Abstract
We present a genome assembly of Ornithopus perpusillus (Bird’s-foot; Streptophyta; Magnoliopsida; Fabales; Fabaceae). The assembly consists of two haplotypes with total lengths of 528.92 megabases and 473.72 megabases. The haplotype 1 assembly and the haplotype 2 assembly each contain 7 chromosomal pseudomolecules; these account for 99.73% and 98.58% of their respective sequences. The mitochondrial genome assembly has a length of 336.14 kilobases and the plastid genome assembly has a length of 151.07 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.
Keywords: Ornithopus perpusillus, Bird’s-foot, genome sequence, chromosomal, Fabales
Species taxonomy
Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade; NPAAA clade; Hologalegina; robinioid clade; Loteae; Ornithopus; Ornithopus perpusillus L. (NCBI:txid181291)
Background
Ornithopus perpusillus L. (Figure 1) is a small, hairy annual legume with prostrate stems up to 30 cm long. Its pinnate leaves have 9 to 27 leaflets, and its white or whitish flowers, marked with red veins, occur in clusters of 3 to 8 ( Griffin et al., 2021). The species is predominantly self-pollinating: pollen is shed and germinates in the bud, although fertilised ovules were observed only after the flowers had opened ( Wojciechowska, 1972). The pods are loments, 10–20 mm long, divided by constrictions into usually 4 to 9 single-seeded segments ( Webb et al., 1988). At maturity, the pods break into these indehiscent segments, which act as the dispersal units ( Fernández-Pascual et al., 2022).
Figure 1. Ornithopus perpusillus near Lake Głębokie, Szczecin, Poland.
Photograph by Krzysztof Ziarnek (Kenraiz).
The clusters of curved pods resemble a bird’s toes, giving rise to the name Ornithopus, which is Greek for ‘bird’s foot’. The species epithet perpusillus means ‘extremely small’: the Latin pusillus, meaning ‘very small’, is strengthened by the intensifying prefix per- ( Eckel, 2011).
Ornithopus perpusillus is native to Macaronesia, northwestern and central Europe, including Britain and Ireland, and parts of southern Europe and Algeria. It has been introduced to parts of eastern Europe, western North America, Australia and New Zealand, among other regions ( POWO, 2026). In Britain, its distribution is concentrated in the south, with records scattered across Scotland; in Ireland, records are mainly coastal, particularly in the east and southwest. It grows in short, open grassland on freely drained acidic sands and gravels, around rock outcrops, on dunes and in bare patches of dry heathland. Sunny banks beside tracks and paths that are prone to drought are frequent habitats ( Pearman, 2023).
The reported sporophytic chromosome count is 2 n = 14 ( Henniges et al. , 2022), consistent with diploidy. In agreement with the haploid chromosome number of n = 7, most of the sequence in each of the two haplotype assemblies reported here is scaffolded into seven chromosomal pseudomolecules.
We sequenced the genome of Ornithopus perpusillus as part of the Darwin Tree of Life Project, which aims to generate high-quality reference genomes for all named eukaryotic species in Britain and Ireland to support research, conservation, and the sustainable use of biodiversity. The wild specimen used for sequencing was collected from a mown lawn in arboretum bed 226 at the Royal Botanic Gardens, Kew. The genus Ornithopus also includes cultivated forage legumes, notably O. sativus and O. compressus. This assembly may therefore support comparative genomics of forage legumes and studies of the genetic basis of traits such as drought tolerance.
Methods
Sample acquisition, flow cytometry and DNA barcoding
A specimen of O. perpusillus (specimen ID KDTOL10328, ToLID drOrnPerp1) was used for genome sequencing. It was collected from Kew Gardens, Surrey, UK (latitude 51.2884, longitude −0.1786) on 2021-08-03. The specimen was collected by Maria Vorontsova and identified by Tom Cope. The herbarium voucher for the sequenced plant (collector number MV2415) is deposited in the Herbarium, Royal Botanic Gardens, Kew (K), as specimen K001400857.
