
==== Front
Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
F1000 Research Limited London, UK

10.12688/wellcomeopenres.20833.1
Data Note
Articles
The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758)
[version 1; peer review: 2 approved]

Boyes Douglas Investigation Resources 1
Holland Peter W. H. Writing – Original Draft Preparation Writing – Review & Editing https://orcid.org/0000-0003-1533-9376
2
University of Oxford and Wytham Woods Genome Acquisition Lab
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
Wellcome Sanger Institute Scientific Operations: Sequencing Operations
Wellcome Sanger Institute Tree of Life Core Informatics team
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 UK Centre for Ecology & Hydrology, Wallingford, England, UK
2 University of Oxford, Oxford, England, UK
a mark.blaxter@sanger.ac.uk
+ Deceased author

No competing interests were disclosed.

12 2 2024
2024
9 318 1 2024
Copyright: © 2024 Boyes D et al.
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

We present a genome assembly from an individual male Callimorpha dominula (the Scarlet Tiger moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 658.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,234 protein coding genes.

Callimorpha dominula
Scarlet Tiger moth
genome sequence
chromosomal
Lepidoptera
Wellcome Trust206194 218328 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (218328). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
==== Body
pmcSpecies taxonomy

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Amphiesmenoptera; Lepidoptera; Glossata; Neolepidoptera; Heteroneura; Ditrysia; Obtectomera; Noctuoidea; Erebidae; Arctiinae; Callimorphini; Callimorpha; Callimorpha dominula (Linnaeus, 1758) (NCBI:txid938182).

Background

The Scarlet Tiger Callimorpha dominula is a day-flying moth with blue-black forewings marked with cream and white spots, and striking red and black hindwings. Several colour variants have been described including the form bimacula with only two forewing spots, proposed to result from a homozygous recessive mutation, and a partially spotted form medionigra proposed to be heterozygous at the same locus ( Ford, 1967). The bimacula allele may also have pleiotropic effects on other traits ( Sheppard & Cook, 1962). C. dominula inhabits damp meadows and riverine habitats where the larval foodplant comfrey, Symphytum officinale, grows. The distribution in Britain is very patchy, with many apparently suitable habitats not favoured by the species. Where present, however, the moth can be abundant, with the weakly flying adults a common sight in June in some riverside towns in the south and west of England and Wales. The moth is found across most of Europe from southern Scandinavia to northern Spain, and also further east to Iran and Russia ( GBIF Secretariat, 2023).

For several decades, the Scarlet Tiger moth C. dominula was at the centre of a fierce academic dispute around the relative importance of natural selection and genetic drift in evolution. From the 1930s to the 1960s, E.B. Ford, Ronald Fisher and Philip Sheppard monitored the frequencies of the normal colour variant, the homozygote bimacula and the heterozygote medionigra at Cothill Fen near Oxford, UK. They argued that radically changing genotype frequencies seen from year to year, in a relatively large population, could only be explained by changing selection pressures and not by genetic drift ( Fisher & Ford, 1947; Ford, 1967). There have been criticisms of these studies, including statistical critique and evidence for variable penetrance of alleles leading to inconsistent genotype inference by observers ( Clarke et al., 1991; Cook & Jones, 1996). One environmental cause of variable penetrance may be the temperature experienced by the larvae or pupae ( Owen & Goulson, 1994), although the relevance of this effect has also been disputed ( Jones, 2000). Current evidence suggests that natural selection, genetic drift and dispersal were all interacting in the Cothill population ( O’Hara, 2005).

The genome sequence of Callimorpha dominula was determined as part of the Darwin Tree of Life project. The complete genome sequence will aid research into the molecular basis of wing colour polymorphisms and facilitate research into habitat choice and larval food preference.

Genome sequence report

The genome was sequenced from one male Callimorpha dominula ( Figure 1) collected from Wytham Woods, Oxfordshire, UK (51.77, –1.33). A total of 39-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 12 missing joins or mis-joins and removed one haplotypic duplication, reducing the scaffold number by 10.81%.

