
==== Front
Wellcome Open Res
Wellcome Open Res
Wellcome Open Research
2398-502X
F1000 Research Limited London, UK

10.12688/wellcomeopenres.22453.1
Data Note
Articles
The genome sequence of the grey gurnard, Eutrigla gurnardus (Linnaeus, 1758)
[version 1; peer review: 2 approved, 1 approved with reservations]

Brittain Rachel Investigation Resources 1
Adkins Patrick Investigation Resources Writing – Original Draft Preparation Writing – Review & Editing 1
Harley Joanna Investigation Resources 1
Marine Biological Association Genome Acquisition Lab
Darwin Tree of Life Barcoding collective
Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team
Wellcome Sanger Institute Scientific Operations: Sequencing Operations
Wellcome Sanger Institute Tree of Life Core Informatics team
Tree of Life Core Informatics collective
Darwin Tree of Life Consortiuma
1 The Marine Biological Association, Plymouth, England, UK
a mark.blaxter@sanger.ac.uk
No competing interests were disclosed.

11 6 2024
2024
9 30720 5 2024
Copyright: © 2024 Brittain R et al.
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

We present a genome assembly from an individual Eutrigla gurnardus (the grey gurnard; Chordata; Actinopteri; Scorpaeniformes; Triglidae). The genome sequence is 680.5 megabases in span. Most of the assembly is scaffolded into 24 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.51 kilobases in length.

Eutrigla gurnardus
grey gurnard
genome sequence
chromosomal
Scorpaeniformes
Wellcome Trust206194 218328 This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328 </a>]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
==== Body
pmcSpecies taxonomy

Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Euteleosteomorpha; Neoteleostei; Eurypterygia; Ctenosquamata; Acanthomorphata; Euacanthomorphacea; Percomorphaceae; Eupercaria; Perciformes; Triglioidei; Triglidae; Eutrigla; Eutrigla gurnardus (Linnaeus, 1758) (NCBI:txid426098).

Background

Eutrigla gurnardus, commonly called the Grey Gurnard, is a demersal teleost fish belonging to the family Triglidae ( Figure 1). It is distributed in shelf seas and coastal waters from Norway, Greenland and Iceland in the north, to as far south as Mauritania and the Azores, including the Mediterranean and black sea ( Blanc & Hureau, 1979; Froese & Pauly, 2023; Hureau, 1986; Neudecker & Stein, 2011). E. gurnardus is commonly found on sandy/muddy-sand bottoms around the entire of the UK. It is traditionally more common in southern sites in the UK. However, its distribution has been shown to be changing in response to climatic changes ( Perry et al., 2005).

Figure 1. Photograph of Eutrigla gurnardus (not the specimen used for genome sequencing) (image by Clumpus).

E. gurnardus is typically grey or brownish in colour (occasionally dull red) and whitish ventrally. As with other members of the Triglidae family it has modified pectoral fins, the first three rays of which form slender tactile processes. It can be distinguished from other members of UK Triglidae by having short pectoral fins which do not reach as far back as the anal fin and by having spines along its lateral line.

A significant predator around much of the UK ( Daan et al., 1990), E. gurnardus feeds on a range of invertebrate species (mostly crustaceans) and small fish ( Weinert et al., 2010). During competition for food, it has been shown to make vocalisations in the form of grunts, growls and knocks ( Amorim et al., 2004).

In the past gurnards have not been split into their respective species when landed and have instead been treated as a single group. It has therefore been difficult to interpret fisheries data when trying to regard individual gurnard species. Even today, due to the low economic value of this species, it is likely that landing data does not accurately reflect the actual numbers of individuals caught, with the majority of gurnards being discarded after being caught alongside target demersal species such as flatfish ( Enever et al., 2007; Enever et al., 2009; ICES, 2006; ICES, 2012).

This genome represents the first of its kind for this Eutrigla gurnardus. It was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.

Genome sequence report

The genome was sequenced from one Eutrigla gurnardus collected using a trawl in Whitsand Bay, English Channel, UK (latitude 50.26, longitude –3.95). A total of 34-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 24 missing joins or mis-joins and removed 3 haplotypic duplications, reducing the scaffold number by 4.20%.

The final assembly has a total length of 680.5 Mb in 318 sequence scaffolds with a scaffold N50 of 29.2 Mb ( Table 1). The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3. The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla. Most (96.33%) of the assembly sequence was assigned to 24 chromosomal-level scaffolds. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 2). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.

Table 1. Genome data for Eutrigla gurnardus, fEutGur1.1.

