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

10.12688/wellcomeopenres.22765.1
Data Note
Articles
The genome sequence of the springtail, Dicyrtomina minuta (O.Fabricius, 1783)
[version 1; peer review: 2 approved]

Jaron Kamil S. Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing 1
Schneider Clément Resources Writing – Original Draft Preparation Writing – Review & Editing 2
Hodson Christina N. Resources 3
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 Tree of Life, Wellcome Sanger Institute, Hinxton, England, UK
2 Senckenberg Museum of Natural History, Görlitz, Germany
3 University of British Columbia, Biodiversity Research Centre, Canada
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

29 7 2024
2024
9 41716 7 2024
Copyright: © 2024 Jaron KS 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 female Dicyrtomina minuta (springtail; Arthropoda; Collembola; Symphypleona; Dicyrtomidae). The genome sequence is 582.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X 1 and X 2 sex chromosomes. The mitochondrial genome has also been assembled and is 15.59 kilobases in length.

Dicyrtomina minuta
springtail
genome sequence
chromosomal
Symphypleona
Wellcome Trust206194 218328 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>] 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.
==== Body
pmcSpecies taxonomy

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Collembola; Symphypleona; Dicyrtomidae; Dicyrtominae; Dicyrtomina; Dicyrtomina minuta (O.Fabricius, 1783) (NCBI:txid1387116).

Background

Springtails are one of the most abundant groups of soil animals, found in all sorts of biomes and habitats worldwide ( Hopkin, 1997). Most of the springtails are truly miniature creatures, often smaller than a millimetre, but there are exceptions. Dicyrtomina minuta is one of the larger globular springtails and is up to 3mm long, which is a paradox given its species name (since minuta means small). These springtails can be found in moist leaf litter in Europe and North America during autumn and winter, alongside other species of the same family Dicyrtomidae ( GBIF Secretariat, 2024). The fourth antenatal segment of Dicyrtomidae is very short, which is a distinct feature that can be used for quick identification to family level. Another remarkable trait of the family is the secretion of numerous rods of wax, secreted by special chaetae ( Massoud & Vannier, 1965). The rods are sheddable, and their function remains unclear, presumably involved in the sensorial system. Three species of the Dicyrtomina genus, D. minuta, D. ornata and D. saudersi differ only in colour pattern variations and therefore were considered by some authors morphs of the same species ( Richards, 1968).

In general, karyotypes of globular springtails (Symphypleona) are thought to be conserved, with 2n=12 chromosomes in females and 2n=10 in males ( Dallai et al., 2004), which was also observed in D. ornate ( Dallai et al., 1999). The only exception is a more distantly related member Dicyrtomidae, Ptenothrix italica, with 2n=14 and 2n=12 in males ( Dallai et al., 1999). However, the karyotype of D. minuta was prior to this study unknown. Based on the overall conservation of the double X chromosome system (X 1X 200) and aberrant spermatogenesis in Symphypleona ( Dallai et al., 1999), it is expected that this species is reproducing via Paternal Genome Elimination ( Jaron et al., 2022), a reproductive mode where males eliminate the paternal genome, and pass only the maternal one to the next generation. However, this hypothesis has not been directly tested in this species yet.

The genome of a springtail, Dicyrtomina minuta, was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland. Here we present a chromosomally complete genome sequence for Dicyrtomina minuta, based on a female specimen from Wytham Woods, Oxfordshire, UK.

Genome sequence report

The genome was sequenced from an adult female Dicyrtomina minuta collected from Wytham Woods, Berkshire, UK (51.78, –1.34). 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 68 missing joins or mis-joins and removed 8 haplotypic duplications, reducing the assembly length by 0.70% and the scaffold number by 6.36%, and increasing the scaffold N50 by 2.24%.

The final assembly has a total length of 582.0 Mb in 485 sequence scaffolds with a scaffold N50 of 89.8 Mb ( Table 1). The snail plot in Figure 1 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 2. The cumulative assembly plot in Figure 3 shows curves for subsets of scaffolds assigned to different phyla. Most (88.88%) of the assembly sequence was assigned to 5 chromosomal-level scaffolds, representing three autosomes and the X 1 and X 2 sex chromosomes. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 4; Table 2). Chromosomes X 1 and X 2 were identified based on synteny with Allacma fusca (GCA_947179485.1) ( Jaron 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 Dicyrtomina minuta, qeDicMinu4.1.

