The genome sequence of the John Dory, Zeus faber Linnaeus, 1758

We present a genome assembly from an individual Zeus faber (the John Dory; Chordata; Actinopteri; Zeiformes; Zeidae). The genome sequence is 804.7 megabases in span. Most of the assembly is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.72 kilobases in length.


Background
John Dory, Zeus faber Linnaeus, 1758, also known as St Peter's fish, is a solitary, demersal marine fish characterised by a laterally compressed body of golden-brown colouration with a black spot on either side and long dorsal spines (Wheeler, 1978).It is widely distributed in the eastern Atlantic, Mediterranean, Pacific and Indian Oceans, and along the entire West African coast, typically occupying depths of 0-200 m (Iwamoto, 2015;Maravelias et al., 2007).Recently, it has been recorded for the first time in the Black Sea (Aydın & Karadurmuş, 2023).John Dory has a large, highly protrusible mouth allowing it to predate on relatively large fish which they target using well-developed eyes (Kim et al., 2020;Stergiou & Fourtouni, 1991).
In the eastern Mediterranean, John Dory begins its life feeding on small zooplankton, such as mysids, until it reaches a total length (TL) of approximately 80 mm (Stergiou & Fourtouni, 1991).It gradually switches to small benthopelagic fishes then, as it grows, it predates on larger schooling pelagic teleosts (Kim et al., 2020;Stergiou & Fourtouni, 1991).In Korean coastal waters there is also varying diet composition with size and age (Kim et al., 2020).Off the Portuguese coast however, there is no prey switching from juvenile to adult life stages (Silva, 1999).Predominantly, evidence suggests it is an opportunistic feeder, switching prey depending on food availability and abundance which can vary seasonally and with life stage (Kim et al., 2020).Recently, meso-and microplastics have been found to occur in the gastrointestinal tracts of Z. faber in the Mediterranean (Bottari et al., 2019).
Z. faber is known to make 'croaking' or 'barking' noises upon capture onboard (Radford et al., 2018).These vocalisations have since been documented in-situ in Australia and were found to induce an escape response in conspecifics and heterospecifics such as the Australian Snapper (Pagurus auratus), suggesting they make sounds as a territorial display against competitors (Radford et al., 2018).
John Dory is a commercially important species valued for human consumption, meal, and fish oil, as well as being important as a gamefish and in the aquarium trade (Iwamoto, 2015).It has been a prominent species in mixed species trawl fisheries in the British Isles and is a notable by-catch species for trawl gears globally (Dunn, 2001;Iwamoto, 2015).Despite being a highly regarded food fish, the only stock assessment for the British Isles, to our knowledge, was carried out between April 1994and March 1996(Dunn, 2001).Dunn describes landings from commercial fisheries in England and Wales alongside biological samples and catch data from the English Channel.John Dory was most abundant in the south and southwest of the British Isles (Dunn, 2001;Wheeler, 1969).Evidence suggests that the English Channel is a seasonal nursery ground for Z. faber: seasonal peaks in landings coincided with the period of recruitment, in this case during quarters three and four, when individuals were just over 1 year old at the transition between juvenile and adult life stages species (Dunn, 2001).Recruitment total length of the species was approximately 23 cm TL.Most commercial landings were in the range 23-29 cm TL with a maximum observed TL of 59 cm.Mean TL of first maturity was approximately 26 cm for males and 34.5 cm for females.The global conservation status of this species was last assessed in 2013, deemed 'Data Deficient' on the IUCN Red List (Iwamoto, 2015), which reflects the lack of historical data and biological information for this species (Dunn, 2001).Because of this, stock status and fishing pressure is uncertain for Z. faber.
In the Northeast Atlantic (FAO area 27), consuming John Dory may prove harmful to human health, as mercury levels of 0.68 ± 0.07 μg g −1 exceed the maximum limit deemed safe for human consumption (0.5 μg g −1 ) (Vieira et al., 2021).John Dory imported from Senegal and sold in Turkish fish markets, as well as individuals caught around Turkey, have also been found to carry larvae of the nematode Anisakis pegreffii, with potential implications for human health if consumed (Pekmezci, 2019;Yardimci et al., 2014).
Molecular investigation of this species has shown significant genetic differentiation (7.44%) between clades in the North Atlantic/Mediterranean region and Australasia, indicating the possibility that they have speciated (Ward et al., 2008).The first genome of Z. faber was generated in 2016 for a study that suggests immune-related genes play an important role in teleost evolution and speciation (Malmstrøm et al., 2016).Here we present the second published genome of John Dory, collected and sequenced as part of the Darwin Tree of Life project (Blaxter et al., 2022).This dataset will be important for furthering our understanding of teleost pathology, immunology, evolution and phylogenetics (Malmstrøm et al., 2016;Ward et al., 2008).

