Abstract
We present a genome assembly from an individual female Clivina fossor (a ground beetle; Arthropoda; Insecta; Coleoptera; Carabidae). The genome sequence spans 612.60 megabases. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.48 kilobases in length.
Keywords: Clivina fossor, a ground beetle, genome sequence, chromosomal, Coleoptera
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Adephaga; Caraboidea; Carabidae; Scaritinae; Clivinini; Clivina; Clivina fossor ( Linnaeus, 1758) (NCBI:txid795047).
Background
Clivina fossor ( Linnaeus, 1758) is a species of ground beetle in the family Scaritinae. This species has a natural range widespread across the Palaearctic region, with an introduced range across North America ( Bousquet, 1997; Nelson & Reynolds, 1987). Its distribution extends across Great Britain and Ireland, including most small islands and Shetland. Adult Clivina fossor are active year-round with new generations appearing in late summer.
Clivina fossor is eurytopic; its habitat preference includes damp areas of grassland, wetland, arable land, woodland and peat bogs. Due to their proclivity for damp and dark areas, adults remain subterranean in the day and become active at night, while their larvae are entirely endogeic ( Desender, 1983).
Clivina fossor is the largest species in its sub-family and is easily distinguished from other members, except for the slightly smaller and flatter Clivina collaris. Adult Clivina fossor have a black or dark brown body with a continuous series of setiferous punctures between the elytral humerus and apex. The tarsal segments on the forelegs are broad, for fossorial activity. The head is elongate with large lateral eyes and short mandibles. The species possesses wings and, as a result, exhibits rapid range expansion locally. There is little sexual dimorphism and sexes can be distinguished by fine setae along the apical margin of the terminal sternite, where the female setae are equidistant from each other and irregular in males.
The genome of Clivina fossor was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.
Genome sequence report
The genome of an adult female Clivina fossor ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating a total of 20.55 Gb (gigabases) from 2.17 million reads, providing approximately 29-fold coverage. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data, which produced 136.64 Gbp from 904.93 million reads, yielding an approximate coverage of 223-fold. Specimen and sequencing information is summarised in Table 1.
Figure 1. Photograph of the Clivina fossor (icCliFoss2) specimen used for genome sequencing.
Table 1. Specimen and sequencing data for Clivina fossor.
| Project information | |||
|---|---|---|---|
| Study title | Clivina fossor | ||
| Umbrella BioProject | PRJEB57316 | ||
| Species | Clivina fossor | ||
| BioSample | SAMEA10107093 | ||
| NCBI taxonomy ID | 795047 | ||
| Specimen information | |||
| Technology | ToLID | BioSample accession | Organism part |
| PacBio long read sequencing | icCliFoss2 | SAMEA10200820 | Whole organism |
| Hi-C sequencing | icCliFoss1 | SAMEA9359544 | Head and thorax |
| Sequencing information | |||
| Platform | Run accession | Read count | Base count (Gb) |
| Hi-C Illumina NovaSeq 6000 | ERR10466822 | 9.05e+08 | 136.64 |
| PacBio Sequel IIe | ERR10480601 | 2.17e+06 | 20.55 |
Manual assembly curation corrected 78 missing joins or mis-joins and six haplotypic duplications, reducing the assembly length by 0.64% and the scaffold number by 7.96%, and increasing the scaffold N50 by 75.31%. The final assembly has a total length of 612.60 Mb in 554 sequence scaffolds with a scaffold N50 of 24.0 Mb ( Table 2), with 201 gaps. The snail plot 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 (86.33%) of the assembly sequence was assigned to 22 chromosomal-level scaffolds, representing 21 autosomes and the X sex chromosome. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 3). The X chromosome was identified via synteny to Agonum fuliginosum (GCA_947534325.1) ( Crowley et al., 2024). The order and orientation of scaffolds are uncertain in the following regions: on chromosome 14 in the region 13–17.8 Mb and on chromosome 17 in the region 0–6.3 Mb. 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.
Figure 2. Genome assembly of Clivina fossor, icCliFoss2.1: 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 612,615,498 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 (85,984,474 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (24,002,212 and 765,083 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 endopterygota_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Clivina_fossor/dataset/GCA_963966155.1/snail.
Figure 3. Genome assembly of Clivina fossor, icCliFoss2.1: BlobToolKit GC-coverage plot.
Blob plot of base coverage in ERR10480601 against GC proportion for sequences in assembly GCA_963966155.1. 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/Clivina_fossor/dataset/GCA_963966155.1/blob.