Figure 1. Photograph of the Callimorpha dominula (ilCalDomi2) specimen used for genome sequencing.

The final assembly has a total length of 658.1 Mb in 32 sequence scaffolds with a scaffold N50 of 24.1 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 (99.99%) of the assembly sequence was assigned to 31 chromosomal-level scaffolds, representing 30 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). Chromosome Z has been assigned based on synteny to Tyria jacobaea (GCA_947561695.1) ( Boyes et al., 2023). 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.

Table 1. Genome data for Callimorpha dominula, ilCalDomi2.1.

Project accession data	
Assembly identifier	ilCalDomi2.1	
Species	Callimorpha dominula	
Specimen	ilCalDomi2	
NCBI taxonomy ID	938182	
BioProject	PRJEB60214	
BioSample ID	SAMEA7701310	
Isolate information	ilCalDomi2, male: head and thorax (DNA and
Hi-C sequencing), abdomen (RNA sequencing)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	65.7	≥ 50	
k-mer completeness	100.0%	≥ 95%	
BUSCO **	C:98.8%[S:98.1%,D:0.7%],
F:0.3%,M:1.0%,n:5,286	C ≥ 95%	
Percentage of assembly
mapped to chromosomes	99.99%	≥ 95%	
Sex chromosomes	Z	localised
homologous pairs	
Organelles	Mitochondrial genome:
15.45 kb	complete single
alleles	
Raw data accessions	
PacificBiosciences SEQUEL II	ERR10934082	
Hi-C Illumina	ERR10936425	
PolyA RNA-Seq Illumina	ERR12245540	
Genome assembly	
Assembly accession	GCA_949752705.1	
Accession of alternate
haplotype	GCA_949752685.1	
Span (Mb)	658.1	
Number of contigs	119	
Contig N50 length (Mb)	9.4	
Number of scaffolds	32	
Scaffold N50 length (Mb)	24.1	
Longest scaffold (Mb)	30.46	
Genome annotation	
Number of protein-coding genes	20,234	
Number of gene transcripts	20,422	
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from ( Rhie et al., 2021).

** BUSCO scores based 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/ilCalDomi2_1/dataset/ilCalDomi2_1/busco.

Figure 2. Genome assembly of Callimorpha dominula, ilCalDomi2.1: 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 658,140,099 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 (30,463,512 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (24,103,837 and 15,029,384 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/ilCalDomi2_1/dataset/ilCalDomi2_1/snail.

Figure 3. Genome assembly of Callimorpha dominula, ilCalDomi2.1: 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/ilCalDomi2_1/dataset/ilCalDomi2_1/blob.

Figure 4. Genome assembly of Callimorpha dominula, ilCalDomi2.1: 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/ilCalDomi2_1/dataset/ilCalDomi2_1/cumulative.

Figure 5. Genome assembly of Callimorpha dominula, ilCalDomi2.1: Hi-C contact map of the ilCalDomi2.1 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=bE1ClM-NQxG8RLymMc8O3w.

Table 2. Chromosomal pseudomolecules in the genome assembly of Callimorpha dominula, ilCalDomi2.

INSDC
accession	Chromosome	Length
(Mb)	GC%	
OX456991.1	1	28.78	36.0	
OX456992.1	2	28.24	35.5	
OX456993.1	3	27.11	36.0	
OX456994.1	4	26.71	35.5	
OX456995.1	5	26.69	35.5	
OX456996.1	6	26.62	35.5	
OX456997.1	7	26.2	35.5	
OX456998.1	8	25.32	35.5	
OX456999.1	9	25.16	35.5	
OX457000.1	10	24.39	35.5	
OX457001.1	11	24.23	35.5	
OX457002.1	12	24.1	35.5	
OX457003.1	13	22.81	35.5	
OX457004.1	14	22.61	35.5	
OX457005.1	15	22.42	35.5	
OX457006.1	16	22.28	36.0	
OX457007.1	17	22.06	35.5	
OX457008.1	18	21.8	36.0	
OX457009.1	19	20.04	36.0	
OX457010.1	20	18.88	36.0	
OX457011.1	21	18.49	35.5	
OX457012.1	22	17.09	36.0	
OX457013.1	23	16.57	36.0	
OX457014.1	24	16.15	36.0	
OX457015.1	25	15.03	36.0	
OX457016.1	26	14.37	36.0	
OX457017.1	27	12.69	37.5	
OX457018.1	28	11.02	37.0	
OX457019.1	29	10.44	37.0	
OX457020.1	30	9.32	37.5	
OX456990.1	Z	30.46	35.5	
OX457021.1	MT	0.02	18.5	