Genome sequence report
The genome was sequenced from an individual Zeus faber (Figure 1) collected from Bigbury Bay, UK (50.27,.A total of 43-fold coverage in Pacific Biosciences singlemolecule HiFi long reads was generated.Primary assembly contigs were scaffolded with chromosome conformation Hi-C data.Manual assembly curation corrected 9 missing joins or mis-joins, reducing the scaffold number by 1.04%. The final assembly has a total length of 804.7 Mb in 190 sequence scaffolds with a scaffold N50 of 34.5 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 (97.08%) of the assembly sequence was assigned to 22 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.

Genome assembly
Assembly accession GCA_960531495.1       mitochondrial contig and to ensure the general quality of the sequence.
Table 3 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

Nastaran Mazloumi
University of Tasmania Institute for Marine and Antarctic Studies, Hobart, Tasmania, Australia

Title:
The chosen title "The genome sequence of the John Dory, Zeus faber Linnaeus, 1758" lacks clarity and intention.You need to choose a better tile to define why you have done this study and what the genome sequestration is going to do! Background: In the background section, this paragraph below is disjointed and very hard to follow: "John Dory is a commercially important species valued for human consumption, meal, and fish oil, as well as being important as a gamefish and in the aquarium trade (Iwamoto, 2015).It has been a prominent species in mixed species trawl fisheries in the British Isles and is a notable by-catch species for trawl gears globally (Dunn, 2001;Iwamoto, 2015).Despite being a highly regarded food fish, the only stock assessment for the British Isles, to our knowledge, was carried out between April 1994and March 1996(Dunn, 2001).Dunn describes landings from commercial fisheries in England and Wales alongside biological samples and catch data from the English Channel.John Dory was most abundant in the south and southwest of the British Isles (Dunn, 2001;Wheeler, 1969).Evidence suggests that the English Channel is a seasonal nursery ground for Z. faber: seasonal peaks in landings coincided with the period of recruitment, in this case during quarters three and four, when individuals were just over 1 year old at the transition between juvenile and adult life stages species (Dunn, 2001).Recruitment total length of the species was approximately 23 cm TL.Most commercial landings were in the range 23-29 cm TL with a maximum observed TL of 59 cm.Mean TL of first maturity was approximately 26 cm for males and 34.5 cm for females.The global conservation status of this species was last assessed in 2013, deemed 'Data Deficient' on the IUCN Red List (Iwamoto, 2015), which reflects the lack of historical data and biological information for this species (Dunn, 2001).Because of this, stock status and fishing pressure is uncertain for Z. faber".
This paragraph provides valuable information for reader but it significantly lacks clarity and confinement.For instance, human health issues with over the threshold elements in the flesh is one argument, data deficient stock assessment is another argument.Similarly, the genetically distinguished populations in different parts of the world that is discussed in the following paragraph, is another statement: "Molecular investigation of this species has shown significant genetic differentiation (7.44%) between clades in the North Atlantic/Mediterranean region and Australasia, indicating the possibility that they have speciated (Ward et al., 2008).The first genome of Z. faber was generated in 2016 for a study that suggests immune-related genes play an important role in teleost evolution and speciation (Malmstrøm et al., 2016).Here we present the second published genome of John Dory, collected and sequenced as part of the Darwin Tree of Life project (Blaxter et al., 2022).This dataset will be important for furthering our understanding of teleost pathology, immunology, evolution and phylogenetics (Malmstrøm et al., 2016;Ward et al., 2008)" -this confuse the reader as to why this study is important and why you made efforts to sequence genomes for John Dory.
Background section, requires substantial revision in term of clarity and confinement and more importantly the message the author want to communicate with the reader as to why they have done this study and what gaps this is going to fill and how it serves the intention of the study.It needs to be specifically clarified as to whether this is for seafood industry and human health matter, or conservation matter?Or even management of the stock?What is the main intention here.without this valuable bit, it is not recommended to jump into the methodology and analysis.