Figure 4. Genome assembly of Clivina fossor icCliFoss2.1: 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/Clivina_fossor/dataset/GCA_963966155.1/cumulative.
Figure 5. Genome assembly of Clivina fossor icCliFoss2.1: Hi-C contact map of the icCliFoss2.1 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=DJuW1ubzQNS77UjswHCgjA.
Table 2. Genome assembly data for Clivina fossor, icCliFoss2.1.
| Genome assembly | ||
|---|---|---|
| Assembly name | icCliFoss2.1 | |
| Assembly accession | GCA_963966155.1 | |
| Accession of alternate haplotype | GCA_963966135.1 | |
| Span (Mb) | 612.60 | |
| Number of contigs | 756 | |
| Contig N50 length (Mb) | 4.8 | |
| Number of scaffolds | 554 | |
| Scaffold N50 length (Mb) | 24.0 | |
| Longest scaffold (Mb) | 86.25 | |
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 56.3 | ≥ 50 |
| k-mer completeness | 99.99% | ≥ 95% |
| BUSCO ** | C:99.0%[S:91.8%,D:7.2%],F:0.6%,M:0.4%,n:2,124 | C ≥ 95% |
| Percentage of assembly mapped to chromosomes | 86.33% | ≥ 95% |
| Sex chromosomes | X | localised homologous pairs |
| Organelles | Mitochondrial genome: 16.48 kb | complete single alleles |
* 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 endopterygota_odb10 BUSCO set using version 5.4.3. 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/Clivina_fossor/dataset/GCA_963966155.1/busco.
Table 3. Chromosomal pseudomolecules in the genome assembly of Clivina fossor, icCliFoss2.
| INSDC accession | Name | Length (Mb) | GC% |
|---|---|---|---|
| OZ014551.1 | 1 | 40.78 | 27.5 |
| OZ014552.1 | 2 | 35.6 | 27.5 |
| OZ014553.1 | 3 | 34.89 | 27.0 |
| OZ014554.1 | 4 | 33.54 | 28.0 |
| OZ014555.1 | 5 | 30.76 | 27.0 |
| OZ014556.1 | 6 | 24.77 | 27.5 |
| OZ014557.1 | 7 | 24.0 | 27.5 |
| OZ014558.1 | 8 | 23.1 | 28.0 |
| OZ014559.1 | 9 | 22.0 | 27.5 |
| OZ014560.1 | 10 | 21.23 | 27.0 |
| OZ014561.1 | 11 | 21.14 | 27.5 |
| OZ014562.1 | 12 | 18.45 | 27.0 |
| OZ014563.1 | 13 | 17.91 | 27.0 |
| OZ014564.1 | 14 | 17.88 | 27.0 |
| OZ014565.1 | 15 | 14.5 | 27.0 |
| OZ014566.1 | 16 | 13.88 | 27.0 |
| OZ014567.1 | 17 | 13.17 | 28.0 |
| OZ014568.1 | 18 | 12.57 | 27.0 |
| OZ014569.1 | 19 | 9.59 | 27.5 |
| OZ014570.1 | 20 | 6.78 | 27.0 |
| OZ014571.1 | 21 | 6.14 | 27.0 |
| OZ014550.1 | X | 85.98 | 28.0 |
| OZ014572.1 | MT | 0.02 | 22.0 |
The estimated Quality Value (QV) of the final assembly is 56.3 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.4.3 completeness of 99.0% (single = 91.8%, duplicated = 7.2%), using the endopterygota_odb10 reference set ( n = 2,124).
Metadata for specimens, BOLD barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/795047.
Methods
Sample acquisition and nucleic acid extraction
The genome was sequenced from an adult female Clivina fossor (specimen ID Ox001175, ToLID icCliFoss2) was collected from Wytham Woods, Oxfordshire (biological vice-county Berkshire), UK (latitude 51.79, longitude –1.32) on 2021-04-13. The specimen was collected by Liam Crowley (University of Oxford) and identified by Mark Telfer (independent researcher), and then preserved on dry ice. The specimen used for Hi-C sequencing (specimen ID NHMUK014433213, ToLID icCliFoss1) was an adult specimen collected from Bookham Common, Leatherhead, UK on 2021-04-18. The specimen was collected and identified by Maxwell Barclay (Natural History Museum), and preserved by dry freezing at –80 °C.
The initial identification of both specimens 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 specimens and preserved in ethanol, while the remaining parts of the specimen were shipped on dry ice to the Wellcome Sanger Institute (WSI). The tissue was lysed before PCR amplification of the COI marker region, and amplicons were sequenced and compared to the BOLD database, confirming 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).
