The genome sequence of the European mole, Talpa europaea Linnaeus, 1758
Nicola Pearce, Michelle F. O’Brien, Rosa Lopez Colom, Phillip A Morin, Frédéric Delsuc, Sadık Demirtaş
TL;DR
This paper presents the genome sequence of the European mole, including two haplotypes and the mitochondrial genome.
Contribution
The study provides a high-quality genome assembly for the European mole, including chromosomal pseudomolecules and the mitochondrial genome.
Findings
The genome assembly includes two haplotypes with lengths of 2,060.98 and 2,056.47 megabases.
Haplotype 1 is mostly scaffolded into 17 chromosomal pseudomolecules, including the X chromosome.
The mitochondrial genome is 16.93 kilobases in length.
Abstract
We present a genome assembly from a female Talpa europaea (European mole; Chordata; Mammalia; Eulipotyphla; Talpidae). The assembly contains two haplotypes with total lengths of 2,060.98 megabases and 2,056.47 megabases. Most of haplotype 1 (98.6%) is scaffolded into 17 chromosomal pseudomolecules, including the X sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled and is 16.93 kilobases in length.
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
Click any figure to enlarge with its caption.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5| Project information | |||
|---|---|---|---|
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| Talpa europaea (European mole) | ||
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| PRJEB71540 | ||
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| SAMEA112468127 | ||
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| 9375 | ||
| Specimen information | |||
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| mTalEur1 | SAMEA112468169 | muscle |
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| mTalEur1 | SAMEA112468169 | muscle |
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| mTalEur1 | SAMEA112468169 | muscle |
| Sequencing information | |||
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| ERR12512734 | 1.47e+09 | 222.28 |
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| ERR12982550 | 1.65e+09 | 248.83 |
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| ERR12408791 | 2.69e+06 | 22.94 |
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| ERR12408790 | 5.70e+06 | 41.29 |
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| ERR12512735 | 3.91e+07 | 5.91 |
| Genome assembly | Haplotype 1 | Haplotype 2 |
|---|---|---|
| Assembly name | mTalEur1.hap1.1 | mTalEur1.hap2.1 |
| Assembly accession | GCA_964194135.1 | GCA_964194205.1 |
| Assembly level | chromosome | scaffold |
| Span (Mb) | 2,060.98 | 2,056.47 |
| Number of contigs | 1,519 | 1,396 |
| Number of scaffolds | 463 | 356 |
| Longest scaffold (Mb) | 158.76 | None |
| Assembly metrics
| Haplotype 1 | Haplotype 2 |
| Contig N50 length
| 3.42 Mb | 3.51 Mb |
| Scaffold N50 length
| 136.89 Mb | 136.52 Mb |
| Consensus quality (QV) (≥ 40) | 60.0 | 60.2 |
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| 97.53% | 97.45% |
| Combined
| 99.65% | |
| BUSCO** (S > 90%; D < 5%) | C:95.4%[S:93.8%,D:1.6%],
|
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| Percentage of assembly mapped to
| 98.6% | - |
| Sex chromosomes (localised
| X | - |
| Organelles
| Mitochondrial genome:
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| INSDC
| Name | Length
| GC% |
|---|---|---|---|
| 1 | 158.76 | 41 | |
| 2 | 157.3 | 41.5 | |
| 3 | 151.62 | 40 | |
| 4 | 147.38 | 39.5 | |
| 5 | 143.94 | 40.5 | |
| 6 | 138.79 | 40.5 | |
| 7 | 136.89 | 43.5 | |
| 8 | 124.17 | 42.5 | |
| 9 | 118.35 | 43.5 | |
| 10 | 118.22 | 42.5 | |
| 11 | 105.44 | 43.5 | |
| 12 | 103.12 | 45 | |
| 13 | 99.97 | 41 | |
| 14 | 92.98 | 43.5 | |
| 15 | 86.6 | 42.5 | |
| 16 | 52.08 | 47.5 | |
| X | 96.47 | 41.5 | |
| MT | 0.02 | 39 |
| Software
| Version | Source |
|---|---|---|
| BEDTools | 2.30.0 |
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| BLAST | 2.14.0 |
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| BlobToolKit | 4.3.9 |
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| BUSCO | 5.5.0 |
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| bwa-mem2 | 2.2.1 |
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| Cooler | 0.8.11 |
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| DIAMOND | 2.1.8 |
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| fasta_
| 0.2.4 |
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| FastK | 427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c |
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| Gfastats | 1.3.6 |
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| GoaT CLI | 0.2.5 |
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| Hifiasm | 0.19.8-r603 |
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| HiGlass | 44086069ee7d4d3f6f3f0012569789ec138f42b84
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| MerquryFK | d00d98157618f4e8d1a9190026b19b471055b22e |
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| Minimap2 | 2.24-r1122 |
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| MitoHiFi | 3 |
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| MultiQC | 1.14, 1.17, and 1.18 |
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| NCBI
| 15.12.0 |
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| Nextflow | 23.10.0 |
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| PretextView | 0.2.5 |