Project accession data	
Assembly identifier	fEutGur1.1	
Species	Eutrigla gurnardus	
Specimen	fEutGur1	
NCBI taxonomy ID	426098	
BioProject	PRJEB64070	
BioSample ID	SAMEA111562159	
Isolate information	fEutGur1, gill tissue (PacBio DNA, Illumina Hi-C and RNA
sequencing)	
Assembly metrics *	Benchmark	
Consensus quality (QV)	55.6	≥ 50	
k-mer completeness	99.99%	≥ 95%	
BUSCO **	C:98.4%[S:97.7%,D:0.7%],F:0.4%,
M:1.3%,n:3,640	C ≥ 95%	
Percentage of assembly
mapped to chromosomes	96.33%	≥ 95%	
Sex chromosomes	None	localised homologous pairs	
Organelles	Mitochondrial genome: 16.51 kb	complete single alleles	
Raw data accessions	
PacificBiosciences Sequel IIe	ERR11673231	
Hi-C Illumina	ERR11679384, ERR11679385	
PolyA RNA-Seq Illumina	ERR11837500	
Genome assembly	
Assembly accession	GCA_963514095.1	
Accession of alternate haplotype	GCA_963514115.1	
Span (Mb)	680.5	
Number of contigs	872	
Contig N50 length (Mb)	2.4	
Number of scaffolds	318	
Scaffold N50 length (Mb)	29.2	
Longest scaffold (Mb)	37.75	
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from Rhie et al. (2021).

** BUSCO scores based on the actinopterygii_odb10 BUSCO set using version 5.3.2. 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/CAUPSS01/dataset/CAUPSS01/busco.

Figure 2. Genome assembly of Eutrigla gurnardus, fEutGur1.1: metrics.

The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 680,483,561 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 (37,750,515 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (29,198,404 and 20,162,171 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/CAUPSS01/dataset/CAUPSS01/snail.

Figure 3. Genome assembly of Eutrigla gurnardus, fEutGur1.1: BlobToolKit GC-coverage plot.

Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAUPSS01/dataset/CAUPSS01/blob.

Figure 4. Genome assembly of Eutrigla gurnardus, fEutGur1.1: BlobToolKit cumulative sequence plot.

The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/CAUPSS01/dataset/CAUPSS01/cumulative.

Figure 5. Genome assembly of Eutrigla gurnardus, fEutGur1.1: Hi-C contact map of the fEutGur1.1 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=T0CMcjkMSfGbGvPjIDJGGg.

Table 2. Chromosomal pseudomolecules in the genome assembly of Eutrigla gurnardus, fEutGur1.

INSDC accession	Chromosome	Length (Mb)	GC%	
OY741264.1	1	37.75	42.5	
OY741265.1	2	33.21	42.5	
OY741266.1	3	33.05	43.0	
OY741267.1	4	32.29	43.0	
OY741268.1	5	32.14	42.5	
OY741269.1	6	31.33	42.5	
OY741270.1	7	30.74	43.5	
OY741271.1	8	30.68	43.5	
OY741272.1	9	30.19	43.0	
OY741273.1	10	29.9	43.0	
OY741274.1	11	29.2	43.0	
OY741275.1	12	28.47	43.0	
OY741276.1	13	28.36	43.0	
OY741277.1	14	27.27	43.0	
OY741278.1	15	25.25	42.5	
OY741279.1	16	25.05	43.5	
OY741280.1	17	24.68	43.0	
OY741281.1	18	24.52	43.0	
OY741282.1	19	24.42	43.0	
OY741283.1	20	23.17	43.5	
OY741284.1	21	20.33	43.5	
OY741285.1	22	20.16	43.5	
OY741286.1	23	19.75	43.5	
OY741287.1	24	13.66	45.0	
OY741288.1	MT	0.02	48.5	

The estimated Quality Value (QV) of the final assembly is 55.6 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.3.2 completeness of 98.4% (single = 97.7%, duplicated = 0.7%), using the actinopterygii_odb10 reference set ( n = 3,640).

Metadata for specimens, BOLD barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://tolqc.cog.sanger.ac.uk/darwin/fish/Eutrigla_gurnardus/.

Methods

Sample acquisition and nucleic acid extraction

A Eutrigla gurnardus specimen (specimen ID MBA-211118-001A, ToLID fEutGur1) was collected from Whitsand Bay, English Channel, UK (latitude 50.26, longitude –3.95) on 29 April 2022. The specimen was taken from its habitat of sand and broken shell using an otter trawl deployed from RV Sepia. The specimen was identified by Rachel Brittain, Patrick Adkins and Joanna Harley (Marine Biological Association) based on gross morphology. The fish was first anesthetised and then overdosed using Aquased (2-phenoxyethanol). Destruction of the brain was used as a secondary method to ensure the animal was deceased before tissue sampling took place as in accordance with Schedule 1 methodology under the home office licence. Samples taken from the animal were preserved on dry ice.