The genome size was estimated by flow cytometry following the ‘one-step’ method outlined in Pellicer et al. (2021) and using propidium iodide as the fluorochrome. The General Purpose Buffer (GPB) supplemented with 3% PVP was used for isolation of nuclei ( Loureiro et al., 2007), and the internal calibration standard was Petroselinum crispum ‘Champion Moss Curled’ with an assumed 1C-value of 2,200 Mb ( Obermayer et al., 2002).
The initial identification was verified by an additional DNA barcoding process according to the framework developed by Twyford et al. (2024). Part of the plant specimen was preserved in silica gel desiccant ( Chase & Hills, 1991). DNA extracted from the dried plant was amplified by PCR for standard barcode markers, with the amplicons sequenced and compared to public sequence databases including GenBank and the Barcode of Life Database (BOLD) ( Ratnasingham & Hebert, 2007). 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 are available on protocols.io.
Nucleic acid extraction
High molecular weight (HMW) DNA extraction protocols developed by the Tree of Life Core Laboratory at the Wellcome Sanger Institute (WSI) are available on protocols.io ( Howard et al., 2025). Tissue from the drOrnPerp1 sample was weighed and triaged to select the appropriate extraction workflow. HMW DNA was prepared for two PacBio HiFi libraries: DTOL13669567 and ToL_PacBio_HiFi010:D2. The tissue input, HMW DNA extraction, downstream fragmentation and clean-up, and post-shearing quality-control measurements for each PacBio library are summarised in Table 1.
The concentration of the sheared and purified DNA was assessed with a NanoDrop spectrophotometer and a Qubit Fluorometer using the Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the Femto Pulse system.
Table 1. DNA extraction and post-extraction processing for each PacBio library used for O. perpusillus.
| PacBio library ID | Tissue preparation | HMW DNA extraction | Fragmentation and clean-up | Post-shearing QC |
|---|---|---|---|---|
| DTOL13669567 | 54.0 mg leaf; cryoPREP | Automated Plant MagAttract v3 | Fragmentation: Covaris g-TUBE for ULI PacBio; clean-up: Automated SPRI | Qubit 4.74 ng/μL; fragment size 9.9 kb |
| ToL_PacBio_HiFi010:D2 | leaf; cryogenic bead beating | Automated Plant Organic Extraction | Fragmentation: Megaruptor®3 for LI PacBio; clean-up: Automated SPRI | Not recorded |
PacBio HiFi library preparation and sequencing
Library preparation and sequencing took place in the WSI Scientific Operations core.
Library ToL_PacBio_HiFi010:D2 was prepared with the SMRTbell Prep Kit 3.0 (Pacific Biosciences) according to the manufacturer’s instructions. The kit includes reagents for end repair/A-tailing, adapter ligation, post-ligation SMRTbell bead clean-up, and nuclease treatment. Size selection and clean-up were performed using diluted AMPure PB beads (Pacific Biosciences). DNA concentration was quantified with a Qubit Fluorometer v4.0 (Thermo Fisher Scientific) and the Qubit 1X dsDNA HS assay kit. Final library fragment size was assessed with the Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies) using the gDNA 55 kb BAC analysis kit. This library was sequenced on a Revio instrument (Pacific Biosciences, California, USA). The prepared libraries selected for multiplexing were pooled based on genome size, library molarity, and the intended plex level. Primers were annealed and polymerases were bound to generate circularised complexes, following the manufacturer’s instructions. Complexes were purified using SMRTbell beads, diluted to the Revio loading concentration, and spiked with a Revio sequencing internal control. The pooled libraries were sequenced on a Revio 25M Plex SMRT cell in a 2-plex run. SMRT Link software (Pacific Biosciences), a web-based workflow manager, was used to configure and monitor the run and to carry out primary and secondary data analysis.