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| samtools | 1.19.2 |
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| sanger-tol/
| - |
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| sanger-tol/
| 0.5.1 |
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| Seqtk | 1.3 |
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| Singularity | 3.9.0 |
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| TreeVal | 1.2.0 |
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| YaHS | 1.2a.2 |
|
- —Wellcome Trust
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Taxonomy
TopicsEvolution and Paleontology Studies · Genomics and Phylogenetic Studies · Chromosomal and Genetic Variations
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Eulipotyphla; Talpidae; Talpa; Talpa europaea Linnaeus, 1758 (NCBI:txid9375)
Background
The European mole ( Talpa europaea) is a small fossorial mammal with a cylindrically-shaped body, 110–160 mm in length, very short legs, and a short tail about ¼ the length of the head and body ( Corbet & Southern, 1977). It is covered in short, black, velvety fur, including on the tail, which will lay in any direction. Tiny, but functional, eyes are hidden by fur and ear pinnae are absent ( Sterry, 2010). Short vibrissae, on the otherwise hairless, long, tapering snout are associated with specialised sensory receptors (Eimer’s organs); the hairs on the tip of the tail are also sensory ( Corbet & Southern, 1977). The European mole’s forelimb is very highly modified with extremely specialised adaptations seen in the skeleton and muscles ( Cornwall, 1964; Matthews, 1968; Morris, 2019) to enable digging, the most visible of which are the large spade-like fore-feet, armed with stout claws. These are rotated with the inner edge of the foot turned downwards and the sole facing backwards ( Couzens et al., 2017). The breadth of the manus is increased further by the presence of an os falciforme at the base of the thumb ( Cornwall, 1964; Matthews, 1968; Morris, 2019). There is little sexual dimorphism between males and females, although males are usually slightly larger, but the sex organs can be differentiated during the short breeding season ( Gorman & Stone, 1990).
The European mole can be found inhabiting meadows and grasslands, arable fields and deciduous woodland, the common factor being well-drained and invertebrate rich soils. Waterlogged and stony ground are less favoured, and they are scarce in acidic soils (pH less than 4.4) where prey animals, particularly earthworms, are scarce or absent ( Sterry, 2010). It does not hibernate or enter torpor when temperature and prey availability deteriorate ( Gorman & Stone, 1990), and is active all year round in an extensive burrow system just below the surface and up to a depth of 1m in suitable substrate. Usually, the only signs of its presence are mole-hills, conical piles of earth, the spoil heaps from burrowing activity ( Couzens et al., 2017).
This species establishes its territory within a subterranean system of tunnels centred around a nest chamber used for sleeping and, in the case of females, raising young. Solitary and highly aggressive to others of either sex, the very short breeding season in early spring is the only time females and males will tolerate one another ( Gorman & Stone, 1990). Females give birth once a year, after a gestation period of c.4 weeks, averaging 3 to 4 young in a litter in late spring ( Sterry, 2010). Young are naked and blind at birth, weighing c.3–5g. Young moles are weaned around 4 to 5 weeks and leave the nest from 6 weeks onwards. They reach sexual maturity by the following spring, and have a lifespan of about 3 years ( Corbet & Southern, 1977).
As an insectivore the diet consists of larger members of soil fauna especially earthworms and beetle and fly larvae ( Corbet & Southern, 1977). Two distinctive features are the double-rooted very large upper canine ( Lawrence & Brown, 1973), unusual in mammals, and the presence of large submandibular glands ( Matthews, 1968), the purpose of which is not clear. Food caches are maintained by this species, principally of the worm Lumbricus terrestris which are not killed but immobilised by removal of the head segments (with nerve ganglia) so that the prey remains paralysed. More research is required to demonstrate whether the European mole produces toxic substances in the salivary glands to disable prey ( Kowalski & Rychlik, 2021) in addition to mutilation ( Berkowitz & Shellis, 2018).
The European mole is the only British representative of the family Talipidae ( Lawrence & Brown, 1973), the ‘true’ or Old-World moles. It is common and widespread throughout mainland Great Britain but absent from Ireland, Shetland and Orkney Islands, Outer Hebrides and the Isle of Man ( Couzens et al., 2017). Across continental Europe, its range extends from Southern Sweden to the Mediterranean, excluding southern Iberia and Balkans, and east as far as the Russian Arctic circle ( Corbet & Southern, 1977). Whilst it is listed as ‘Least Concern’ globally and widely distributed across Europe, the current population trend is unknown. Historically hunted in large numbers for its fur, it remains heavily persecuted as a pest by agricultural and horticultural industries across much of its range ( Gazzard & Atkinson, 2023). The European mole has no legal protection in the UK currently ( The Mammal Society, 2024).