The estimated Quality Value (QV) of the final assembly is 65.7 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 98.8% (single = 98.1%, duplicated = 0.7%), using the lepidoptera_odb10 reference set ( n = 5,286).

Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/938182.

Genome annotation report

The Callimorpha dominula genome assembly (GCA_949752705.1) was annotated using the Ensembl rapid annotation pipeline ( Table 1; https://rapid.ensembl.org/Callimorpha_dominula_GCA_949752705.1/Info/Index). The resulting annotation includes 20,422 transcribed mRNAs from 20,234 protein-coding genes.

Methods

Sample acquisition and nucleic acid extraction

A male Callimorpha dominula (specimen ID Ox000543, ToLID ilCalDomi2) was collected from Wytham Woods, Oxfordshire, UK (latitude 51.77, longitude –1.33) on 2020-06-25 using a light trap. The specimen was collected and identified by Douglas Boyes (University of Oxford) and preserved on dry ice.

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 ilCalDomi2 sample was weighed and dissected on dry ice ( Jay et al., 2023). Tissue from the head and thorax 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 ( Oatley et al., 2023). The DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 31 ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 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.

RNA was extracted from abdomen tissue of ilCalDomi2 in the Tree of Life Laboratory at the WSI using the RNA Extraction: Automated MagMax™ mirVana protocol ( do Amaral et al., 2023). The RNA concentration was assessed using a Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit RNA Broad-Range Assay kit. Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023b).

Sequencing

Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit. DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from remaining head and thorax tissue of ilCalDomi2 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 using the TreeVal pipeline ( Pointon et al., 2023). Manual curation was performed using JBrowse2 ( Diesh et al., 2023), HiGlass ( Kerpedjiev et al., 2018) and Pretext ( Harry, 2022). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) or MITOS ( Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

A Hi-C map for the final assembly was produced using bwa-mem2 ( Vasimuddin et al., 2019) in the Cooler file format ( Abdennur & Mirny, 2020). To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury ( Rhie et al., 2020). This work was done using Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a) and “sanger-tol/genomenote” ( Surana et al., 2023b). The genome was analysed within the BlobToolKit environment ( Challis et al., 2020) and BUSCO scores ( Manni et al., 2021; Simão et al., 2015) were calculated.

Table 3 contains a list of relevant software tool versions and sources.

Table 3. Software tools: versions and sources.

Software tool	Version	Source	
BlobToolKit	4.2.1	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.3.2	https://gitlab.com/ezlab/busco	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
Merqury	MerquryFK	https://github.com/thegenemyers/MERQURY.FK	
MitoHiFi	3	https://github.com/marcelauliano/MitoHiFi	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
purge_dups	1.2.3	https://github.com/dfguan/purge_dups	
sanger-tol/
genomenote	v1.0	https://github.com/sanger-tol/genomenote	
sanger-tol/
readmapping	1.1.0	https://github.com/sanger-tol/readmapping/tree/1.1.0	
TreeVal	-	https://github.com/sanger-tol/treeval	
YaHS	1.2a	https://github.com/c-zhou/yahs	

Genome annotation

The BRAKER2 pipeline ( Brůna et al., 2021) was used in the default protein mode to generate annotation for the Callimorpha dominula assembly (GCA_949752705.1) 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

• 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.

Data availability

European Nucleotide Archive: Callimorpha dominula (scarlet tiger). Accession number PRJEB60214; https://identifiers.org/ena.embl/PRJEB60214 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Callimorpha dominula 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. Raw data and assembly accession identifiers are reported in Table 1.

Author information

Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7125292.

Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.

Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.

Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.

Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.

Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.

Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.

10.21956/wellcomeopenres.23052.r96842
Reviewer response for version 1
Wulff Juan 1Referee https://orcid.org/0000-0002-5773-4684

1 North Carolina State University, Raleigh, USA
3 9 2024 Copyright: © 2024 Wulff J
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
Abstract: please add the word of in between as follows … “a male individual” of “ Callimorpha dominula”…

Abstract: since genetic annotation is one of the weaknesses of this work I recommend to the authors removing the sentence “Gene annotation of this assembly on Ensembl identified 20,234 protein coding genes.” from it.

Please rephrase to clarify if “ bimacula” is another species or just a variant, e.g. “Several colour variants of the same species”

For future reports, using a scale bar in the pictures could be useful to see the actual specimens’ size.

Keywords: chromosomal is not a word that provides more visualization, or a strong keyword associated with the study; given the background, a word more related to the evolution of the species or those factors that drive the evolution of the species might be a better choice.

It may be useful for future studies if the DNA of bacteria and other microorganisms is provided separately from the genome assembly but all together with an associated ID within the same Bioproject.

It is recommended to use a transcriptomic approach to improve gene annotation in future studies.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

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

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Entomology; Molecular Biology; Genetics

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.

10.21956/wellcomeopenres.23052.r83182
Reviewer response for version 1
Sucháčková Alena 1Referee
1 Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
13 6 2024 Copyright: © 2024 Sucháčková A
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
The article represents yet another Lepidopteran genome assembly, this time of Callimorpha dominula, including mitogenome assembly and gene annotation. The manuscript is standard and the text is clear. The data are stored in a standard way.

I have only one minor text change suggestion:

Background - Specify the range: further east to NW Iran and Ural Mountains.

Are sufficient details of methods and materials provided to allow replication by others?