Summary:
Despite my encouragement for scientists to publish their work, I must admit that this particular research lacks clarity and conciseness.Therefore, I have no choice but to recommend rejection and suggest resubmission after thorough revisions, including expanding the research and writing in a more concise manner.This manuscript presents the genome sequence of a fish species (John Dory) that is in general poorly studied and for which conservation strategies can not be appropriately defined.
Considering that understanding the genetic connectivity is critical for defining management units, and that full genomes facilitate the analysis and interpretation of population genomic data, this study is considered important for improving the conservation of the John Dory.The methods are well described and the results are pertinent.I have only one comment that I think the authors can address easily: -In the introduction they should better explain what is the knowledge of this species in terms of how many populations exist and potential subspecies.The data of "significant genetic differentiation (7.44%) between clades in the North Atlantic/Mediterranean region and Australasia" seem to be taken from the abstract of a cited paper, but there is not much information here to understand what is the main issue that could be resolved with the help of a full genome sequence.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Population genomics, molecular evolution, high-throughput sequencing data analysis 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.

Shawn M. Burgess
National Human Genome Research Institute, Bethesda, USA Adkins and colleagues have submitted a manuscript describing the genomic assembly of a John Dory fish (Zeus faber).The sequencing was performed using PacBio HiFi and Hi-C data and the assembly using hifiasm and manual curation.The resulting assembly exceeds general benchmarks for high-quality assemblies including scoring for BUSCO, k-mer completeness, and percentage of sequence mapped to chromosomes.All raw and analyzed datasets are deposited in publicly available repositories.The data are clear, the approaches adequately documented.I have no substantial objections to any of the data presented.It should be a very useful assembly for researchers who are interested in John Dory biology.

Is the rationale for creating the dataset(s) clearly described? Yes
Are the protocols appropriate and is the work technically sound?Yes

Are sufficient details of methods and materials provided to allow replication by others? Yes
Are the datasets clearly presented in a useable and accessible format?Yes Competing Interests: No competing interests were disclosed.
Reviewer Expertise: Zebrafish genetics and genomics.Fish genome assembly.
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.

Figure 1 .
Figure 1.Photograph of the Zeus faber (fZeuFab8) specimen used for genome sequencing.

Figure 2 .
Figure 2. Genome assembly of Zeus faber, fZeuFab8.1: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 804,731,948 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 (65,762,550 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (34,476,449 and 28,869,016 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/fZeuFab8_1/dataset/fZeuFab8_1/snail.

Figure 3 .
Figure 3. Genome assembly of Zeus faber, fZeuFab8.1: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/fZeuFab8_1/dataset/fZeuFab8_1/blob.

Figure 4 .
Figure 4. Genome assembly of Zeus faber, fZeuFab8.1: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/fZeuFab8_1/dataset/fZeuFab8_1/cumulative.

Figure 5 .
Figure 5. Genome assembly of Zeus faber, fZeuFab8.1:Hi-C contact map of the fZeuFab8.1 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=ODHdK-fnRfy3tLmo69JGwQ.

Is the rationale for creating the dataset(s) clearly described? No Are the protocols appropriate and is the work technically sound? Partly Are sufficient details of methods and materials provided to allow replication by others? No Are the datasets clearly presented in a useable and accessible format? No Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.