Abstract
We present a genome assembly from an individual Trachurus trachurus (the Atlantic horse mackerel; Chordata; Actinopteri; Carangiformes; Carangidae). The genome sequence is 801 megabases in span. The majority of the assembly, 98.68%, is scaffolded into 24 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 25,797 protein coding genes.
Keywords: Trachurus trachurus, Atlantic horse mackerel, genome sequence, chromosomal
Species taxonomy
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata; Carangaria; Carangiformes; Carangidae; Trachurus; Trachurus trachurus (Linnaeus, 1758) (NCBI txid:36212).
Background
The Atlantic horse mackerel Trachurus trachurus (Linnaeus, 1758), also known as European horse mackerel or common scad, is northern Europe’s only resident representative of the Carangidae, a ray-finned fish family that includes the jacks, pompanos and trevallies. Trachurus trachurus is a benthopelagic shoaling species and is typically found at depths of less than 200 m. The species has a broad distribution, including Iceland, Northeast Atlantic continental shelf waters, the Mediterranean, and north-western African coastal waters at least as far as Ghana ( Healey et al., 2020). Atlantic horse mackerel are targeted by commercial fisheries using trawls, purse seines and long-lines. Major fished stocks are managed regionally. Those in Northeast Atlantic continental shelf waters are separated into a southern stock (Atlantic waters of the Iberian Peninsula), a western stock (shelf-edge seas from Bay of Biscay to the Norwegian coast, including spawning grounds of the Celtic Sea), and a North Sea stock (central and southern North Sea, including the Skagerrak and Kattegat) ( ICES, 2019). Total landings of 140,000 metric tonnes were reported in 2018, down from catches of over 450,000 metric tonnes in the mid 1990s. On the basis of declining abundance over sections of the species range, it has been listed as Vulnerable by the International Union for the Conservation of Nature ( Smith-Vaniz et al., 2015).
Genome sequence report
The genome was sequenced from a single T. trachurus of unknown sex collected from Southampton Water, off the coast of Hampshire, UK. A total of 105-fold coverage in Pacific Biosciences single-molecule long reads (N50 23 kb) and 64-fold coverage in 10X Genomics read clouds (from molecules with an estimated N50 of 22 kb) were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 141 missing/misjoins and removed 43 haplotypic duplications, reducing the scaffold number by 22.14%, increasing the scaffold N50 by 19.37% and decreasing the assembly length by 1.57%.
The final assembly has a total length of 801 Mb in 152 sequence scaffolds with a scaffold N50 of 35.4 Mb ( Table 1). The majority, 98.68%, of the assembly sequence was assigned to 24 chromosomal-level scaffolds, representing 24 autosomes (numbered by synteny to Oryzias latipes (Japanese medaka); GCF_002234675.1) ( Figure 1– Figure 4; Table 2). The assembly has a BUSCO v5.1.2 ( Manni et al., 2021) completeness of 98.6% using the actinopterygii_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.
Figure 1. Genome assembly of Trachurus trachurus, fTraTra1.2: metrics.
The BlobToolKit Snailplot 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 801,243,942 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 (40,754,244 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (35,447,499 and 25,462,409 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 actinopterygii_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/fTraTra1.2/dataset/CAJIMH02/snail.
Figure 4. Genome assembly of Trachurus trachurus, fTraTra1.2: Hi-C contact map.
Hi-C contact map of the fTraTra1.2 assembly, visualised in HiGlass. Chromosomes are given in order of size from top to bottom and left to right. The interactive Hi-C map can be viewed here.
