The genome sequence of the short-beaked common dolphin, Delphinus delphis Linnaeus, 1758
Nicholas J Davison, Phillip A. Morin, Annabel Whibley, Takushi Kishida
TL;DR
This paper presents the genome sequence of the short-beaked common dolphin, including detailed assembly and gene annotation.
Contribution
The study provides a high-quality genome assembly and gene annotation for Delphinus delphis, including sex chromosomes and mitochondrial DNA.
Findings
The genome assembly is 2,663.52 megabases long with 88.76% scaffolded into 23 chromosomal pseudomolecules.
The mitochondrial genome is 16.39 kilobases long and fully assembled.
Gene annotation identified 17,797 protein-coding genes using Ensembl.
Abstract
We present a genome assembly from a male specimen of Delphinus delphis (short-beaked common dolphin; Chordata; Mammalia; Artiodactyla; Delphinidae). The genome sequence has a total length of 2,663.52 megabases. Most of the assembly (88.76%) is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.39 kilobases. Gene annotation of this assembly at Ensembl identified 17,797 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
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Figure 5| Project information | |||
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| Delphinus delphis (saddleback dolphin) | ||
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| PRJEB60667 | ||
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| SAMEA111380534 | ||
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| 9728 | ||
| Specimen information | |||
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| mDelDel1 | SAMEA111380542 | lung |
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| mDelDel1 | SAMEA111380542 | lung |
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| mDelDel1 | SAMEA111380542 | lung |
| Sequencing information | |||
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| ERR11040185 | 2.98e+09 | 450.46 |
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| ERR11029689 | 2.95e+06 | 26.36 |
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| ERR11029687 | 3.07e+06 | 25.73 |
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| ERR11029690 | 2.97e+06 | 25.62 |
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| ERR11029688 | 2.91e+06 | 23.88 |
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| ERR11837480 | 4.32e+07 | 6.53 |
| Genome assembly | ||
|---|---|---|
| Assembly name | mDelDel1.2 | |
| Assembly accession | GCA_949987515.2 | |
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| Assembly level for primary
| chromosome | |
| Span (Mb) | 2,663.52 | |
| Number of contigs | 1,598 | |
| Number of scaffolds | 630 | |
| Longest scaffold (Mb) | 184.87 | |
| Assembly metric | Measure |
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| Contig N50 length | 3.63 Mb |
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| Scaffold N50 length | 107.08 Mb |
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| Consensus quality (QV) | Primary: 66.4; alternate:
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| Primary: 94.23%; alternate:
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| BUSCO
| C:95.4%[S:93.3%,D:2.1%],
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| Percentage of assembly
| 88.77% |
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| Sex chromosomes | X and Y |
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| Organelles | Mitochondrial genome:
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| INSDC accession | Name | Length (Mb) | GC% |
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| 1 | 184.87 | 42 | |
| 2 | 178.37 | 41.5 | |
| 3 | 173.06 | 41 | |
| 4 | 144.52 | 39.5 | |
| 5 | 139.21 | 39 | |
| 6 | 116.6 | 42 | |
| 7 | 115.54 | 40 | |
| 8 | 110.53 | 42.5 | |
| 9 | 107.08 | 40.5 | |
| 10 | 104.91 | 43.5 | |
| 11 | 102.45 | 41.5 | |
| 12 | 89.89 | 42 | |
| 13 | 89.81 | 43 | |
| 14 | 88.85 | 39.5 | |
| 15 | 88.04 | 46 | |
| 16 | 85.33 | 43 | |
| 17 | 80.67 | 40.5 | |
| 18 | 78.82 | 39.5 | |
| 19 | 60.21 | 46.5 | |
| 20 | 59.47 | 45.5 | |
| 21 | 35.59 | 41 | |
| X | 126.48 | 40 | |
| Y | 4.08 | 39.5 | |
| MT | 0.02 | 38.5 |
| Software tool | Version | Source |
|---|---|---|
| BLAST | 2.14.0 | ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ |
| BlobToolKit | 4.3.9 |
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| BUSCO | 5.5.0 |
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| bwa-mem2 | 2.2.1 |
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| DIAMOND | 2.1.8 |
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| fasta_windows | 0.2.4 |
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| FastK | 666652151335353eef2fcd58880bcef5bc2928e1 |
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| Gfastats | 1.3.6 |
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| GoaT CLI | 0.2.5 |
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| Hifiasm | 0.16.1-r375 |
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| HiGlass | 44086069ee7d4d3f6f3f0012569789ec138f42b84
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| MerquryFK | d00d98157618f4e8d1a9190026b19b471055b22e |
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| Minimap2 | 2.24-r1122 |
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| MitoHiFi | 3 |
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| MultiQC | 1.14, 1.17, and 1.18 |
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| Nextflow | 23.10.0 |
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| PretextView | 0.2.5 |
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| purge_dups | 1.2.5 |
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| samtools | 1.19.2 |
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| sanger-tol/ascc | - |
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| sanger-tol/blobtoolkit | 0.6.0 |
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| Seqtk | 1.3 |
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| Singularity | 3.9.0 |
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| TreeVal | 1.2.0 |
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| YaHS | 1.2a |
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- —Wellcome Trust
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Taxonomy
TopicsMarine animal studies overview · Genomics and Phylogenetic Studies · Identification and Quantification in Food
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Artiodactyla; Whippomorpha; Cetacea; Odontoceti; Delphinidae; Delphinus; Delphinus delphis Linnaeus, 1758 (NCBI:txid9728).