Project accession data	
Assembly identifier	qeDicMinu4.1	
Species	Dicyrtomina minuta	
Specimen	qeDicMinu4	
NCBI taxonomy ID	1387116	
BioProject	PRJEB58248	
BioSample ID	Genome sequencing: SAMEA7701774
Hi-C scaffolding: SAMEA7701781	
Isolate information	qeDicMinu4: whole organism (genome sequence)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	60.5	≥ 50	
k-mer completeness	100.0%	≥ 95%	
BUSCO **	C:95.1%[S:91.8%,D:3.3%],F:2.0%,M:2.9%,n:1013	C ≥ 95%	
Percentage of assembly
mapped to chromosomes	88.88%	≥ 95%	
Sex chromosomes	X 1, X 2	localised homologous pairs	
Organelles	Mitochondrial genome: 15.59 kb	complete single alleles	
Raw data accessions	
PacificBiosciences Sequel IIe	ERR10879914	
Hi-C Illumina	ERR10684080	
Genome assembly	
Assembly accession	GCA_949802685.1	
Accession of alternate haplotype	GCA_951387605.1	
Span (Mb)	582.0	
Number of contigs	1325	
Contig N50 length (Mb)	1.0	
Number of scaffolds	485	
Scaffold N50 length (Mb)	89.8	
Longest scaffold (Mb)	181.99	
* 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 arthropoda_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/GCA_949802685.1/dataset/qeDicMinu4_1/busco.

Figure 1. Genome assembly of Dicyrtomina minuta, qeDicMinu4.1: metrics.

The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 581,995,013 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 (181,988,040 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (89,754,956 and 1,302,000 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 arthropoda_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Dicyrtomina%20minuta/dataset/qeDicMinu4_1/snail.

Figure 2. Genome assembly of Dicyrtomina minuta, qeDicMinu4.1: BlobToolKit GC-coverage plot.

Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Dicyrtomina%20minuta/dataset/qeDicMinu4_1/blob.

Figure 3. Genome assembly of Dicyrtomina minuta qeDicMinu4.1: BlobToolKit cumulative sequence plot.

The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Dicyrtomina%20minuta/dataset/qeDicMinu4_1/cumulative.

Figure 4. Genome assembly of Dicyrtomina minuta qeDicMinu4.1: Hi-C contact map of the qeDicMinu4.1 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=cRUc7wPZQ9e5NHpn5R-dYg.

Table 2. Chromosomal pseudomolecules in the genome assembly of Dicyrtomina minuta, qeDicMinu4.

INSDC accession	Name	Length (Mb)	GC%	
OX461808.1	1	181.99	35.0	
OX461810.1	2	89.75	35.5	
OX461811.1	3	74.52	35.5	
OX461813.1	MT	0.02	27.5	
OX461809.1	X1	101.2	36.0	
OX461812.1	X2	69.85	36.5	

The estimated Quality Value (QV) of the final assembly is 60.5 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.3.2 completeness of 95.1% (single = 91.8%, duplicated = 3.3%), using the arthropoda_odb10 reference set ( n = 1,013).

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/1387116.

Methods

Sample acquisition and nucleic acid extraction

Specimens of Dicyrtomina minuta were collected from Wytham Woods, Oxfordshire, UK (latitude 51.78, longitude –1.34) on 2020-08-03 by aspiration. The specimens were collected and identified by Kamil Jaron (Wellcome Sanger Institute) and preserved on dry ice. The specimen used for genome sequencing was a female adult Dicyrtomina minuta (specimen ID Ox000721, ToLID qeDicMinu4), and a second specimen (ID Ox000728, ToLID qeDicMinu3) was used for Hi-C sequencing.

The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. In sample preparation, the qeDicMinu4 sample was weighed and dissected 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 v1 protocol ( Sheerin et al., 2023). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 30 ( Todorovic et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): in brief, the method employs AMPure PB beads to eliminate shorter fragments and concentrate the DNA. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

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

Sequencing

Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on a Pacific Biosciences Sequel IIe instrument. Hi-C data were also generated from whole organism tissue of qeDicMinu3 using the Arima v2 kit. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp on the Illumina NovaSeq 6000 instrument.

Genome assembly and curation

Assembly was carried out with Hifiasm ( Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups, without the -e option ( Guan et al., 2020). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using YaHS ( Zhou et al., 2023). The assembly was checked for contamination and corrected as described previously ( Howe et al., 2021). Manual curation was performed using HiGlass ( Kerpedjiev et al., 2018) and PretextView ( 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.

Evaluation of final assembly

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 QVy 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	2	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	
YaHS	1.2a	https://github.com/c-zhou/yahs	

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: Dicyrtomina minuta. Accession number PRJEB58248; https://identifiers.org/ena.embl/PRJEB58248 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Dicyrtomina minuta 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.

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.25069.r97699
Reviewer response for version 1
Martín-Durán José M 1Referee https://orcid.org/0000-0002-2572-1061

1 Queen Mary University of London, London, UK
18 9 2024 Copyright: © 2024 Martín-Durán JM
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
This Genome Note reports the sequencing and assembly of the genome of the springtail (Collembola)  Dicyrtomina minuta. Collembolans are fascinating animals that occupy a key phylogenetic position to investigate the evolution of Insecta, the most diverse animal clade on Earth.