The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. The sample was prepared for extraction at the Tree of Life Core Laboratory: tissue from the gills of fEutGur1 sample was weighed and dissected on dry ice ( Jay et al., 2023) and 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 with speed setting 31 ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Strickland et al., 2023): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.

RNA was extracted from gill tissue of fEutGur1 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.

Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023b).

Sequencing

Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit. DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences Sequel IIe (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from gill tissue of fEutGur1 using the Arima v2 kit. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation

Assembly was carried out with Hifiasm ( Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups ( Guan et al., 2020). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using YaHS ( Zhou et al., 2023). The assembly was checked for contamination and corrected using the TreeVal pipeline ( Pointon et al., 2023). Manual curation was performed using JBrowse2 ( Diesh et al., 2023), HiGlass ( Kerpedjiev et al., 2018) and PretextView ( Harry, 2022). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) or MITOS ( Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.

Final assembly evaluation

The final assembly was post-processed and evaluated with the three Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a), “sanger-tol/genomenote” ( Surana et al., 2023b), and “sanger-tol/blobtoolkit” ( Muffato et al., 2024). The pipeline sanger-tol/readmapping aligns the Hi-C reads with bwa-mem2 ( Vasimuddin et al., 2019) and combines the alignment files with SAMtools ( Danecek et al., 2021). The sanger-tol/genomenote pipeline transforms the Hi-C alignments into a contact map with BEDTools ( Quinlan & Hall, 2010) and the Cooler tool suite ( Abdennur & Mirny, 2020), which is then visualised with HiGlass ( Kerpedjiev et al., 2018). It also provides statistics about the assembly with the NCBI datasets ( Sayers et al., 2024) report, computes k-mer completeness and QV consensus quality values with FastK and MerquryFK, and a completeness assessment with BUSCO ( Manni et al., 2021).

The sanger-tol/blobtoolkit pipeline is a Nextflow port of the previous Snakemake Blobtoolkit pipeline ( Challis et al., 2020). It aligns the PacBio reads with SAMtools and minimap2 ( Li, 2018) and generates coverage tracks for regions of fixed size. In parallel, it queries the GoaT database ( Challis et al., 2023) to identify all matching BUSCO lineages to run BUSCO ( Manni et al., 2021). For the three domain-level BUSCO lineage, the pipeline aligns the BUSCO genes to the Uniprot Reference Proteomes database ( Bateman et al., 2023) with DIAMOND ( Buchfink et al., 2021) blastp. The genome is also split into chunks according to the density of the BUSCO genes from the closest taxonomically lineage, and each chunk is aligned to the Uniprot Reference Proteomes database with DIAMOND blastx. Genome sequences that have no hit are then chunked with seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). All those outputs are combined with the blobtools suite into a blobdir for visualisation.

All three pipelines were developed using the nf-core tooling ( Ewels et al., 2020), use MultiQC ( Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), and the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.

Table 3 contains a list of relevant software tool versions and sources.

Table 3. Software tools: versions and sources.

Software tool	Version	Source	
BEDTools	2.30.0	https://github.com/arq5x/bedtools2	
Blast	2.14.0	ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/	
BlobToolKit	4.3.7	https://github.com/blobtoolkit/blobtoolkit	
BUSCO	5.4.3	https://gitlab.com/ezlab/busco	
BUSCO	5.4.3 and 5.5.0	https://gitlab.com/ezlab/busco	
bwa-mem2	2.2.1	https://github.com/bwa-mem2/bwa-mem2	
Cooler	0.8.11	https://github.com/open2c/cooler	
DIAMOND	2.1.8	https://github.com/bbuchfink/diamond	
fasta_windows	0.2.4	https://github.com/tolkit/fasta_windows	
FastK	427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c	https://github.com/thegenemyers/FASTK	
GoaT CLI	0.2.5	https://github.com/genomehubs/goat-cli	
Hifiasm	0.16.1-r375	https://github.com/chhylp123/hifiasm	
HiGlass	1.11.6	https://github.com/higlass/higlass	
HiGlass	44086069ee7d4d3f6f3f0012569789ec138f42b84aa44357826c0b6753eb28de	https://github.com/higlass/higlass	
MerquryFK	d00d98157618f4e8d1a9190026b19b471055b22e	https://github.com/thegenemyers/MERQURY.FK	
MitoHiFi	3	https://github.com/marcelauliano/MitoHiFi	
MultiQC	1.14, 1.17, and 1.18	https://github.com/MultiQC/MultiQC	
NCBI Datasets	15.12.0	https://github.com/ncbi/datasets	
Nextflow	23.04.0-5857	https://github.com/nextflow-io/nextflow	
PretextView	0.2	https://github.com/wtsi-hpag/PretextView	
purge_dups	1.2.5	https://github.com/dfguan/purge_dups	
samtools	1.16.1, 1.17, and 1.18	https://github.com/samtools/samtools	
sanger-tol/genomenote	1.1.1	https://github.com/sanger-tol/genomenote	
sanger-tol/readmapping	1.2.1	https://github.com/sanger-tol/readmapping	
Seqtk	1.3	https://github.com/lh3/seqtk	
Singularity	3.9.0	https://github.com/sylabs/singularity	
TreeVal	1.0.0	https://github.com/sanger-tol/treeval	
YaHS	1.2a.2	https://github.com/c-zhou/yahs	

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.

