The genome sequence of the Dune Robberfly, Philonicus albiceps (Meigen, 1820)
Olga Sivell, Erica McAlister, Ryan Mitchell, Arun Arumugaperumal, Laurence Despres, Darren Obbard
TL;DR
This paper presents the genome sequence of the Dune Robberfly, including a detailed assembly and gene annotation.
Contribution
The study provides a high-quality genome assembly and gene annotation for Philonicus albiceps, a species in the Asilidae family.
Findings
The genome assembly is 253.92 megabases long with 98.91% scaffolded into 6 chromosomal pseudomolecules.
The mitochondrial genome is 16.9 kilobases long and has been assembled.
Gene annotation identified 11,887 protein-coding genes using Ensembl.
Abstract
We present a genome assembly from a female specimen of Philonicus albiceps (Dune Robberfly; Arthropoda; Insecta; Diptera; Asilidae). The genome sequence has a total length of 253.92 megabases. Most of the assembly (98.91%) is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.9 kilobases. Gene annotation of this assembly on Ensembl identified 11,887 protein-coding genes.
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 | |||
|---|---|---|---|
|
| Philonicus albiceps | ||
|
| PRJEB62736 | ||
|
|
| ||
|
| SAMEA11024992 | ||
|
| 468783 | ||
| Specimen information | |||
|
|
|
|
|
|
| idPhiAlbi1 | SAMEA11025198 | head and thorax |
|
| idPhiAlbi2 | SAMEA11025423 | head |
|
| idPhiAlbi1 | SAMEA11025201 | abdomen |
| Sequencing information | |||
|
|
|
|
|
|
| ERR11526210 | 7.33e+08 | 110.71 |
|
| ERR11512321 | 2.69e+06 | 25.14 |
|
| ERR11641140 | 7.62e+07 | 11.5 |
| Genome assembly | ||
|---|---|---|
| Assembly name | idPhiAlbi1.1 | |
| Assembly accession | GCA_963969385.1 | |
|
|
| |
| Assembly level for primary assembly | chromosome | |
| Span (Mb) | 253.92 | |
| Number of contigs | 229 | |
| Number of scaffolds | 28 | |
| Longest scaffold (Mb) | 75.08 | |
| Assembly metric | Measure |
|
| Contig N50 length | 2.5 Mb |
|
| Scaffold N50 length | 57.53 Mb |
|
| Consensus quality (QV) | Primary: 63.7; alternate: 63.8; combined: 63.7 |
|
|
| Primary: 88.89%; alternate: 75.90%; combined: 99.34% |
|
| BUSCO
| C:96.3%[S:95.8%,D:0.5%],
|
|
| Percentage of assembly assigned to
| 98.91% |
|
| Sex chromosomes | Not identified |
|
| Organelles | Mitochondrial genome: 16.9 kb |
|
| INSDC accession | Name | Length (Mb) | GC% |
|---|---|---|---|
| 1 | 75.08 | 35 | |
| 2 | 57.53 | 34 | |
| 3 | 45.56 | 34.5 | |
| 4 | 35.33 | 35.5 | |
| 5 | 32.05 | 34 | |
| 6 | 5.6 | 34.5 | |
| MT | 0.02 | 29 |
| Software tool | Version | Source |
|---|---|---|
| BLAST | 2.14.0 |
|
| BlobToolKit | 4.3.9 |
|
| BUSCO | 5.5.0 |
|
| bwa-mem2 | 2.2.1 |
|
| DIAMOND | 2.1.8 |
|
| fasta_windows | 0.2.4 |
|
| FastK | 666652151335353eef2fcd58880bcef5bc2928e1 |
|
| Gfastats | 1.3.6 |
|
| GoaT CLI | 0.2.5 |
|
| Hifiasm | 0.16.1-r375 |
|
| HiGlass | 44086069ee7d4d3f6f3f0012569789ec138f42b84aa4
|
|
| MerquryFK | d00d98157618f4e8d1a9190026b19b471055b22e |
|
| Minimap2 | 2.24-r1122 |
|
| MitoHiFi | 3 |
|
| MultiQC | 1.14, 1.17, and 1.18 |
|
| Nextflow | 23.04.1 |
|
| PretextView | 0.2.5 |
|
| PretextSnapshot | - |
|
| purge_dups | 1.2.5 |
|
| samtools | 1.19.2 |
|
| sanger-tol/ascc | 0.1.0 |
|
| sanger-tol/blobtoolkit | 0.4.0 |
|
| Seqtk | 1.3 |
|
| Singularity | 3.9.0 |
|
| TreeVal | 1.2.0 |
|
| YaHS | 1.2a.2 |
|
- —Wellcome Trust
Peer Reviews
No public reviews on file for this paper yet. If you reviewed it on a platform where reviews are public (OpenReview, ICLR, NeurIPS, ICML), you can paste yours below so the community can read it here.
