038/s41592-020-01056-5 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Crowley L, Allen H, Barnes I, et al. : A sampling strategy for genome sequencing the British terrestrial arthropod fauna [version 1; peer review: 2 approved]. Wellcome Open Res. 2023;8:123. 10.12688/wellcomeopenres.18925.1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- da Veiga Leprevost F, Grüning BA, Alves Aflitos S, et al. : BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017;33(16):2580–2582. 10.1093/bioinformatics/btx192 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Danecek P, Bonfield JK, Liddle J, et al. : Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2): giab008. 10.1093/gigascience/giab008 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Denton A, Oatley G, Cornwell C, et al. : Sanger Tree of Life sample homogenisation: PowerMash. protocols.io. 2023a. 10.17504/protocols.io.5qpvo3r19v4o/v1 [DOI] [Google Scholar]
- Denton A, Yatsenko H, Jay J, et al. : Sanger Tree of Life wet laboratory protocol collection V.1. protocols.io. 2023b. 10.17504/protocols.io.8epv5xxy6g1b/v1 [DOI] [Google Scholar]
- Diesh C, Stevens GJ, Xie P, et al. : JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biol. 2023;24(1): 74. 10.1186/s13059-023-02914-z [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ewels PA, Peltzer A, Fillinger S, et al. : The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276–278. 10.1038/s41587-020-0439-x [DOI] [PubMed] [Google Scholar]
- Ewels P, Magnusson M, Lundin S, et al. : MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048. 10.1093/bioinformatics/btw354 [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]
- GBIF Secretariat: Ancylis achatana (Denis & Schiffermüller), 1775 checklist dataset. GBIF Backbone Taxonomy. 2025; [Accessed 8 February 2025]. Reference Source
- Grüning B, Dale R, Sjödin A, et al. : Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018;15(7):475–476. 10.1038/s41592-018-0046-7 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guan D, McCarthy SA, Wood J, et al. : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896–2898. 10.1093/bioinformatics/btaa025 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hancock EF, Bland KP, Razowski J: The Moths and Butterflies of Great Britain and Ireland Tortricidae Olethreutinae. Leiden: Brill,2015. [Google Scholar]
- Harry E: PretextView (Paired REad TEXTure Viewer): a desktop application for viewing pretext contact maps. 2022. Reference Source
- 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]
- Jay J, Yatsenko H, Narváez-Gómez JP, et al. : Sanger Tree of Life sample preparation: triage and dissection. protocols.io. 2023. 10.17504/protocols.io.x54v9prmqg3e/v1 [DOI] [Google Scholar]
- Kerpedjiev P, Abdennur N, Lekschas F, et al. : HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19(1): 125. 10.1186/s13059-018-1486-1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kurtzer GM, Sochat V, Bauer MW: 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]
- Langmaid JR, Palmer S, Young MR: A field guide to the smaller moths of Great Britain and Ireland. 3rd ed., British Entomological and Natural History Society,2018. Reference Source [Google Scholar]
- Lawniczak MKN, Davey RP, Rajan J, et al. : Specimen and sample metadata standards for biodiversity genomics: a proposal from the Darwin Tree of Life project [version 1; peer review: 2 approved with reservations]. Wellcome Open Res. 2022;7:187. 10.12688/wellcomeopenres.17605.1 [DOI] [Google Scholar]
- Li H: Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–3100. 10.1093/bioinformatics/bty191 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Manni M, Berkeley MR, Seppey M, et al. : BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38(10):4647–4654. 10.1093/molbev/msab199 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Merkel D: Docker: lightweight Linux containers for consistent development and deployment. Linux J. 2014;2014(239): 2, [Accessed 2 April 2024]. Reference Source [Google Scholar]
- Oatley G, Denton A, Howard C: Sanger Tree of Life HMW DNA extraction: automated MagAttract v.2. protocols.io. 2023a. 10.17504/protocols.io.kxygx3y4dg8j/v1 [DOI] [Google Scholar]
- Oatley G, Sampaio F, Howard C: Sanger Tree of Life fragmented DNA clean up: automated SPRI. protocols.io. 2023b. 10.17504/protocols.io.q26g7p1wkgwz/v1 [DOI] [Google Scholar]
- Pereira L, Sivell O, Sivess L, et al. : DToL taxon-specific standard operating procedure for the terrestrial and freshwater arthropods working group.2022. 10.17504/protocols.io.261gennyog47/v1 [DOI] [Google Scholar]
- Pointon DL, Eagles W, Sims Y, et al. : sanger-tol/treeval v1.0.0 – Ancient Atlantis. 2023. Reference Source [Google Scholar]
- Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–842. 10.1093/bioinformatics/btq033 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ranallo-Benavidez TR, Jaron KS, Schatz MC: GenomeScope 2.0 and smudgeplot for reference-free profiling of polyploid genomes. Nat Commun. 2020;11(1): 1432. 10.1038/s41467-020-14998-3 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rao SSP, Huntley MH, Durand NC, 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]
- Rhie A, McCarthy SA, 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]
- Rhie A, Walenz BP, Koren S, et al. : Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21(1): 245. 10.1186/s13059-020-02134-9 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sterling P, Parsons M, Lewington R: Field guide to the micro-moths of Great Britain and Ireland. Second Edition. London: Bloomsbury Publishing,2023. Reference Source [Google Scholar]
- Twyford AD, Beasley J, Barnes I, et al. : A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life project [version 1; peer review: 2 approved]. Wellcome Open Res. 2024;9:339. 10.12688/wellcomeopenres.21143.1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Uliano-Silva M, Ferreira JGRN, 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 M, Misra S, Li H, et al. : Efficient architecture-aware acceleration of BWA-MEM for multicore systems.In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).IEEE,2019;314–324. 10.1109/IPDPS.2019.00041 [DOI] [Google Scholar]
- Zhou C, McCarthy SA, 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]