Nucleic acid extraction
The workflow for high molecular weight (HMW) DNA extraction at the WSI Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation and homogenisation, DNA extraction, fragmentation and purification. Detailed protocols are available on protocols.io ( Denton et al., 2023b).
The sample was prepared for DNA extraction at the Tree of Life Core Laboratory: the icCliFoss2 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 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 ( 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 ( Strickland 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.
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 head and thorax tissue of icCliFoss1 using the Arima-HiC 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, curation and evaluation
Assembly
The HiFi reads were first assembled using Hifiasm ( Cheng et al., 2021) with the --primary option. Haplotypic duplications were identified and removed using purge_dups ( Guan et al., 2020). The Hi-C reads were mapped to the primary contigs using bwa-mem2 ( Vasimuddin et al., 2019). The contigs were further scaffolded using the provided Hi-C data ( Rao et al., 2014) in YaHS ( Zhou et al., 2023) using the --break option. 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. The sex chromosome was identified by synteny. The entire process is documented at https://gitlab.com/wtsi-grit/rapid-curation (article in preparation).
Evaluation of the final assembly
The final assembly was post-processed and evaluated with the three Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a), “sanger-tol/genomenote” ( Surana et al., 2023b), and “sanger-tol/blobtoolkit” ( Muffato et al., 2024). The pipeline sanger-tol/readmapping aligns the Hi-C reads with bwa-mem2 ( Vasimuddin et al., 2019) and combines the alignment files with SAMtools ( Danecek et al., 2021). The sanger-tol/genomenote pipeline transforms the Hi-C alignments into a contact map with BEDTools ( Quinlan & Hall, 2010) and the Cooler tool suite ( Abdennur & Mirny, 2020), which is then visualised with HiGlass ( Kerpedjiev et al., 2018). It also provides statistics about the assembly with the NCBI datasets ( Sayers et al., 2024) report, computes k-mer completeness and QV consensus quality values with FastK and MERQURY.FK, and a completeness assessment with BUSCO ( Manni et al., 2021).
The sanger-tol/blobtoolkit pipeline is a Nextflow port of the previous Snakemake Blobtoolkit pipeline ( Challis et al., 2020). It aligns the PacBio reads with 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 lineage, the pipeline aligns the BUSCO genes to the Uniprot Reference Proteomes database ( Bateman et al., 2023) with DIAMOND ( Buchfink et al., 2021) blastp. The genome is also split into chunks according to the density of the BUSCO genes from the closest taxonomically lineage, and each chunk is aligned to the Uniprot Reference Proteomes database with DIAMOND blastx. Genome sequences that have no hit are then chunked with seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). All those outputs are combined with the blobtools suite into a blobdir for visualisation.
The evaluation pipelines were developed using the nf-core tooling ( Ewels et al., 2020), use MultiQC ( Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), and the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.
Table 4 contains a list of relevant software tool versions and sources.
Table 4. Software tools: versions and sources.
Wellcome Sanger Institute – Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. The submission of materials by a Darwin Tree of Life Partner is subject to the ‘Darwin Tree of Life Project Sampling Code of Practice’, which can be found in full on the Darwin Tree of Life website here. By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are:
• Ethical review of provenance and sourcing of the material
• Legality of collection, transfer and use (national and international)
Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.
Funding Statement
This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [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>]. XRB is supported by grant NERC – QUADRAT DTP.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
[version 1; peer review: 2 approved]
Data availability
European Nucleotide Archive: Clivina fossor. Accession number PRJEB57316; https://identifiers.org/ena.embl/PRJEB57316 ( Wellcome Sanger Institute, 2024). The genome sequence is released openly for reuse. The Clivina fossor genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1 and Table 2.
Author information
Members of the University of Oxford and Wytham Woods Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7125292.
Members of the Natural History Museum Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.7139035.
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.