Strengths

- High-quality genome for an important and understudied animal group.

- Important resource to investigate sex determination and karyotype evolution in Collembola.

Weaknesses

- None for this resource. The fact that the karyotype inferred from genome sequence differs so dramatically from those observed in other species warrants further investigations and experimental validations.

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:

Comparative genomics, evolutionary developmental biology, invertebrates

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.25069.r95172
Reviewer response for version 1
Makunin Alex 1Referee https://orcid.org/0000-0002-9555-5097

1 Wellcome Sanger Institute, Hinxton, England, UK
1 9 2024 Copyright: © 2024 Makunin 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 data note by Jaron et al. presents a high quality chromosome scale assembly for Collembola species Dicyrtomina minuta. This is the first chromosomal genome assembly for Dicyrtomidae family. The presentation of the results and methods is standardized and overall very transparent. 

I have a few minor suggestions: Is it possible to specify the amount of DNA used for PacBio sequencing? From the methods section it seems that the no amplification was done prior to sequencing, i.e. low input protocol was used.

The identification of X1 and X2 chromosomes is based on genome alignment to Allacma fusca, also from DToL project (Jaron et al., 2023). However, in that publication the source of chromosome identities is not specified, so it seems reasonable to include more information on sex chromosomes delineation - I assume it was based on coverage given that a male Allacma fusca was used for assembly.

It might be worth including a synteny plot as a figure, possibly accompanied by information on expected divergence times between Dicyrtomina (Dicyrtomidae) and Allacma (Sminthuridae), e.g. estimate of ca 280MY from mitochondrial genomes (Leo et al., 2019).

It might be interesting to include a short discussion around expected chromosome numbers and their evolutionary variability. For example, D. ornata females were reported to have 2n = 12 (Dallai et al 1999) - one chromosome more than reported for D. minuta here, although in introduction it is mentioned that both were considered as a single species at some point

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

Partly

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:

Comparative genomics

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
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
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
Dallai R Fanciulli PP Frati F : Chromosome elimination and sex determination in springtails (Insecta, Collembola). J Exp Zool. 1999;285 (3 ):215–225. 10.1002/(sici)1097-010x(19991015)285:3<215::aid-jez4>3.0.co;2-5 10497320
Dallai R Fanciulli PP Frati F : New data on the aberrant spermatogenesis of Collembola. Pedobiologia. 2004;48 (5–6 ):487–492. 10.1016/j.pedobi.2004.05.006
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
GBIF Secretariat: Dicyrtomina minuta Occurrence download. gbif.org. 2024; [Accessed 30 June 2024]. 10.15468/dl.kkxysj
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
Hopkin SP : Biology of the Springtails (Insecta: Collembola).Oxford: Oxford University Press,1997. Reference Source
Howe K Chow W Collins J : Significantly improving the quality of genome assemblies through curation. GigaScience. Oxford University Press,2021;10 (1 ): giaa153. 10.1093/gigascience/giaa153 33420778
Jaron KS Berg MP Ellers J : The genome sequence of the springtail Allacma fusca (Linnaeus, 1758) [version 1; peer review: 2 approved, 1 approved with reservations]. Wellcome Open Res. 2023;8 :319. 10.12688/wellcomeopenres.19690.1 37593568
Jaron KS Hodson CN Ellers J : Genomic evidence of paternal genome elimination in the globular springtail Allacma fusca . Genetics. 2022;222 (3 ): iyac117. 10.1093/genetics/iyac117 35946560
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
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
Massoud Z Vannier G : Présence des sécrétions cireuses chez les Collemboles.Paris: Comptes Rendus de l’Académie des Sciences,1965;260.
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
Richards WR : Generic classification, evolution, and biogeography of the sminthuridae of the world (Collembola). Memoirs of the Entomological Society of Canada. 1968;100 (S53 ):3–54. 10.4039/entm10053fv
Sheerin E Sampaio F Oatley G : Sanger Tree of Life HMW DNA Extraction: Automated MagAttract v.1. protocols.io. 2023. 10.17504/protocols.io.x54v9p2z1g3e/v1
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.7755669
Surana P Muffato M Sadasivan Baby C : sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b. 10.5281/zenodo.6785935
Todorovic M Sampaio F Howard C : Sanger Tree of Life HMW DNA Fragmentation: Diagenode Megaruptor ®3 for PacBio HiFi. protocols.io. 2023. 10.17504/protocols.io.8epv5x2zjg1b/v1
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 springtail, Dicyrtomina minuta (O.Fabricius, 1783). European Nucleotide Archive, [dataset], accession number PRJEB58248,2023.
Zhou C McCarthy SA Durbin R : YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39 (1 ): btac808. 10.1093/bioinformatics/btac808 36525368