Videos
No videos yet. Explain this paper in a talk, walkthrough, or lecture? Add one.
Taxonomy
TopicsInsect and Arachnid Ecology and Behavior · Plant and animal studies · Species Distribution and Climate Change
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Asiloidea; Asilidae; Asilinae; Philonicus; Philonicus albiceps ( Meigen, 1820) (NCBI:txid468783)
Background
Philonicus albiceps ( Meigen, 1820) is a large, stout fly, with a body length of 13–18 mm and wing length 10–13 mm. It is quite dark, greyish or greyish yellow brown without a tessellated pattern on abdomen and has black legs with mostly white bristles. It is a habitat specific and morphologically very distinctive species, readily identifiable by the single pair of white bristles on scutellum. Other similar looking species have black bristles on the legs and scutellum or a larger number of white bristles on the scutellum. The male and female genitalia are also distinctive ( Stubbs & Drake, 2014).
Philonicus albiceps has a Palaearctic distribution. It is common and widespread on coast in England, Wales and Ireland, and in Scotland up to Ayr and the Firth of Forth. P. albiceps is common on sand dunes, usually close to the shore where it can be spotted sitting on bare sand and among marram grass. This species is occasionally collected from inland heathland near the coast of Norfolk and Suffolk. The adults appear from mid-May to mid-October, peaking from mid-June to mid-July ( Stubbs & Drake, 2014).
The eggs are laid in the sand among marram grass roots. Once the female finishes ovipositing, she sweeps the sand back to cover the hole with a “brush” of short spines and two long upturned bristles on the anal lamellae and with the hardened tip of the eighth sternite ( Oldroyd, 1969). The larva and pupa of P. albiceps have been described by Melin (1923). Adult asilids are venomous and inject their prey with specially adapted mouthparts leading to quick death ( Drukewitz et al., 2018; Whitfield, 1925). They hunt flying insects, mainly fairly large species such as calyptrate flies, hoverflies, craneflies and other robberflies. Prey records also include a grasshopper, a shield bug, a beetle, solitary bees and the Common Blue Damselfly Enallagma cyathigerum ( Stubbs & Drake, 2014; Yarrow, 1937).
The high-quality genome of Philonicus albiceps was sequenced from a single specimen (NHMUK014438339, SAMEA11024992) from Penhale Dunes, England ( Figure 1). 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. It will aid research into phylogeny of Asilidae, as well as biology and ecology of the species.
Photograph of the Philonicus albiceps (idPhiAlbi1) specimen used for genome sequencing.
Genome sequence report
Sequencing data
The genome of a specimen of Philonicus albiceps ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating 25.14 Gb (gigabases) from 2.69 million reads, which were used to assemble the genome. GenomeScope analysis estimated the haploid genome size at 250.80 Mb, with a heterozygosity of 0.54% and repeat content of 9.87%. These estimates guided expectations for the assembly. Based on the estimated genome size, the sequencing data provided approximately 91× coverage. Hi-C sequencing produced 110.71 Gb from 733.19 million reads, used to scaffold the assembly. RNA sequencing data were also generated and are available in public sequence repositories. Table 1 summarises the specimen and sequencing details.