Table 1. Genome data for Trachurus trachurus, fTraTra1.2.
| Project accession data | |
|---|---|
| Assembly identifier | fTraTra1.2 |
| Species | Trachurus trachurus |
| Specimen | BMNH 2021.3.19.1; fTraTra1 |
| NCBI taxonomy ID | NCBI:txid36212 |
| BioProject | PRJEB42240 |
| BioSample ID | SAMEA7524396 |
| Isolate information | Muscle |
| Raw data accessions | |
| PacificBiosciences SEQUEL II | ERR6445210 |
| 10X Genomics Illumina | ERX5643309, ERX5643310,
ERX5693250, ERX5693251 |
| Hi-C Illumina | ERR6054366-ERR6054368 |
| Genome assembly | |
| Assembly accession | GCA_905171665.2 |
| Accession of alternate haplotype | GCA_905171655.2 |
| Span (Mb) | 801 |
| Number of contigs | 374 |
| Contig N50 length (Mb) | 6.49 |
| Number of scaffolds | 152 |
| Scaffold N50 length (Mb) | 35.45 |
| Longest scaffold (Mb) | 40.75 |
| BUSCO * genome score | C:98.6%[S:97.8%,D:0.8%],
F:0.3%,M:1.1%,n:3640 |
| Genome annotation ** | |
| Number of protein-coding genes | 25,797 |
| Average length of protein-coding
gene (bp) |
1,811 |
| Average number of exons per
gene |
12 |
| Average exon size (bp) | 178 |
| Average intron size (bp) | 1,755 |
*BUSCO scores based on the actinopterygii_odb10 BUSCO set using v5.1.2. 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/fTraTra1.2/dataset/CAJIMH02/busco.
**Genome annotation provided for assembly fTraTra1.1.
Figure 2. Genome assembly of Trachurus trachurus, fTraTra1.2: GC coverage.
BlobToolKit GC-coverage plot. Scaffolds are coloured by phylum. Circles are sized in proportion to scaffold length. Histograms show the distribution of scaffold length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/fTraTra1.2/dataset/CAJIMH02/blob.
Figure 3. Genome assembly of Trachurus trachurus, fTraTra1.2: cumulative sequence.
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/fTraTra1.2/dataset/CAJIMH02/cumulative.
Table 2. Chromosomal pseudomolecules in the genome assembly of Trachurus trachurus, fTraTra1.2.
| INSDC accession | Chromosome | Size (Mb) | GC% |
|---|---|---|---|
| LR991628.1 | 1 | 40.75 | 41.8 |
| LR991651.1 | 2 | 15.47 | 42.7 |
| LR991630.1 | 3 | 40.66 | 41.5 |
| LR991635.1 | 4 | 36.09 | 41.9 |
| LR991633.1 | 5 | 36.89 | 41.7 |
| LR991634.1 | 6 | 36.28 | 41.9 |
| LR991638.1 | 7 | 35.45 | 42.0 |
| LR991642.1 | 8 | 33.05 | 42.4 |
| LR991632.1 | 9 | 37.40 | 41.9 |
| LR991631.1 | 10 | 38.57 | 41.8 |
| LR991641.1 | 11 | 33.39 | 42.1 |
| LR991645.1 | 12 | 29.58 | 41.6 |
| LR991629.1 | 13 | 40.70 | 42.2 |
| LR991640.1 | 14 | 33.71 | 41.8 |
| LR991643.1 | 15 | 31.05 | 41.9 |
| LR991639.1 | 16 | 35.01 | 41.9 |
| LR991637.1 | 17 | 35.71 | 42.0 |
| LR991646.1 | 18 | 29.25 | 42.0 |
| LR991650.1 | 19 | 25.33 | 42.2 |
| LR991648.1 | 20 | 25.46 | 42.2 |
| LR991636.1 | 21 | 35.83 | 41.7 |
| LR991644.1 | 22 | 30.60 | 42.2 |
| LR991649.1 | 23 | 25.35 | 42.1 |
| LR991647.1 | 24 | 29.13 | 42.0 |
| LR991652.1 | MT | 0.02 | 46.5 |
| - | Unplaced | 10.50 | 31.6 |
Gene annotation
The Ensembl gene annotation system ( Aken et al., 2016) was used to generate annotation for the T. trachurus assembly (GCA_905171665.1). 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 vertebrate proteins from UniProt ( UniProt Consortium, 2019) and coordinate mapping of GENCODE ( Frankish et al., 2019) mouse reference annotations via a pairwise whole genome alignment. The resulting Ensembl annotation includes 60,310 transcripts assigned to 25,797 coding and 2,264 non-coding genes ( Trachurus trachurus - Ensembl Rapid Release).