Library DTOL13669567 was prepared with the ultra-low-input (ULI) PacBio HiFi workflow. Prior to library preparation, the DNA was fragmented to ~10 kb. Ultra-low-input (ULI) libraries were prepared with the PacBio SMRTbell® Express Template Prep Kit 2.0 and gDNA Sample Amplification Kit. Samples were normalised to 20 ng DNA. Single-strand overhang removal, DNA damage repair, and end-repair/A-tailing were performed according to the manufacturer’s instructions, followed by adapter ligation. A 0.85× pre-PCR clean-up was carried out with Promega ProNex beads. The DNA was evenly divided into two aliquots for dual PCR (reactions A and B), both following the manufacturer’s protocol. A 0.85× post-PCR clean-up was performed with ProNex beads. DNA concentration was measured with a Qubit Fluorometer v4.0 (Thermo Fisher Scientific) with the Qubit HS Assay Kit, and fragment size was assessed on an Agilent Femto Pulse Automated Pulsed Field CE Instrument (Agilent Technologies) using the gDNA 55 kb BAC analysis kit. PCR reactions A and B were then pooled, ensuring a total mass of ≥500 ng in 47.4 μL. The pooled sample underwent another round of DNA damage repair, end-repair/A-tailing, and hairpin adapter ligation. A 1× clean-up was performed with ProNex beads, followed by DNA quantification using the Qubit and fragment size analysis using the Agilent Femto Pulse. Size selection was performed on the Sage Sciences PippinHT system, with target fragment size determined by Femto Pulse analysis (typically 4–9 kb). Size-selected libraries were cleaned with 1.0× ProNex beads and normalised to 2 nM before sequencing. This library was sequenced using the Sequel IIe system (Pacific Biosciences, California, USA). The concentration of the library loaded onto the Sequel system was in the range 40–135 pM. SMRT Link software, a PacBio web-based workflow manager, was used to set up and monitor the run, and to perform primary and secondary analysis of the data upon completion.
Hi-C
Sample preparation and crosslinking
Hi-C data were generated from the drOrnPerp1 leaf sample using the Arima-HiC v2 kit (Arima Genomics). Tissue was finely ground using the Covaris cryoPREP Dry Pulverizer (Covaris), and then subjected to nuclei isolation. Nuclei were isolated using a modified protocol based on the Qiagen QProteome Cell Compartment Kit (Qiagen), in which only the Lysis and CE2 buffers were used, with QIAshredder spin columns. After isolation, nuclei were fixed using formaldehyde to a final concentration of 2% to crosslink the DNA. The crosslinked DNA was then digested and biotinylated according to the manufacturer’s instructions. A clean-up step was performed with SPRIselect beads before library preparation. DNA concentration was quantified using the Qubit Fluorometer v4.0 (Thermo Fisher Scientific) and the Qubit HS Assay Kit, following the manufacturer’s instructions.
Hi-C library preparation and sequencing
Biotinylated DNA constructs were fragmented using a Covaris E220 sonicator and size-selected to 400–600 bp using SPRISelect beads. DNA was enriched with Arima-HiC v2 kit Enrichment beads. End repair, A-tailing, and adapter ligation were carried out with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs), following a modified protocol where library preparation occurs while DNA remains bound to the Enrichment beads. Libraries were amplified with KAPA HiFi HotStart mix and a custom Unique Dual Index (UDI) barcode set (Integrated DNA Technologies). Depending on sample concentration and biotinylation percentage determined at the crosslinking stage, libraries were amplified with 10–16 PCR cycles. Post-PCR clean-up was performed with SPRISelect beads. Libraries were quantified using the AccuClear Ultra High Sensitivity dsDNA Standards Assay Kit (Biotium) and a FLUOstar Omega plate reader (BMG Labtech).
Prior to sequencing, libraries were normalised to 10 ng/μL. Normalised libraries were quantified again to create equimolar and/or weighted 2.8 nM pools. Pool concentrations were checked using the Agilent 4200 TapeStation (Agilent) with High Sensitivity D500 reagents before sequencing. Libraries were sequenced on the Illumina NovaSeq 6000, generating paired-end 150-bp reads.
Genome 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. The k-mer frequency distribution was analysed with GenomeScope (version 2.1.0) ( Ranallo-Benavidez et al., 2020), providing fitted point estimates of genome size, heterozygosity and repeat content.
The HiFi reads were assembled using Hifiasm in Hi-C phasing mode ( Cheng et al., 2021, 2022), producing two haplotypes. Hi-C reads ( Rao et al. , 2014) were mapped to contigs using bwa-mem2 ( Vasimuddin et al., 2019). Contigs were further scaffolded with Hi-C data 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 MerquryFK ( Rhie et al., 2020). The organelle genomes were assembled using OATK ( Zhou et al., 2025). The comparator for the mitochondrial assembly was the mitochondrial genome of Lotus japonicus (NC_016743.2).