Yes

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

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

biogeography, population genetics, phylogeography, Lepidopteran ecology

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.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
==== Refs
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 31290943
Allio R Schomaker-Bastos A Romiguier J : 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 32243090
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.8epv5x2zjg1b/v1
Bernt M Donath A Jühling F : MITOS: Improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013;69 (2 ):313–319. 10.1016/j.ympev.2012.08.023 22982435
Boyes D Sivell O Holland PWH : The genome sequence of the Cinnabar Moth, Tyria jacobaeae (Linnaeus, 1758) [version 1; peer review: awaiting peer review]. Wellcome Open Res. 2023;8 :255. 10.12688/wellcomeopenres.19545.1
Brůna T Hoff KJ Lomsadze A : BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom Bioinform. 2021;3 (1 ): lqaa108. 10.1093/nargab/lqaa108 33575650
Challis R Richards E Rajan J : BlobToolKit - interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10 (4 ):1361–1374. 10.1534/g3.119.400908 32071071
Cheng H Concepcion GT Feng X : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18 (2 ):170–175. 10.1038/s41592-020-01056-5 33526886
Clarke CA Clarke FMM Owen DF : Natural selection and the scarlet tiger moth, Panaxia dominula: Inconsistencies in the scoring of the heterozygote, f. medionigra. Proceedings of the Royal Society B: Biological Sciences. 1991;244 (1311 ):203–205. 10.1098/rspb.1991.0071
Cook LM Jones DA : The medionigra gene in the moth Panaxia dominula: The case for selection. Philosophical Transactions of the Royal Society B: Biological Sciences. 1996;351 (1347 ):1623–1635. 10.1098/rstb.1996.0146
Denton A Oatley G Cornwell C : Sanger Tree of Life Sample Homogenisation: PowerMash. protocols.io. 2023a. 10.17504/protocols.io.5qpvo3r19v4o/v1
Denton A Yatsenko H Jay J : Sanger Tree of Life Wet Laboratory Protocol Collection V.1. protocols.io. 2023b. 10.17504/protocols.io.8epv5xxy6g1b/v1
Di Tommaso P Chatzou M Floden EW : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35 (4 ):316–319. 10.1038/nbt.3820 28398311
Diesh C Stevens GJ Xie P : 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 37069644
do Amaral RJV Bates A Denton A : Sanger Tree of Life RNA Extraction: Automated MagMax™ mirVana. protocols.io. 2023. 10.17504/protocols.io.6qpvr36n3vmk/v1
Fisher RA Ford EB : The spread of a gene in natural conditions in a colony of the moth Panaxia dominula L. Heredity. 1947;1 (2 ):143–174. 10.1038/hdy.1947.11
Ford EB : Moths.London: New Naturalist, Collins,1967.
GBIF Secretariat: Callimorpha dominula (Linnaeus, 1758) GBIF Backbone Taxonomy. 2023; [Accessed 30 December 2023]. Reference Source
Guan D McCarthy SA Wood J : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36 (9 ):2896–2898. 10.1093/bioinformatics/btaa025 31971576
Harry E : PretextView (Paired REad TEXTure Viewer): A desktop application for viewing pretext contact maps. 2022; [Accessed 19 October 2022]. Reference Source
Jay J Yatsenko H Narváez-Gómez JP : Sanger Tree of Life Sample Preparation: Triage and Dissection. protocols.io. 2023. 10.17504/protocols.io.x54v9prmqg3e/v1
Jones DA : Temperatures in the Cothill habitat of Panaxia (Callimorpha) dominula L. (the scarlet tiger moth). Heredity (Edinb). 2000;84 (Pt 5 ):578–586. 10.1046/j.1365-2540.2000.00700.x 10849083
Kerpedjiev P Abdennur N Lekschas F : HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19 (1 ): 125. 10.1186/s13059-018-1486-1 30143029
Manni M Berkeley MR Seppey M : 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 34320186
Oatley G Denton A Howard C : Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.2. protocols.io. 2023. 10.17504/protocols.io.kxygx3y4dg8j/v1
O’Hara RB : Comparing the effects of genetic drift and fluctuating selection on genotype frequency changes in the scarlet tiger moth. Proc Biol Sci. 2005;272 (1559 ):211–217. 10.1098/rspb.2004.2929 15695213
Owen DF Goulson D : Effect of Temperature on the Expression of the medionigra Phenotype of the Moth Panaxia dominula (Lepidoptera: Arctiidae). Oikos. 1994;71 (1 ):107. 10.2307/3546177
Pointon DL Eagles W Sims Y : sanger-tol/treeval v1.0.0 – Ancient Atlantis. 2023. 10.5281/zenodo.10047653
Rao SSP Huntley MH Durand NC : 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 25497547
Rhie A McCarthy SA Fedrigo O : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592 (7856 ):737–746. 10.1038/s41586-021-03451-0 33911273
Rhie A Walenz BP Koren S : Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21 (1 ): 245. 10.1186/s13059-020-02134-9 32928274
Sheppard PM Cook LM : The manifold effects of the medionigra gene of the moth Panaxia dominula and the maintenance of a polymorphism. Heredity. 1962;17 (3 ):415–426. 10.1038/hdy.1962.41
Simão FA Waterhouse RM Ioannidis P : BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31 (19 ):3210–3212. 10.1093/bioinformatics/btv351 26059717
Strickland M Cornwell C Howard C : Sanger Tree of Life Fragmented DNA clean up: Manual SPRI. protocols.io. 2023. 10.17504/protocols.io.kxygx3y1dg8j/v1
Surana P Muffato M Qi G : sanger-tol/readmapping: sanger-tol/readmapping v1.1.0 - Hebridean Black (1.1.0). Zenodo. 2023a. 10.5281/zenodo.7755665
Surana P Muffato M Sadasivan Baby C : sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b; [Accessed 21 July 2023]. 10.5281/zenodo.6785935
Uliano-Silva M Ferreira JGRN Krasheninnikova K : 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 37464285
Vasimuddin M Misra S Li H : 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
Wellcome Sanger Institute: The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758). European Nucleotide Archive.[dataset], accession number PRJEB60214,2023.
Zhou C McCarthy SA Durbin R : YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39 (1 ): btac808. 10.1093/bioinformatics/btac808 36525368