Table 1.: Specimen and sequencing data for Philonicus albiceps.
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 37 misjoins or missing joins and removed four haplotypic duplications. These interventions decreased the scaffold count by 40.82%. The final assembly has a total length of 253.92 Mb in 28 scaffolds, with 201 gaps, and a scaffold N50 of 57.53 Mb ( Table 2).
Table 2.: Genome assembly data for Philonicus albiceps.
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 Philonicus albiceps, idPhiAlbi1.1: 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 diptera_odb10 set is presented at the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_963969385.1/dataset/GCA_963969385.1/snail.
Genome assembly of Philonicus albiceps, idPhiAlbi1.1: 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_963969385.1/dataset/GCA_963969385.1/blob.
Genome assembly of Philonicus albiceps, idPhiAlbi1.1: 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_963969385.1/dataset/GCA_963969385.1/cumulative.
Most of the assembly sequence (98.91%) was assigned to 6 chromosomal-level scaffolds. These chromosome-level scaffolds, confirmed by Hi-C data, are named according to size ( Figure 5; Table 3). During curation, we noted that read coverage suggests this is the homogametic sex, but we did not identify the sex chromosome(s) as sequence data from the heterogametic sex was not available and homology is unreliable for sex chromosome identification in Diptera due to frequent sex chromosome turnover ( Vicoso & Bachtrog, 2015).
Genome assembly of Philonicus albiceps: Hi-C contact map of the idPhiAlbi1.1 assembly, generated using PretextSnapshot.Chromosomes are shown in order of size and labelled with chromosome numbers (top) and chromosome accession numbers (left).
Table 3.: Chromosomal pseudomolecules in the genome assembly of Philonicus albiceps, idPhiAlbi1.
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 63.7. The k-mer completeness is 88.89% for the primary haplotype and 75.90% for the alternate haplotype; and 99.34% for the combined primary and alternate assemblies. BUSCO v.5.5.0 analysis using the diptera_odb10 reference set ( n = 3,285) identified 96.3% of the expected gene set (single = 95.8%, duplicated = 0.5%).
Table 2 provides assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project Report on Assembly Standards September 2024. The primary assembly achieves the EBP reference standard of 6.C.Q63.
Genome annotation report
The Philonicus albiceps genome assembly (GCA_963969385.1) was annotated externally by Ensembl at the European Bioinformatics Institute (EBI). This annotation includes 20,109 transcribed mRNAs from 11,887 protein-coding and 392 non-coding genes. The average transcript length is 10,937.85 bp. There are 1.64 coding transcripts per gene and 6.16 exons per transcript. For further information about the annotation, please refer to https://beta.ensembl.org/species/8e00c00e-705a-45a5-8db3-c90a26a78799.
Methods
Sample acquisition and DNA barcoding
The specimen used for genome sequencing was a female Philonicus albiceps (specimen ID NHMUK014438339, ToLID idPhiAlbi1). The specimen was collected by Charles Griffiths (Dipterists Forum) and identified by Brian Levey (OUMNH). A second specimen used for Hi-C sequencing (specimen ID NHMUK014438340, ToLID idPhiAlbi2) was collected by Olga Sivell and Erica McAlister and identified by Ryan Mitchell. Both specimens were collected from Penhale Dunes, England, United Kingdom (latitude 50.3705, longitude –5.1373) on 2021-06-30, using an aerial net, and were 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 each 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 ( Howard et al., 2025). Detailed protocols are available on protocols.io ( Denton et al., 2023b). The idPhiAlbi1 sample was prepared for DNA extraction by weighing and dissecting it 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 using the Automated MagAttract v1 protocol ( Sheerin et al., 2023). For ultra-low input (ULI) PacBio sequencing, DNA was fragmented using the Covaris g-TUBE method ( Oatley et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation, using AMPure PB beads to eliminate shorter fragments and concentrate the DNA ( Strickland et al., 2023). The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit dsDNA High Sensitivity Assay kit. The fragment size distribution was evaluated by running the sample on the FemtoPulse system. For this sample, the extracted DNA had a Qubit concentration of 1.78 ng/μL and a yield of 694.20 ng. Spectrophotometric measurements indicated 260/280 and 260/230 ratios of 2.25 and 1.98, respectively.