References
- Abdennur N, Mirny LA: Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 10.1093/bioinformatics/btz540 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Allio R, Schomaker-Bastos A, Romiguier J, et al. : MitoFinder: efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020;20(4):892–905. 10.1111/1755-0998.13160 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Altschul SF, Gish W, Miller W, et al. : Basic local alignment search tool. J Mol Biol. 1990;215(3):403–410. 10.1016/S0022-2836(05)80360-2 [DOI] [PubMed] [Google Scholar]
- Bateman A, Martin MJ, Orchard S, et al. : UniProt: the universal protein knowledgebase in 2023. Nucleic Acids Res. 2023;51(D1):D523–D531. 10.1093/nar/gkac1052 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bates A, Clayton-Lucey I, Howard C: Sanger Tree of Life HMW DNA fragmentation: diagenode megaruptor ®3 for LI PacBio. protocols.io. 2023. 10.17504/protocols.io.81wgbxzq3lpk/v1 [DOI] [Google Scholar]
- Beasley J, Uhl R, Forrest LL, et al. : DNA barcoding SOPs for the Darwin Tree of Life project. protocols.io. 2023; [Accessed 25 June 2024]. 10.17504/protocols.io.261ged91jv47/v1 [DOI] [Google Scholar]
- Bousquet Y: Description of a new species of Clivina Latreille from Southeastern United States with a key to North American species of the fossor group (Coleoptera: Carabidae: Clivinini). Coleopterists Bulletin. 1997;51(4):343–349. Reference Source [Google Scholar]
- Buchfink B, Reuter K, Drost HG: Sensitive protein alignments at Tree-of-Life scale using DIAMOND. Nat Methods. 2021;18(4):366–368. 10.1038/s41592-021-01101-x [DOI] [PMC free article] [PubMed] [Google Scholar]
- Challis R, Kumar S, Sotero-Caio C, et al. : Genomes on a Tree (GoaT): a versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic Tree of Life [version 1; peer review: 2 approved]. Wellcome Open Res. 2023;8:24. 10.12688/wellcomeopenres.18658.1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Challis R, Richards E, Rajan J, et al. : BlobToolKit – interactive quality assessment of genome assemblies. G3 (Bethesda). 2020;10(4):1361–1374. 10.1534/g3.119.400908 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cheng H, Concepcion GT, Feng X, et al. : Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021;18(2):170–175. 10.1038/s41592-020-01056-5 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Crowley L, Allen H, Barnes I, et al. : A sampling strategy for genome sequencing the British terrestrial arthropod fauna [version 1; peer review: 2 approved]. Wellcome Open Res. 2023;8:123. 10.12688/wellcomeopenres.18925.1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Crowley LM, Telfer MG, Escalona HE, et al. : The genome sequence of a ground beetle, Agonum fuliginosum (Panzer, 1809) [version 1; peer review: awaiting peer review]. Wellcome Open Res. 2024;9:81. 10.12688/wellcomeopenres.20912.1 [DOI] [Google Scholar]
- da Veiga Leprevost F, Grüning BA, Alves Aflitos S, et al. : BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017;33(16):2580–2582. 10.1093/bioinformatics/btx192 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Danecek P, Bonfield JK, Liddle J, et al. : Twelve years of SAMtools and BCFtools. GigaScience. 2021;10(2): giab008. 10.1093/gigascience/giab008 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Denton A, Oatley G, Cornwell C, et al. : Sanger Tree of Life sample homogenisation: PowerMash. protocols.io. 2023a. 10.17504/protocols.io.5qpvo3r19v4o/v1 [DOI] [Google Scholar]
- Denton A, Yatsenko H, Jay J, et al. : Sanger Tree of Life wet laboratory protocol collection. protocols.io. 2023b. 10.17504/protocols.io.8epv5xxy6g1b/v1 [DOI] [Google Scholar]
- Desender K: Ecological data on Clivina fossor (Coleoptera, Carabidae) from a pasture ecosystem 1. Adult and larval abundance, seasonal and diurnal activity. Pedobiologia. 1983;25(3):157–167. 10.1016/S0031-4056(23)05919-X [DOI] [Google Scholar]
- Di Tommaso P, Chatzou M, Floden EW, et al. : Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316–319. 10.1038/nbt.3820 [DOI] [PubMed] [Google Scholar]
- Diesh C, Stevens GJ, Xie P, et al. : JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biol. 2023;24(1): 74. 10.1186/s13059-023-02914-z [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ewels P, Magnusson M, Lundin S, et al. : MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32(19):3047–3048. 10.1093/bioinformatics/btw354 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ewels PA, Peltzer A, Fillinger S, et al. : The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276–278. 10.1038/s41587-020-0439-x [DOI] [PubMed] [Google Scholar]