Background
The saddleback dolphin ( Delphinus delphis), also referred to as the common dolphin, is a highly abundant species consisting of four recognized subspecies. The taxonomy of common dolphins has been controversial, with two species, the short-beaked ( D. delphis) and long-beaked ( D. capensis) common dolphins, previously recognized but recently synonymized as D. delphis globally ( Society for Marine Mammalogy Committee on Taxonomy, 2024). The long-beaked common dolphin in the eastern Pacific Ocean has recently been suggested to represent a separate species, Delphinus bairdii ( Jefferson et al., 2024).
Common dolphin populations occur in warm-temperate and tropical waters globally, often divided into regional long-beaked and short-beaked forms, with the long-beaked forms typically most coastal while short-beaked forms are pelagic. The specimen sampled for the Darwin Tree of Life Project was of the short-beaked form. While common dolphins are listed as “Least Concern” globally by the IUCN (IUCNredlist.org, consulted 11 September, 2024), potential threats include bycatch in fishing gear, direct take by humans for food and shark bait, prey depletion, sonar produced by naval vessels, pollution, and climate change, especially for regional populations and ecotypes ( Perrin, 2018).
The genome of the saddleback dolphin, Delphinus delphis, 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. Here we present a chromosomally complete genome sequence for Delphinus delphis, based on one juvenile male specimen from Scrabster, Scotland, UK.
Genome sequence report
Sequencing data
The genome of a specimen of Delphinus delphis ( Figure 1) was sequenced using Pacific Biosciences single-molecule HiFi long reads, generating 101.59 Gb (gigabases) from 11.89 million reads. GenomeScope analysis of the PacBio HiFi data estimated the haploid genome size at 2,543.29 Mb, with a heterozygosity of 0.28% and repeat content of 22.24%. 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 29.0x coverage of the genome. Chromosome conformation Hi-C sequencing produced 450.46 Gb from 2,983.17 million reads. Table 1 summarises the specimen and sequencing information.
Photograph of the Delphinus delphis (mDelDel1) specimen used for genome sequencing.
Table 1.: Specimen and sequencing data for Delphinus delphis.
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 seven misjoins or missing joins. These interventions decreased the scaffold count by 0.32% and increased the scaffold N50 by 19.12%. The final assembly has a total length of 2,663.52 Mb in 630 scaffolds, with 968 gaps, and a scaffold N50 of 107.08 Mb ( Table 2).
Table 2.: Genome assembly data for Delphinus delphis.
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 Delphinus delphis, mDelDel1.2: 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 cetartiodactyla_odb10 set is presented at the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/GCA_949987515.2/dataset/GCA_949987515.2/snail.
Genome assembly of Delphinus delphis, mDelDel1.2: 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_949987515.2/dataset/GCA_949987515.2/blob.
Genome assembly of Delphinus delphis, mDelDel1.2: 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_949987515.2/dataset/GCA_949987515.2/cumulative.
Most of the assembly sequence (88.77%) was assigned to 23 chromosomal-level scaffolds, representing 21 autosomes and the X and Y sex chromosome. These chromosome-level scaffolds, confirmed by Hi-C data, are named according to size ( Figure 5; Table 3).
