The genome sequence of the corkwing wrasse, Symphodus melops (Linnaeus, 1758) [version 1; peer review: awaiting peer review]

We present a genome assembly from an individual Symphodus melops (the corkwing wrasse; Chordata; Actinopteri; Labriformes; Labridae). The genome sequence is 636.4 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.5 kilobases in length.


Background
The corkwing wrasse Symphodus melops is a reef-associated fish. S. melops is non-migratory, occurring in the Eastern Atlantic from Norway to the Azores, and the Western Mediterranean and Adriatic seas, usually at depths ranging from 1 to 30 m (Froese & Pauly, 2023).
S. melops grow to 24 cm in length and live for nine years, and although they are not hermaphroditic, sex reversal has been observed (Darwall et al., 1992;Froese & Pauly, 2023;Uglem & Rosenqvist, 2002). As well as being sexually dimorphic, females generally being smaller and having less colourful brown colouring, Reproductive males also exhibit dimorphism: with 'sneaker' males mimicking the females' brown/grey colouring and dark blue urogenital papilla, whilst also being smaller than other males and females. This morph makes up 3 to 20% of all males (Uglem & Rosenqvist, 2002). Males of the second colour morph have a distinctive blue green colouration and are larger than female fish. The two different morphs additionally exhibit different reproductive behaviour, with the more colourful morph being territorial and building elaborate nests out of layers of algae, while the female mimic is non-territorial and does not build nests (Uglem & Rosenqvist, 2002). Since 1988, S. melops has been used commercially for its ability to remove parasite from other fish. Today, it is heavily fished in the British Isles and Scandinavia for use in salmonid aquaculture to reduce parasitic copepod loads (Halvorsen et al., 2016;Halvorsen et al., 2017).
Researchers suspect that the distribution of the corkwing wrasse is shifting northwards due to climatic changes, with significant genetic differences in microsatellite DNA fragments between the southern and northern conspecifics, where genetic separation has occurred due to morphological and depth changes to the seabed (Knutsen et al., 2013). The genome sequence reported here provides the basis for understanding the genetic diversity and phylogeography of this species.

Genome sequence report
The genome was sequenced from a Symphodus melops specimen ( Figure 1) collected from Hannafore Point, Looe, Cornwall,UK (50.34,. A total of 32-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 286 missing joins or mis-joins and removed 13 haplotypic duplications, reducing the scaffold number by 32%, and increasing the scaffold N50 by 9.25%. The final assembly has a total length of 636.4 Mb in 395 sequence scaffolds with a scaffold N50 of 27.6 Mb (Table 1). Most (98.48%) of the assembly sequence was assigned to 23 chromosomal-level scaffolds. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2- 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.
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/171736.

Sample acquisition and nucleic acid extraction
A Symphodus melops (specimen no. MBA-210624-004A, ToLID fSymMel2) was collected from Hannafore Point, Looe, Cornwall, UK (latitude 50.34, longitude -4.45) on 24 June 2021. The specimen was collected with a net from beneath Fucus serratus by Patrick Adkins (Marine Biological Association). The specimen was identified by Patrick Adkins and Joanna Harley based on gross morphology. The fish was first anaesthetised 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. The samples taken from the fish were preserved in liquid nitrogen.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The fSymMel2 sample  was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Muscle tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. HMW DNA was sheared into an average fragment size of 12-20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solidphase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample. 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 muscle tissue of fSymMel2 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer's instructions. RNA was then eluted in 50 μl RNAse-free water and its concentration assessed using a Nanodrop spectrophotometer and Qubit Fluorometer using the Qubit RNA Broad-Range (BR) Assay kit. Analysis of the integrity of the RNA was done using Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.

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 were performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from muscle tissue of fSymMel2

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 as described previously (Howe et al., 2021). Manual curation was performed using HiGlass (Kerpedjiev et al., 2018) and Pretext (Harry, 2022). The mitochondrial genome was assembled using MitoHiFi (Uliano-Silva et al., 2022), 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.
To evaluate the assembly, MerquryFK was used to estimate consensus quality (QV) scores and k-mer completeness (Rhie et al., 2020). The genome was analysed within the Blob-ToolKit environment (Challis et al., 2020) and BUSCO scores (Manni et al., 2021;Simão et al., 2015) were calculated. Table 3 contains a list of software tool versions and sources. 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  The genome sequence is released openly for reuse. The Symphodus melops 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.