Assembly curation
The assembly was decontaminated using the Assembly Screen for Cobionts and Contaminants ( ASCC) pipeline. The flat files and maps for curation were generated with TreeVal. Manual curation was conducted primarily in PretextView and HiGlass ( Kerpedjiev et al. , 2018). Scaffolds were visually inspected and corrected as described by Howe et al. (2021). The two haplotype assemblies were combined for curation. Manual corrections included 61 breaks and 116 joins. This reduced the scaffold count by 48.8%, increased the scaffold N50 by 55.4%, and increased the total assembly length by 7.3%. The curation process is described at sanger-tol/curation-resources. A Hi-C contact map of the haplotype 1 assembly was generated with PretextSnapshot.
Assembly quality assessment
The MerquryFK tool ( Rhie et al., 2020) was run in a Singularity container ( Kurtzer et al., 2017) to evaluate k-mer completeness and assembly quality for both haplotypes using the k-mer database ( k = 31) computed prior to genome assembly. The analysis outputs included assembly QV scores and completeness statistics.
The haplotype 1 assembly was assessed using BlobToolKit ( Challis et al., 2020). PacBio reads were mapped to the haplotype 1 assembly to derive sequence coverage, and BUSCO ( Manni et al., 2021) was used to assess gene-set completeness. DIAMOND BLASTp searches of extracted BUSCO proteins and DIAMOND BLASTx searches of assembly sequences against UniProt Reference Proteomes ( Buchfink et al., 2021), followed by BLASTn searches of sequences without DIAMOND BLASTx hits against the NCBI nt database ( Altschul et al., 1990), supported taxonomic assignment. Coverage, sequence composition, taxonomic assignment and BUSCO results were integrated into a BlobDir for interactive inspection and visualisation. The snail and blob plots were rendered locally from this hosted BlobDir using BlobTk v0.8.3. The scaffold-length radial scale function for the snail plot was set to linear ( Challis & Blaxter, 2026). The blob plot used circular markers with area proportional to scaffold length ( Challis et al., 2020).
Genome sequence report
Sequence data
The genome of a specimen of O. perpusillus was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating 18.39 Gb (gigabases) from 1.67 million reads. We assembled the genome from these reads. GenomeScope analysis using a p = 2 model gave a k-mer-based haploid genome size estimate of 572.16 Mb, with heterozygosity of 0.00% and repeat content of 46.30%; the full-model fit was 98.60% (Figure 2). Using flow cytometry, the genome size (1C‐value) of the sample was estimated to be 0.69 pg, equivalent to 670.00 Mb. These estimates guided expectations for the assembly. The sequencing data provided approximately 30× coverage of the haplotype 1 assembly. Hi-C sequencing produced 106.94 Gb from 354.09 million read pairs, which were used to scaffold the haplotype 1 assembly. Table 2 summarises the specimen and sequencing details.
Figure 2. GenomeScope model fitted to the k-mer frequency distribution.
The plot shows the observed and modelled k-mer spectra used to estimate genome size, heterozygosity and repeat content from unassembled sequencing reads.
Table 2. Specimen and sequencing data for O. perpusillus (BioProject PRJEB80118).
| Platform | PacBio HiFi | Hi-C |
|---|---|---|
| ToLID | drOrnPerp1 | drOrnPerp1 |
| Specimen ID | KDTOL10328 | KDTOL10328 |
| BioSample (source individual) | SAMEA10369524 | SAMEA10369524 |
| BioSample (tissue) | SAMEA10369581; SAMEA10369582 | SAMEA10369581 |
| Tissue | leaf | leaf |
| Instrument | Sequel IIe; Revio | Illumina NovaSeq 6000 |
| Library ID & run accession(s) | DTOL13669567: ERR13698302; ToL_PacBio_HiFi010:D2: ERR13698301 | ERR13670062 |
| Read count total | 1.67 million reads | 354.09 million read pairs |
| Base count total | 18.39 Gb | 106.94 Gb |
Assembly statistics
The genome was assembled into two haplotypes using Hi-C phasing. The haplotype 1 assembly was curated to chromosome level, and haplotype 2 was also scaffolded to chromosome level. The haplotype 1 assembly, which is proposed as the reference assembly for this species, has a total length of 528.92 Mb in 42 scaffolds (excluding organelle sequences), with 223 gaps, and a scaffold N50 of 82.81 Mb (Table 3). The haplotype 1 assembly has a scaffold auN of 79.3 Mb.
