The genome sequence of a beetle, Pycnomerus fuliginosus Erichson, 1842
Olga Sivell, Susan C. Taylor, Maxwell V. L. Barclay, Stephanie Skipp, Michael F. Geiser, Chenyang Cai, Lapo Ragionieri
TL;DR
This paper reports the genome sequence of the beetle Pycnomerus fuliginosus, including chromosomal scaffolds and gene annotations.
Contribution
The study provides a high-quality genome assembly and gene annotation for Pycnomerus fuliginosus.
Findings
The genome assembly is 359.22 megabases long with 95.81% scaffolded into 11 chromosomal pseudomolecules.
The mitochondrial genome is 17.21 kilobases in length.
Gene annotation identified 11,547 protein-coding genes.
Abstract
We present a genome assembly from a female Pycnomerus fuliginosus (beetle; Arthropoda; Insecta; Coleoptera; Zopheridae). The genome sequence has a total length of 359.22 megabases. Most of the assembly (95.81%) is scaffolded into 11 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.21 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,547 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 | |||
|---|---|---|---|
|
| Pycnomerus fuliginosus | ||
|
| PRJEB59804 | ||
|
|
| ||
|
| SAMEA11024993 | ||
|
| 878397 | ||
| Specimen information | |||
|
|
|
|
|
|
| icPycFuli2 | SAMEA11025200 | abdomen |
|
| icPycFuli1 | SAMEA9359522 | head and thorax |
|
| icPycFuli3 | SAMEA114806053 | whole organism |
| Sequencing information | |||
|
|
|
|
|
|
| ERR10890754 | 1.32e+09 | 199.06 |
|
| ERR10879942 | 1.84e+06 | 22.55 |
|
| ERR13999062 | 8.69e+07 | 13.13 |
| Genome assembly | ||
|---|---|---|
| Assembly name | icPycFuli2.1 | |
| Assembly accession | GCA_963924575.1 | |
|
|
| |
| Assembly level for primary assembly | chromosome | |
| Span (Mb) | 359.22 | |
| Number of contigs | 109 | |
| Number of scaffolds | 50 | |
| Longest scaffold (Mb) | 56.25 | |
| Assembly metric | Measure |
|
| Contig N50 length | 7.63 Mb |
|
| Scaffold N50 length | 37.94 Mb |
|
| Consensus quality (QV) | Primary: 69.3; alternate: 68.5; combined 68.9 |
|
|
| Primary: 83.08%; alternate: 75.60%;
|
|
| BUSCO
| C:99.3%[S:98.7%,D:0.6%],
|
|
| Percentage of assembly mapped
| 95.83% |
|
| Sex chromosomes | X |
|
| Organelles | Mitochondrial genome: 17.21 kb |
|
| Genome annotation of assembly GCA_963924575.1 at Ensembl | ||
| Number of protein-coding genes | 11,547 | |
| Number of non-coding genes | 1,002 | |
| Number of gene transcripts | 17,565 | |
|
|
|
|
|
|---|---|---|---|
| 1 | 56.25 | 37.5 | |
| 2 | 52.38 | 37 | |
| 3 | 50.57 | 37 | |
| 4 | 37.94 | 36.5 | |
| 5 | 36.06 | 37 | |
| 6 | 31.7 | 37 | |
| 7 | 26.06 | 37 | |
| 8 | 19.45 | 37 | |
| 9 | 17.57 | 37 | |
| 10 | 1.33 | 38.5 | |
| X | 14.89 | 36 | |
| MT | 0.02 | 31.5 |
|
|
|
|
|---|---|---|
| BEDTools | 2.30.0 |
|
| BLAST | 2.14.0 |
|
| BlobToolKit | 4.3.9 |
|
| BUSCO | 5.5.0 |
|
| bwa-mem2 | 2.2.1 |
|
| Cooler | 0.8.11 |
|
| DIAMOND | 2.1.8 |
|
| fasta_windows | 0.2.4 |
|
| FastK | 427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c |
|
| Gfastats | 1.3.6 |
|
| GoaT CLI | 0.2.5 |
|
| Hifiasm | 0.16.1-r375 |
|
| HiGlass | 44086069ee7d4d3f6f3f0012569789ec138f42b84aa44357826c0b6753eb28de |
|
| MerquryFK | d00d98157618f4e8d1a9190026b19b471055b22e |
|
| Minimap2 | 2.24-r1122 |
|
| MitoHiFi | 2 |
|
| MultiQC | 1.14, 1.17, and 1.18 |
|
| NCBI Datasets | 15.12.0 |
|
| Nextflow | 23.04.1 |
|
| PretextView | 0.2.5 |
|
| purge_dups | 1.2.3 |
|
| samtools | 1.19.2 |
|
| sanger-tol/ascc | - |
|
| sanger-tol/blobtoolkit | 0.5.1 |
|
| Seqtk | 1.3 |
|
| Singularity | 3.9.0 |
|
| TreeVal | 1.2.0 |
|
| YaHS | 1.2a |
|
- —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
TopicsForest Insect Ecology and Management · Coleoptera Taxonomy and Distribution · Insect Resistance and Genetics
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Protostomia; Ecdysozoa; Panarthropoda; Arthropoda; Mandibulata; Pancrustacea; Hexapoda; Insecta; Dicondylia; Pterygota; Neoptera; Endopterygota; Coleoptera; Polyphaga; Cucujiformia; Tenebrionoidea; Zopheridae; Zopherinae; Pycnomerini; Pycnomerus; Pycnomerus fuliginosus Erichson, 1842 (NCBI:txid878397)
Background
Pycnomerus fuliginosus Erichson, 1842 is a species of a beetle from the family Zopheridae, commonly called ironclad beetles. This species is elongated, parallel sided, tenebrionid-like in appearance with expanded genae, reddish-brown in colour, with striatopunctate elytra with single rows of golden setae and tarsi 4-4-4. It is a small species measuring 5.5–6.0 mm ( Ivie, 2002; O’Connor et al., 1983).