Data availability

European Nucleotide Archive: Eutrigla gurnardus (grey gurnard). Accession number PRJEB64070; https://identifiers.org/ena.embl/PRJEB64070 ( Wellcome Sanger Institute, 2023). The genome sequence is released openly for reuse. The Eutrigla gurnardus genome sequencing initiative is part of the Darwin Tree of Life (DToL) project. All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1.

Author information

Members of the Marine Biological Association Genome Acquisition Lab are listed here: https://doi.org/10.5281/zenodo.8382513.

Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.

Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.

Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.

Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.

Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.

Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.

10.21956/wellcomeopenres.24740.r88060
Reviewer response for version 1
Cruz Fernando 1Referee https://orcid.org/0000-0003-4098-8829

1 Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
5 9 2024 Copyright: © 2024 Cruz F
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
Congratultaions to the authors. After  Chelidonichthys spinosus, this is the second chromosome-level reference genome available for the gunards (Family Triglidae) to date. The fEutGur1.1 assembly constitutes a valuable reference genome for this group and for Fish Genomics in general. The assembly meets by far the quality standards of the EBP and VGP.

I have three comments and recommendations about this note:

1. Please specify that by gunards you refer to Family Triglidae in the text. Non experts in fish taxonomy will appreciate this.

2. Please distinguish or split the total 24 missing joins or miss-joins into missing joins (to my knowledge "translocations) and mis-joins (to my knowledeg miss-assemblies).

3. Please add the version of PretextView PretexMap etc to Table 3.

Sincerely,

Fernando Cruz

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Genome Assembly and Population Genomics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

10.21956/wellcomeopenres.24740.r89427
Reviewer response for version 1
Bernardi Giacomo 1Referee https://orcid.org/0000-0002-8249-4678

1 University of California Santa Cruz, Santa Cruz, California, USA
13 8 2024 Copyright: © 2024 Bernardi G
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove
This is a very straightforward report of a genome assembly.

I have two very minor comments that pertain to the introduction: Fig 1. is the picture of the fish used for the genome not available?

what does 'this' mean in the sentence : This genome represents the first of its kind for this Eutrigla gurnardus my interpretation is that there might be crytic species that are expected and 'this' is the genome of 'this' cryptic species?

Are sufficient details of methods and materials provided to allow replication by others?

Yes

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Fish genomics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

10.21956/wellcomeopenres.24740.r89419
Reviewer response for version 1
Parey Elise 1Referee
1 University College London, London, England, UK
31 7 2024 Copyright: © 2024 Parey E
2024
https://creativecommons.org/licenses/by/4.0/ This is an open access peer review report distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Version 1recommendationapprove-with-reservations
This data note from the Darwin Tree of Life Consortium presents a high-quality chromosomes-scale genome assembly for the grey gurnard, as part of the consortium’s efforts to comprehensively sequence the UK eukaryotic biodiversity.

The reported completeness and contiguity statistics support the excellent quality of this new genomic resource. I only have one main concern: the presented Hi-C contact map (Figure 5) does not show the correct scaffolding of contigs into chromosomes. On this contact map, no chromosomes are visible, only the diagonal. Inspecting the complete set of supplemental QC figures available online ( https://tolqc.cog.sanger.ac.uk/darwin/fish/Eutrigla_gurnardus/), the post-scaffolding Hi-C map "Juicebox YaHS Hi-C map: fEutGur1" appears more informative, with chromosomes clearly visible. However, a small mis-assembly can be suspected on this map: the first ~third of chr1 seems to have more contact with chr24 than with the rest of chr1. This might have been corrected during the described manual curation rounds, but it cannot be verified on the presented contact map.

The methods are overall comprehensive. The Hi-C scaffolding steps could maybe be explained in more details: before scaffolding with YaHS, how were the Hi-C reads mapped and filtered? Finally, regarding the Quality Value (QV) it might be worth specifying that this relates to base accuracy (as opposed to structural accuracy), if I understood correctly.

Are sufficient details of methods and materials provided to allow replication by others?

Partly

Is the rationale for creating the dataset(s) clearly described?

Yes

Are the datasets clearly presented in a useable and accessible format?

Yes

Are the protocols appropriate and is the work technically sound?

Yes

Reviewer Expertise:

Genomics

I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Competing interests: No competing interests were disclosed.
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