Table 3. Genome assembly statistics for O. perpusillus .
| Genome assembly | Haplotype 1 | Haplotype 2 |
|---|---|---|
| Assembly name | drOrnPerp1.hap1.1 | drOrnPerp1.hap2.1 |
| Assembly accession | GCA_965278115.1 | GCA_965278145.1 |
| Assembly level | chromosome | chromosome |
| Span (Mb) | 528.92 | 473.72 |
| Number of chromosomes | 7 | 7 |
| Number of contigs | 265 | 281 |
| Contig N50 (Mb) | 3.66 | 3.82 |
| Number of scaffolds (excluding organelle sequences) | 42 | 68 |
| Scaffold N50 (Mb) | 82.81 | 73.66 |
| Scaffold auN (Mb) | 79.3 | 70.2 |
| Longest scaffold length (Mb) | 110.46 | 100.66 |
| Organelles | Mitochondrial genome: 336.14 kb; Plastid genome: 151.07 kb | - |
Most of the haplotype 1 assembly sequence (99.73%) was assigned to 7 chromosome-level scaffolds. These chromosome-level scaffolds, confirmed by Hi-C data, are named according to size (Figure 3; Table 4).
Figure 3. Hi-C contact map of the O. perpusillus haplotype 1 assembly.
Assembled chromosomes are shown in order of size and labelled along the axes, with a megabase scale shown below. The plot was generated using PretextSnapshot.
The mitochondrial genome (length 336.14 kb, OZ256224.1) and plastid genome (length 151.07 kb, OZ256225.1) were also assembled. These sequences are included as contigs in the multifasta file of the haplotype 1 genome submission and as standalone records.
Table 4. Chromosomal pseudomolecules in the haplotype 1 genome assembly of O. perpusillus drOrnPerp1 (haplotype 2 also at chromosome level).
| INSDC accession | Molecule | Length (Mb) | GC% |
|---|---|---|---|
| OZ256217.1 | 1 | 110.46 | 38 |
| OZ256218.1 | 2 | 84.50 | 38.50 |
| OZ256219.1 | 3 | 82.81 | 38 |
| OZ256220.1 | 4 | 69.68 | 37.50 |
| OZ256221.1 | 5 | 68.84 | 37.50 |
| OZ256222.1 | 6 | 57.72 | 37.50 |
| OZ256223.1 | 7 | 53.51 | 38 |
Assembly quality metrics
For the haplotype 1 assembly, the estimated QV is 67.0, and for the haplotype 2 assembly, 65.8. When the two haplotypes are combined, the assembly achieves an estimated QV of 66.4. The k-mer completeness is 98.99% for the haplotype 1 assembly, 93.15% for the haplotype 2 assembly, and 99.23% for the combined haplotypes (Figure 4).
Figure 4. Evaluation of k-mer completeness using MerquryFK.
This plot illustrates the recovery of k‐mers from the original read data in the haplotype 1 assembly, the haplotype 2 assembly and the combined haplotypes. The horizontal axis represents k‐mer multiplicity, and the vertical axis shows the number of k‐mers. The black curve represents k‐mers that appear in the reads but are not assembled, while the remaining curves correspond to k‐mers recovered in the assemblies shown.
BUSCO analysis using the fabales_odb10 reference set ( n = 5,366) identified 97.4% of the expected gene set (single = 92.4%, duplicated = 5.1%) in the haplotype 1 assembly. For the haplotype 2 assembly, BUSCO v.5.7.1 analysis identified 94.3% of the expected gene set (single = 89.5%, duplicated = 4.8%).