RNA was extracted from abdomen tissue of idPhiAlbi1 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 and crosslinking
Hi-C data were generated from the head of the idPhiAlbi2 sample using the Arima-HiC v2 kit (Arima Genomics) with 20–50 mg of frozen tissue (stored at –80 °C). As per manufacturer’s instructions, tissue was fixed, and the DNA crosslinked using a TC buffer with a final formaldehyde concentration of 2%. The tissue was then homogenised using the Diagnocine Power Masher-II. The crosslinked DNA was digested using a restriction enzyme master mix, then biotinylated and ligated. A clean up was performed with SPRIselect beads prior to library preparation. DNA concentration was quantified using the Qubit Fluorometer v4.0 (Thermo Fisher Scientific) and Qubit HS Assay Kit, and sample biotinylation percentage was estimated using the Arima-HiC v2 QC beads.
Library preparation and sequencing
Library preparation and sequencing were performed at the WSI Scientific Operations core.
** PacBio HiFi **
The sample requires Covaris g-TUBE shearing to approximately 10 kb prior to library preparation. Ultra-low input libraries were prepared using PacBio SMRTbell® Express Template Prep Kit 2.0 and PacBio SMRTbell® gDNA Sample Amplification Kit. To begin, samples were normalised to 20 ng of DNA. Initial removal of single-strand overhangs, DNA damage repair, and end repair/A-tailing were performed per manufacturer’s instructions. From the SMRTbell® gDNA Sample Amplification Kit, amplification adapters were then ligated. A 0.85X pre-PCR clean-up was performed with Promega ProNex beads and the sample was then divided into two for a dual PCR. PCR reactions A and B each followed the PCR programs as described in the manufacturer’s protocol. A 0.85X post-PCR clean-up was performed with ProNex beads for PCR reactions A and B and DNA concentration was quantified using the Qubit Fluorometer v4.0 (Thermo Fisher Scientific) and Qubit HS Assay Kit and fragment size analysis was carried out using the Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies) and gDNA 55kb BAC analysis kit. PCR reactions A and B were then pooled, ensuring the total mass was ≥500 ng in 47.4 μl. The pooled sample then repeated the process for DNA damage repair, end repair/A-tailing and additional hairpin adapter ligation. A 1X clean-up was performed with ProNex beads and DNA concentration was quantified using the Qubit and fragment size analysis was carried out using the Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies). Size selection was performed using Sage Sciences' PippinHT system with target fragment size determined by analysis from the Femto Pulse, usually a value between 4000 and 9000 bp. Size selected libraries were then cleaned-up using 1.0X ProNex beads and normalised to 2 nM before proceeding to sequencing.
Samples were sequenced using the Sequel IIe system (Pacific Biosciences, California, USA). The concentration of the library loaded onto the Sequel IIe was in the range 40–135 pM. 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, the biotinylated DNA constructs were fragmented using a Covaris E220 sonicator and size-selected to 400–600 bp using SPRISelect beads. DNA was then enriched using Arima-HiC v2 Enrichment beads. The NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) was used for end repair, A-tailing, and adapter ligation, following a modified protocol in which library preparation is carried out while the DNA remains bound to the enrichment beads. PCR amplification was performed using KAPA HiFi HotStart mix and custom dual-indexed adapters (Integrated DNA Technologies) in a 96-well plate format. Depending on sample concentration and biotinylation percentage determined at the crosslinking stage, samples were amplified for 10–16 PCR cycles. Post-PCR clean-up was carried out using SPRISelect beads. The libraries were quantified using the Accuclear Ultra High Sensitivity dsDNA Standards Assay kit (Biotium) and normalised to 10 ng/μL before sequencing. Hi-C sequencing was performed on the Illumina NovaSeq 6000 instrument.