The tribe Pycnomerini Erichson 1845, previously in Colydiidae (Ivie, M.A.), was revised by Ślipiński and Lawrence (1999) and moved to Zopheridae. Keys to genera of Zopheridae are provided by Ślipiński and Lawrence (1999) and Ivie (2002). Zopheridae and Colydiidae have now both been downgraded to subfamilies of a broader Zopheridae (e.g. see Duff, 2018), and Pycnomerus is the only genus of subfamily Zopherinae occurring in Britain and Ireland.
The genus Pycnomerus Erichson 1842 includes 34 species worldwide, including five species occurring in Europe: P. italicus Ganglbauer, 1899, endemic to Italy ( Pezzi et al., 2022); P. terebrans (Olivier, 1790); P. inexspectus Jacquelin du Val, 1858, found in greenhouses in a few countries; P. angulatus Broun, 1893 introduced to Ireland from New Zealand in recent years ( Alexander & Anderson, 2012), and P. fuliginosus, established in Britain and Ireland ( Iwan & Löbl, 2020). Numerous invertebrate species have been recently imported to Britain and Ireland from Australia and New Zealand (e.g. see Walters et al., 2016).
Pycnomerus fuliginosus was accidentally introduced to Britain from Australia and was first reported in Britain in 1964. It has been suggested it was possibly brought in with horticultural commerce ( O’Connor et al., 1983). Since then, it became established and has been expanding its distribution. It has been recorded mostly from southern England and Wales, with few records from the Midlands and one near Manchester ( Alexander, 2019; Allen, 1968; Morgan, 1979; Twinn & Hunter, 1967; Welch, 1964). It has been known in Ireland since 1981 ( Alexander & Anderson, 2012; O’Connor et al., 1983). It is a relatively uncommon species, living under the bark of conifers and hardwood trees ( James, 2018), but adults were observed flying in sunlight around a pile of cut branches at Bookham Common Surrey (MVL Barclay, personal observation). Both larvae and adults of Pycomerini are associated with rotten plant material. According to Denux and Zagatti (2010), they are likely predatory on saproxylic insects.
Relatively little is known about the biology of P. fuliginosus, and many related species await description. The high-quality genome of P. fuliginosus presented here was sequenced from a single specimen (NHMUK014452846; SAMEA11024993) from Penryn, England. 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 on taxonomy, phylogeny and biology of Pycnomerus, family Zopheridae and the superfamily Tenebrionoidea.
Genome sequence report
Sequencing data
The genome of a specimen of Pycnomerus fuliginosus ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating 22.55 Gb from 1.84 million reads. GenomeScope analysis of the PacBio HiFi data estimated the haploid genome size at 365.18 Mb, with a heterozygosity of 0.71% and repeat content of 46.84%. 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 59.0x coverage of the genome. Chromosome conformation Hi-C sequencing produced 199.06 Gb from 1,318.25 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 Pycnomerus fuliginosus (icPycFuli2) specimen used for genome sequencing.
Table 1.: Specimen and sequencing data for Pycnomerus fuliginosus.
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 14 misjoins or missing joins and removed three haplotypic duplications. These interventions reduced the total assembly length by 1.79% and decreased the scaffold count by 10.53%. The final assembly has a total length of 359.22 Mb in 50 scaffolds, with 59 gaps, and a scaffold N50 of 37.94 Mb ( Table 2).
Table 2.: Genome assembly data for Pycnomerus fuliginosus.
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 Pycnomerus fuliginosus, icPycFuli2.1: 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 endopterygota_odb10 set is presented at the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_963924575.1/dataset/GCA_963924575.1/snail.
Genome assembly of Pycnomerus fuliginosus, icPycFuli2.1: 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_963924575.1/blob.