The snail plot in Figure 5 provides a summary of assembly contiguity, cumulative scaffold count, sequence composition and BUSCO completeness for the haplotype 1 assembly ( Challis & Blaxter, 2026). The relative sizes of the longest scaffold, scaffold N50 and N90, together with the dark-grey scaffold-length distribution, show how much of the assembly is contained in long scaffolds. The outer composition track shows variation in GC, AT and N content, while the central track shows the cumulative scaffold count and the BUSCO inset summarises gene-set completeness.
Figure 5. Assembly metrics for drOrnPerp1.hap1.1, the haplotype 1 assembly.
The BlobToolKit snail plot provides an overview of assembly metrics and BUSCO gene completeness. The circumference represents the length of the haplotype 1 assembly, 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. Scaffold length is shown on a linear radial scale, scaled to the longest scaffold. Red shading indicates the longest scaffold, and the deeper orange and pale orange shading represent the N50 and N90 lengths. The summary statistics include scaffold auN, the area under the scaffold Nx curve. The 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 fabales_odb10 set is presented at the top right. The assembly can be explored interactively in the BlobToolKit viewer.
The blob plot in Figure 6 displays scaffolds from the haplotype 1 assembly by GC proportion and base coverage. Marker area is proportional to scaffold length, and colour indicates taxonomic assignment ( Challis et al., 2020).
Figure 6. BlobToolKit blob plot for drOrnPerp1.hap1.1, the haplotype 1 assembly.
The plot shows base coverage (vertical axis) and GC content (horizontal axis). Circles represent scaffolds; marker area is proportional to scaffold length, and colour indicates taxonomic assignment. The histograms along the axes display the total length of sequences distributed across different levels of coverage and GC content. The assembly can be explored interactively in the BlobToolKit viewer.
Table 5 lists the assembly metric benchmarks adapted from Rhie et al.. (2021) and the Earth BioGenome Project (EBP) Report on Assembly Standards. The three-part EBP metric calculated for the haplotype 1 assembly is 6.C.Q67.
Table 5. Earth BioGenome Project summary metrics for the O. perpusillus assembly.
| Measure | Value | Benchmark |
|---|---|---|
| EBP summary (haplotype 1) | 6.C.Q67 | 6.C.Q40 |
| Contig N50 length | 3.66 Mb | > 1 Mb |
| Scaffold N50 length | 82.81 Mb | = chromosome N50 |
| Consensus quality (QV) | Haplotype 1: 67.0; haplotype 2: 65.8; combined: 66.4 | ≥ 40 |
| k-mer completeness | Haplotype 1: 98.99%; Haplotype 2: 93.15%; combined: 99.23% | > 90% |
| BUSCO | Haplotype 1: C:97.4% [S:92.4%, D:5.1%], F:0.2%, M:2.3%, n:5,366; Haplotype 2: C:94.3% [S:89.5%, D:4.8%], F:0.3%, M:5.5%, n:5,366 | S > 90%; D < 5% |
| Percentage of assembly assigned to chromosomes | 99.73% | ≥ 90% |
Notes: The EBP summary uses log10(Contig N50); chromosome-level (C) or log10(Scaffold N50); Q (Merqury QV). BUSCO v5.7.1 using the fabales_odb10 lineage dataset: C=complete; S=single-copy; D=duplicated; F=fragmented; M=missing; n=orthologues.
Data availability
European Nucleotide Archive: Ornithopus perpusillus. Accession number PRJEB80118; https://identifiers.org/ena.embl/PRJEB80118. The genome sequence is released openly for reuse. The O. perpusillus genome sequencing initiative is part of the Darwin Tree of Life Project ( PRJEB40665) and the Sanger Institute Tree of Life Programme ( PRJEB43745). All raw sequence data and the haplotype assemblies 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 2 and Table 3.
Pipelines used for genome assembly at the WSI Tree of Life are available at https://pipelines.tol.sanger.ac.uk/pipelines. Table 6 lists software versions used in this study.
Table 6. Software versions and sources used for O. perpusillus .
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. 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 [220540, https://doi.org/10.35802/220540] and the Darwin Tree of Life Discretionary Award [218328, https://doi.org/10.35802/218328].
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]
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