** RNA **
Poly(A) RNA-Seq libraries were prepared using the NEBNext ^®^ Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs), following the manufacturer’s instructions. Poly(A) mRNA in the total RNA solution was isolated using oligo(dT) beads, converted to cDNA, and uniquely indexed; 14 PCR cycles were performed. Libraries were size-selected to produce fragments between 100–300 bp. Libraries were quantified, normalised, pooled to a final concentration of 2.8 nM, and diluted to 150 pM for loading. Sequencing was carried out 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 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 ( Rao et al., 2014) were mapped to the primary contigs using bwa-mem2 ( Vasimuddin et al., 2019), and the contigs were scaffolded 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. 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) computed prior to genome assembly. The analysis outputs included assembly QV scores and completeness statistics.
The genome was analysed using the BlobToolKit pipeline, a Nextflow ( Di Tommaso et al., 2017) implementation of the earlier Snakemake BlobToolKit pipeline ( Challis et al., 2020). The pipeline aligns PacBio reads using minimap2 ( Li, 2018) and SAMtools ( Danecek et al., 2021) to generate coverage tracks. Simultaneously, it queries the GoaT database ( Challis et al., 2023) to identify relevant BUSCO lineages and runs BUSCO ( Manni et al., 2021). For the three domain-level BUSCO lineages, BUSCO genes are aligned to the UniProt Reference Proteomes database ( Bateman et al., 2023) using DIAMOND blastp ( Buchfink et al., 2021). The genome is divided into chunks based on the density of BUSCO genes from the closest taxonomic lineage, and each chunk is aligned to the UniProt Reference Proteomes database with DIAMOND blastx. Sequences without hits are chunked using seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). The BlobToolKit suite consolidates all 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), with package management via Conda and Bioconda ( Grüning et al., 2018), and containerisation through Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017).
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.
The reference list from the paper itself. Each links out to its DOI / PubMed record.
- 1Allio R Schomaker-Bastos A Romiguier J : Mito Finder: 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 PMC 7497042 · doi ↗ · pubmed ↗
- 2Altschul SF Gish W Miller W : Basic Local Alignment Search Tool. J Mol Biol. 1990;215(3):403–410. 10.1016/S 0022-2836(05)80360-2 2231712 · doi ↗ · pubmed ↗
- 3Bateman A Martin MJ Orchard S : Uni Prot: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2023;51(D 1):D 523–D 531. 10.1093/nar/gkac 1052 36408920 PMC 9825514 · doi ↗ · pubmed ↗
- 4Beasley J Uhl R Forrest LL : DNA barcoding SO Ps for the Darwin Tree of Life project. protocols.io. 2023; [Accessed 25 June 2024]. 10.17504/protocols.io.261ged 91jv 47/v 1 · doi ↗
- 5Buchfink B Reuter K Drost HG : Sensitive protein alignments at Tree-of-Life scale using DIAMOND. Nat Methods. 2021;18(4):366–368. 10.1038/s 41592-021-01101-x 33828273 PMC 8026399 · doi ↗ · pubmed ↗
- 6Challis R Kumar S Sotero-Caio C : Genomes on a Tree (Goa T): 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 36864925 PMC 9971660 · doi ↗ · pubmed ↗
- 7Challis R Richards E Rajan J : Blob Tool Kit – interactive quality assessment of genome assemblies. G 3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g 3.119.400908 32071071 PMC 7144090 · doi ↗ · pubmed ↗
- 8Cheng 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/s 41592-020-01056-5 33526886 PMC 7961889 · doi ↗ · pubmed ↗