- Formenti G, Abueg L, Brajuka A, et al. : Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics. 2022;38(17):4214–4216. 10.1093/bioinformatics/btac460 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Grüning B, Dale R, Sjödin A, et al. : Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018;15(7):475–476. 10.1038/s41592-018-0046-7 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Guan D, McCarthy SA, Wood J, et al. : Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020;36(9):2896–2898. 10.1093/bioinformatics/btaa025 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Harry E: PretextView (Paired Read Texture Viewer): a desktop application for viewing pretext contact maps. 2022; [Accessed 19 October 2022]. Reference Source
- Howe K, Chow W, Collins J, et al. : Significantly improving the quality of genome assemblies through curation. GigaScience. 2021;10(1): giaa153. 10.1093/gigascience/giaa153 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jay J, Yatsenko H, Narváez-Gómez JP, et al. : Sanger Tree of Life sample preparation: triage and dissection. protocols.io. 2023. 10.17504/protocols.io.x54v9prmqg3e/v1 [DOI] [Google Scholar]
- Kerpedjiev P, Abdennur N, Lekschas F, et al. : HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018;19(1): 125. 10.1186/s13059-018-1486-1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kurtzer GM, Sochat V, Bauer MW: Singularity: scientific containers for mobility of compute. PLoS One. 2017;12(5): e0177459. 10.1371/journal.pone.0177459 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Li H: Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34(18):3094–3100. 10.1093/bioinformatics/bty191 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Linnaeus C: Systema naturae per regna tria naturae, secundum classes, ordines, genera, species cum characteribus, differentiis, synonymis locis.10th revised edn., Stockholm: Lars Salvius,1758;1. Reference Source [Google Scholar]
- Manni M, Berkeley MR, Seppey M, et al. : BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol. 2021;38(10):4647–4654. 10.1093/molbev/msab199 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Merkel D: Docker: lightweight Linux containers for consistent development and deployment. Linux J. 2014;2014(239): 2, [Accessed 2 April 2024]. Reference Source [Google Scholar]
- Muffato M, Butt Z, Challis R, et al. : Sanger-tol/blobtoolkit: v0.3.0 – poliwag.2024. 10.5281/zenodo.10649272 [DOI] [Google Scholar]
- Nelson RE, Reynolds RA: Carabus auratus L. and Clivina fossor L. (Coleoptera: Carabidae): new records of two introduced taxa in the northwest and northeast U.S.A. Journal of the New York Entomological Society. 1987;95(1):10–13. Reference Source [Google Scholar]
- 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 [DOI] [Google Scholar]
- Pointon DL, Eagles W, Sims Y, et al. : Sanger-tol/treeval v1.0.0 – Ancient Atlantis.2023. 10.5281/zenodo.10047654 [DOI] [Google Scholar]
- Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–842. 10.1093/bioinformatics/btq033 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rao SSP, Huntley MH, Durand NC, et al. : A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159(7):1665–1680. 10.1016/j.cell.2014.11.021 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhie A, McCarthy SA, Fedrigo O, et al. : Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021;592(7856):737–746. 10.1038/s41586-021-03451-0 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rhie A, Walenz BP, Koren S, et al. : Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020;21(1): 245. 10.1186/s13059-020-02134-9 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sayers EW, Cavanaugh M, Clark K, et al. : GenBank 2024 update. Nucleic Acids Res. 2024;52(D1):D134–D137. 10.1093/nar/gkad903 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 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 [DOI] [Google Scholar]
- 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 [DOI] [Google Scholar]
- Surana P, Muffato M, Sadasivan Baby C: Sanger-tol/genomenote (v1.0.dev). Zenodo. 2023b. 10.5281/zenodo.6785935 [DOI] [Google Scholar]
- Twyford AD, Beasley J, Barnes I, et al. : A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life project [version 1; peer review: awaiting peer review]. Wellcome Open Res. 2024;9:339. 10.12688/wellcomeopenres.21143.1 [DOI] [PMC free article] [PubMed] [Google Scholar]
- Uliano-Silva M, Ferreira JGRN, Krasheninnikova K, et al. : MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics. 2023;24(1): 288. 10.1186/s12859-023-05385-y [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vasimuddin M, Misra S, Li H, et al. : Efficient architecture-aware acceleration of BWA-MEM for multicore systems. In: 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS). IEEE,2019;314–324. 10.1109/IPDPS.2019.00041 [DOI] [Google Scholar]
- Wellcome Sanger Institute: The genome sequence of a ground beetle, Clivina fossor (Linnaeus, 1758). European Nucleotide Archive. [dataset], accession number PRJEB57316,2024.
- Zhou C, McCarthy SA, Durbin R: YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2023;39(1): btac808. 10.1093/bioinformatics/btac808 [DOI] [PMC free article] [PubMed] [Google Scholar]