Genome assembly of Delphinus delphis: Hi-C contact map of the mDelDel1.2 assembly, produced in PretextView.Chromosomes are shown in order of size from left to right and top to bottom.
Table 3.: Chromosomal pseudomolecules in the genome assembly of Delphinus delphis, mDelDel1.
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 66.5. The k-mer recovery for the primary haplotype is 94.23%, and for the alternate haplotype 88.80%; the combined primary and alternate assemblies have a k-mer recovery of 99.59%. BUSCO v.5.5.0 analysis using the cetartiodactyla_odb10 reference set ( n = 13,335) identified 95.4% of the expected gene set (single = 93.3%, duplicated = 2.1%).
Table 2 provides assembly metric benchmarks adapted from Rhie et al. (2021) and the Earth BioGenome Project Report on Assembly Standards September 2024. The assembly achieves the EBP reference standard of 6.8.Q66.
Genome annotation report
The Delphinus delphis genome assembly (GCA_949987515.1) was annotated externally by Ensembl at the European Bioinformatics Institute (EBI). This annotation includes 37,871 transcribed mRNAs from 17,797 protein-coding and 4,628 non-coding genes. The average transcript length is 56,044.60. There are 1.66 coding transcripts per gene and 9.83 exons per transcript. For further information about the annotation, please refer to https://beta.ensembl.org/species/71bf5139-12df-415e-864d-b1bcb3e72746.
Methods
Sample acquisition
A juvenile male Delphinus delphis (specimen ID SAN00002608, ToLID mDelDel1) was collected from Scrabster, Highland, Scotland (latitude 58.6067, longitude –3.5503) on 2021-12-22. The specimen was collected and identified by Nick Davison (Scottish Marine Animal Stranding Scheme, University of Glasgow). A sample of lung tissue was collected at necropsy and preserved by freezing at –80 °C.
Metadata collection for samples adhered to the Darwin Tree of Life project standards described by Lawniczak et al. (2022).
Nucleic acid extraction
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of procedures: sample preparation and homogenisation, DNA extraction, fragmentation and purification. Detailed protocols are available on protocols.io ( Denton et al., 2023). The mDelDel1 sample was prepared for DNA extraction by weighing and dissecting it on dry ice ( Jay et al., 2023). Tissue from the lung was cryogenically disrupted using the Covaris cryoPREP ^®^ Automated Dry Pulverizer ( Narváez-Gómez et al., 2023). HMW DNA was extracted using the Manual MagAttract v1 protocol ( Strickland et al., 2023b). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system ( Todorovic 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., 2023a). 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 lung tissue of mDelDel1 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
Tissue from the lung of the mDelDel1 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 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 using 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 blobtoolkit pipeline is a Nextflow ( Di Tommaso et al., 2017) port of the previous Snakemake Blobtoolkit pipeline ( Challis et al., 2020). It aligns the PacBio reads in SAMtools and minimap2 ( Li, 2018) and generates coverage tracks for regions of fixed size. In parallel, it queries the GoaT database ( Challis et al., 2023) to identify all matching BUSCO lineages to run BUSCO ( Manni et al., 2021). For the three domain-level BUSCO lineages, the pipeline aligns the BUSCO genes to the UniProt Reference Proteomes database ( Bateman et al., 2023) with DIAMOND blastp ( Buchfink et al., 2021). The genome is also divided into chunks according to the density of the BUSCO genes from the closest taxonomic lineage, and each chunk is aligned to the UniProt Reference Proteomes database using DIAMOND blastx. Genome sequences without a hit are chunked using seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). The blobtools suite combines all these outputs into a blobdir for visualisation.
The blobtoolkit pipeline was developed using nf-core tooling ( Ewels et al., 2020) and MultiQC ( Ewels et al., 2016), relying on the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), as well as the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.
Table 4 contains a list of relevant software tool versions and sources.
Wellcome Sanger Institute – Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. The submission of materials by a Darwin Tree of Life Partner is subject to the ‘Darwin Tree of Life Project Sampling Code of Practice’, which can be found in full on the Darwin Tree of Life website here. By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are:
• Ethical review of provenance and sourcing of the material
• Legality of collection, transfer and use (national and international)
Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.
The reference list from the paper itself. Each links out to its DOI / PubMed record.
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