Previous molecular studies include sequencing of mitochondrial DNA to define Talpa europaea lineages ( Feuda et al., 2015), and inclusion of the species in the examination of the genes in gonadal development in mammals, as females of talpid moles possess ovotestes ( Carmona et al., 2008).
Genome sequence report
Sequencing data
The genome of a specimen of Talpa europaea ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating 64.23 Gb from 8.39 million reads. GenomeScope analysis of the PacBio HiFi data estimated the haploid genome size at 2,049.22 Mb, with a heterozygosity of 0.10% and repeat content of 15.36%. 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 30.0x coverage of the genome. Chromosome conformation Hi-C sequencing produced 471.10 Gb from 3,119.88 million reads. Table 1 summarises the specimen and sequencing information, including the BioProject, study name, BioSample numbers, and sequencing data for each technology.
Photograph of the Talpa europaea (mTalEur1) specimen used for genome sequencing.
Table 1.: Specimen and sequencing data for Talpa europaea.
Assembly statistics
The genome was assembled into two haplotypes using Hi-C phasing. Haplotype 1 was curated to chromosome level, while haplotype 2 was assembled to scaffold level. The assembly was improved by manual curation, which corrected 145 misjoins or missing joins. These interventions decreased the scaffold count by 10.08%, and increased the scaffold N50 by 15.79%. The final assembly has a total length of 2,060.98 Mb in 463 scaffolds, with 1,056 gaps, and a scaffold N50 of 136.89 Mb ( Table 2).
Table 2.: Genome assembly data for Talpa europaea.
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.
Genome assembly of Talpa europaea, mTalEur1.hap1.1: 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 set is presented at the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_964194135.1/dataset/GCA_964194135.1/snail.
Genome assembly of Talpa europaea, mTalEur1.hap1.1: 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_964194135.1/blob.
Genome assembly of Talpa europaea, mTalEur1.hap1.1: 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_964194135.1/dataset/GCA_964194135.1/cumulative.
Most of the assembly sequence (98.6%) was assigned to 17 chromosomal-level scaffolds, representing 16 autosomes and the X sex chromosome. These chromosome-level scaffolds, confirmed by Hi-C data, are named according to size ( Figure 5; Table 3). During curation, the X chromosome was assigned based on synteny to the genome of Erinaceus europaeus (GCA_950295315.1).
Genome assembly of Talpa europaea: Hi-C contact map of the mTalEur1.hap1.1 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=Co0YN1lnTGeRxrh76mDtdw.
Table 3.: Chromosomal pseudomolecules in the genome assembly of Talpa europaea, mTalEur1.
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 in GenBank.
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.
For haplotype 1, the estimated QV is 60.0, and for haplotype 2, the QV is 60.2. When the two haplotypes are combined, the assembly achieves an estimated QV of 60.1. The k-mer completeness for haplotype 1 is 97.53%, and for haplotype 2, 97.45%, while the combined haplotypes achieve a k-mer completeness of 99.65%. BUSCO 5.5.0 analysis using the laurasiatheria_odb10 reference set ( n = 12,234) achieved a completeness score of 95.4% (single = 93.8%, duplicated = 1.6%) for haplotype 1.
Table 2 provides assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project Report on Assembly Standards September 2024. The assembly achieves the EBP reference standard of 6.C.Q60.
Methods
Sample acquisition and DNA barcoding
The sample used for sequencing (specimen ID NHMUK014551519, ToLID mTalEur1) was collected from a deceased wild individual that was found at WWT Slimbridge on 2021-12-26 and stored at –20 °C. The specimen was collected and identified by Michelle O'Brien (Wildfowl & Wetlands Trust). Muscle tissue samples were taken from areas of the thigh and the back, and preserved by dry freezing (–80 °C).
The initial identification by morphology 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). 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., 2023). The mTalEur1 sample was prepared for DNA extraction by weighing and dissecting it on dry ice ( Jay et al., 2023). Tissue from the muscle was cryogenically disrupted using the Covaris cryoPREP ^®^ Automated Dry Pulverizer ( Narváez-Gómez et al., 2023).
HMW DNA was extracted using the manual MagAttract v2 protocol ( Strickland et al., 2023). 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., 2023). 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.
RNA was extracted from muscle tissue of mTalEur1 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.
Hi-C sample preparation
Tissue from the muscle of the mTalEur1 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.
** RNA **
Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit, following the manufacturer’s instructions. RNA sequencing was performed on the Illumina NovaSeq 6000 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 assembled using Hifiasm in Hi-C phasing mode ( Cheng et al., 2021; Cheng et al., 2022), resulting in a pair of haplotype-resolved assemblies. 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 (article in preparation). Flat files and maps used in curation were generated in TreeVal ( Pointon et al., 2023). Manual curation was primarily conducted using PretextView ( Harry, 2022), with additional insights provided by JBrowse2 ( Diesh et al., 2023) and HiGlass ( Kerpedjiev et al., 2018). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). Any identified contamination, missed joins, and mis-joins were corrected, 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 (article in preparation).
** 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.
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.
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