Methods
Sample acquisition, DNA extraction and sequencing
A single T. trachurus of unknown sex was collected in January 2017 from near Marchwood Power Station in Southampton Water, off the coast of Hampshire, UK (latitude 50.901563, longitude -1.440836) by Rupert Collins as part of the SeaDNA project.
DNA was extracted using an agarose plug extraction from muscle tissue following the Bionano Prep Animal Tissue DNA Isolation Soft Tissue Protocol. Pacific Biosciences CLR long read and 10X Genomics read cloud sequencing libraries were constructed according to the manufacturers’ instructions. Sequencing was performed by the Scientific Operations core at the Wellcome Sanger Institute on Pacific Biosciences SEQUEL II and Illumina HiSeq X instruments. Hi-C data were generated from muscle tissue using the Arima Hi-C kit and sequenced using a HiSeq X instrument.
Genome assembly
Assembly was carried out following the Vertebrate Genome Project pipeline ( Rhie et al., 2020) with Falcon-unzip ( Chin et al., 2016). Haplotypic duplication was identified and removed with purge_dups ( Guan et al., 2020) and a first round of scaffolding carried out with 10X Genomics read clouds using scaff10x. Scaffolding with Hi-C data ( Rao et al., 2014) was carried out with SALSA2 ( Ghurye et al., 2019). The Hi-C scaffolded assembly was polished with arrow using the PacBio data, then polished with the 10X Genomics Illumina data by aligning to the assembly with longranger align, calling variants with freebayes ( Garrison & Marth, 2012) and applying homozygous non-reference edits using bcftools consensus. Two rounds of the Illumina polishing were applied. The mitochondrial genome was assembled using the mitoVGP pipeline ( Formenti et al., 2021). The assembly was checked for contamination and corrected using the gEVAL system ( Chow et al., 2016) as described previously ( Howe et al., 2021). Manual curation ( Howe et al., 2021) was performed using gEVAL, HiGlass ( Kerpedjiev et al., 2018) and Pretext. The genome was analysed and BUSCO scores generated using BlobToolKit ( Challis et al., 2020). Table 3 contains a list of all software tool versions used, where appropriate.
Table 3. Software tools used.
| Software tool | Version | Source |
|---|---|---|
| Falcon_unzip | 1.4.2 | Chin et al., 2016 |
| purge_dups | 1.0.1 | Guan et al., 2020 |
| scaff10x | 4.1 | https://github.com/wtsi-hpag/Scaff10X |
| SALSA2 | 2.2 | Ghurye et al., 2019 |
| arrow | GCpp-1.9.0 | https://github.com/PacificBiosciences/GenomicConsensus |
| freebayes | 1.3.1-17-gaa2ace8 | Garrison & Marth, 2012 |
| mitoVGP | 2.2 | Formenti et al., 2021 |
| gEVAL | N/A | Chow et al., 2016 |
| HiGlass | 1.11.6 | Kerpedjiev et al., 2018 |
| PretextView | 0.1.x | https://github.com/wtsi-hpag/PretextView |
| BlobToolKit | 2.6.4 | Challis et al., 2020 |
Data availability
European Nucleotide Archive: Trachurus trachurus (Atlantic horse mackerel). Accession number PRJEB42240; https://identifiers.org/ena.embl/PRJEB42240.
The genome sequence is released openly for reuse. The T. trachurus genome sequencing initiative is part of the Darwin Tree of Life (DToL) project and Vertebrate Genome Project (VGP). The specimen has been frozen and deposited with the Natural History Museum, London under registration number BMNH 2021.3.19.1, where it will remain accessible to the research community for posterity. All raw sequence data and the assembly have been deposited in INSDC databases. Raw data and assembly accession identifiers are reported in Table 1.
Funding Statement
This work was supported by the Wellcome Trust through core funding to the Wellcome Sanger Institute (206194) and the Darwin Tree of Life Discretionary Award (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: 3 approved]
Author information
Members of the Wellcome Sanger Institute Tree of Life programme are listed here: https://doi.org/10.5281/zenodo.6125027.
Members of Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective are listed here: https://doi.org/10.5281/zenodo.5746904.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.6125046.
Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.5638618.
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