Genome assembly of Pycnomerus fuliginosus, icPycFuli2.1: 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_963924575.1/dataset/GCA_963924575.1/cumulative.
Most of the assembly sequence (95.83%) was assigned to 11 chromosomal-level scaffolds, representing 10 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 X was assigned by synteny to Schizotus pectinicornis (GCA_951805265.1) ( Lyszkowski et al., 2024).
Genome assembly of Pycnomerus fuliginosus: Hi-C contact map of the icPycFuli2.1 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=HQQV4a_CQc6bvNKIzgJKYA.
Table 3.: Chromosomal pseudomolecules in the genome assembly of Pycnomerus fuliginosus, icPycFuli2.
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.
The primary haplotype has a QV of 69.3, and the combined primary and alternate assemblies achieve an estimated QV of 68.9. The k-mer completeness for the primary haplotype is 83.08%, and for the alternate haplotype it is 75.60%. The combined primary and alternate assemblies achieve a k-mer completeness of 98.25%. BUSCO analysis using the endopterygota_odb10 reference set ( n = 2,124) indicated a completeness score of 99.3% (single = 98.7%, duplicated = 0.6%).
Table 2 provides assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project (EBP) Report on Assembly Standards September 2024. The assembly achieves the EBP reference standard of 6.C.Q69.
Genome annotation report
The Pycnomerus fuliginosus genome assembly (GCA_963924575.1) was annotated at the European Bioinformatics Institute (EBI) on Ensembl Rapid Release. The resulting annotation includes 17,565 transcribed mRNAs from 11,547 protein-coding and 1,002 non-coding genes ( Table 2; https://rapid.ensembl.org/Pycnomerus_fuliginosus_GCA_963924575.1/Info/Index). The average transcript length is 9,484.21. There are 1.40 coding transcripts per gene and 4.75 exons per transcript.
Methods
Sample acquisition and DNA barcoding
An adult female Pycnomerus fuliginosus (specimen ID NHMUK014452846, ToLID icPycFuli2) was collected from University of Exeter Falmouth Campus, Penryn, England, UK (latitude 50.17, longitude –5.12) on 2021-06-29, using an aerial net. The specimen was collected by Olga Sivell (Natural History Museum), identified by Sue Taylor (Dipterists Forum) and preserved by dry freezing (–80 °C).
The specimen used for Hi-C sequencing (specimen ID NHMUK014433208, ToLID icPycFuli1) was collected from Bookham Common, Leatherhead, England, UK on 2021-04-18 by handpicking. The specimen was collected and identified by Maxwell Barclay (Natural History Museum) and preserved by dry freezing (–80 °C).
The specimen used for RNA sequencing (specimen ID NHMUK014440698, ToLID icPycFuli3) was collected from Wimbledon Common, England, United Kingdom (latitude 51.44, longitude –0.23) on 2022-03-06. The specimen was collected by Michael Geiser and Stephanie Skipp (Natural History Museum), identified by Michael Geiser 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) ( 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. Detailed protocols are available on protocols.io ( Denton et al., 2023b). The icPycFuli2 sample was prepared for DNA extraction by weighing and dissecting it on dry ice ( Jay et al., 2023). Tissue from the abdomen 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.
RNA was extracted from whole organism tissue of icPycFuli3 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 head and thorax of the icPycFuli1 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 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, 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 6000 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 X 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 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. The sex chromosome was assigned 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.
Genome annotation
The Ensembl Genebuild annotation system ( Aken et al., 2016) was used to generate annotation for the Pycnomerus fuliginosus assembly (GCA_963924575.1) in Ensembl Rapid Release at the EBI. Annotation was created primarily through alignment of transcriptomic data to the genome, with gap filling via protein-to-genome alignments of a select set of proteins from UniProt ( UniProt Consortium, 2019).
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.
- 1Abdennur N Mirny LA : Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020;36(1):311–316. 10.1093/bioinformatics/btz 540 31290943 PMC 8205516 · doi ↗ · pubmed ↗
- 2Aken BL Ayling S Barrell D : The Ensembl gene annotation system. Database (Oxford). 2016;2016: baw 093. 10.1093/database/baw 093 27337980 PMC 4919035 · doi ↗ · pubmed ↗
- 3Alexander KN : Saproxylic invertebrate survey of Wye Valley Woodlands Special Area of Conservation (SAC) in 2017. 2019. Reference Source
- 4Alexander KNA Anderson R : The beetles of decaying wood in Ireland: a provisional annotated checklist of saproxylic Coleoptera. 2012. Reference Source
- 5Allen A : A note on Pycnomerus fuliginosus Er.(Colydiidae) in Epping forest, Essex. Entomologist’s Monthly Magazine. 1968;104:160.
- 6Allio 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 ↗
- 7Altschul 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 ↗
- 8Bateman 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 ↗