The genome sequence of the brown sea anemone, Metridium senile (Linnaeus, 1761)

We present a genome assembly from an individual Metridium senile (the brown sea anemone; Cnidaria; Anthozoa; Actiniaria; Metridiidae). The genome sequence is 390.9 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.44 kilobases in length.


Background
Metridium senile, the frilled or plumose sea anemone, is among the largest sea anemones, reaching up to one metre in height (Stephenson, 1928).Sea anemones, corals, jellyfish, and hydras constitute the oldest eumetazoan phylum, the Cnidaria.The class Anthozoa encompasses sea anemones (Actinaria) and reef-building scleractinian corals.Molecular phylogenetic analyses suggest that corals and sea anemones diverged approximately 500 million years ago (the late Cambrian or early Ordovician) (Shinzato et al., 2011).Metridium species are commonly found in coastal waters across the Northern Hemisphere, at depths ranging from the shallows to depths of up to 100 metres.
Metridium senile exhibits both sexual and asexual reproduction through pedal laceration (Glon et al., 2020;Hoffmann, 1976).The species is an oviparous broadcast spawner, undergoing external fertilisation upon release of gametes in late summer to early fall to produce free-swimming planula larvae (Lombardi & Lesser, 2010).The larva spends several months in the planktonic form before settling into a juvenile polyp (Sebens, 1981).
Metridium senile prevalence and distribution have made it a familiar sight to many marine enthusiasts and researchers alike (Glon et al., 2020).Metridium senile (Linné, 1761) was first described from Scandinavia and has since become well-documented in various regions, including the British Isles, northern Europe, and North America's Atlantic and Pacific coasts (Verrill, 1865;Verrill, 1870).Metridium was one of the first anemone species to be the subject of genetic research due to its accessibility as intertidal species and the known diversity in their body size, colour, and biotic processes as incidence or asexual reproduction (Bucklin & Hedgecock, 1982).The taxonomic history of the species has been challenging, as there has been long-term confusion about how to identify and apply the names of Metridium senile and Metridium dianthus (Ellis, 1768) of the north-eastern Atlantic.The name Metridium senile has been used for populations on both the northwestern and north-eastern Atlantic coasts and for populations in the North Pacific (Glon et al., 2020).Earlier biochemical genetic studies have corroborated morphological evidence that European populations constitute the subspecies M. s. senile (Linnaeus).North-western Atlantic representatives belong to the subspecies M. s. marginatum (Le Sueur), and southwestern Atlantic ones to M. s. lobatum (Carlgren).Furthermore, Metridium senile was classified into two distinct clusters, one containing clonal and one containing solitary individuals, with the large and solitary form later being raised to species level as Metridium farcimen (Brandt, 1834;Fautin et al., 1989).Of the six putative species in the genus Metridium, M. senile has the broadest range, with a circumboreal distribution that overlaps the distribution of nearly every other species in the genus (Fautin, 2016;Stephenson, 1928).Its high intra-population variation in anatomy, reproduction, and genetics, along with its geographic distribution, make the genome of Metridium senile an effective system in investigating the connection of genetic and morphological diversity.

Genome sequence report
The genome was sequenced one Metridium senile (Figure 1) collected from Queen Anne's Battery Marina visitors' pontoon, Plymouth, UK (50.36,.A total of 59-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 137 missing joins or mis-joins and removed 33 haplotypic duplications, reducing the assembly length by 1.44% and the scaffold number by 13.45%, and increasing the scaffold N50 by 0.86%. The final assembly has a total length of 390.9 Mb in 250 sequence scaffolds with a scaffold N50 of 20.8 Mb (Table 1).Most (97.85%) of the assembly sequence was assigned to 16 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.The estimated Quality Value (QV) of the final assembly is 55 with k-mer completeness of 99.99%, and the assembly has a BUSCO v5.3.2 completeness of 96.6% (single = 96.0%,duplicated = 0.6%), using the metazoa_odb10 reference set (n = 954).
Metadata for specimens, spectral estimates, sequencing runs, contaminants and pre-curation assembly statistics can be found at https://links.tol.sanger.ac.uk/species/6116.

Sample acquisition and nucleic acid extraction
A Metridium senile (specimen ID MBA-210326-002A, individual jaMetSeni4) was collected from Queen Anne's Battery Marina visitors' pontoon, Plymouth, UK (latitude 50.36, longitude -4.13) on 2021-03-26.The specimen was collected by John Bishop and Patrick Adkins, and identified by Rob Mrowicki and Patrick Adkins (all Marine Biological Association), and then preserved in liquid nitrogen.The specimen DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The jaMetSeni4 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.
Bodywall 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.Low molecular weight DNA was removed from a 20 ng aliquot of extracted DNA using the 0.8X AMpure XP  A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019) in the Cooler file format (Abdennur & Mirny, 2020).To assess the assembly metrics, the k-mer completeness and QV consensus quality values were calculated in Merqury (Rhie et al., 2020).This work was done using Nextflow (Di Tommaso et al., 2017) DSL2 pipelines   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

Christian Voolstra
Department of Biology, University of Konstanz, Konstanz, Germany The manuscript is a rather brief genome report on the sequencing and assembly of the Metridium senile genome; The background section lists rather old studies; it would be nice to add some more recent references for the last sentence/statement in the background section; For the Methods, it would be nice to provide a GitHub repo or similar that actually describe the detailed code used; for instance, the manual assembly curation is very brief: how were haplotypic duplications identified and removed?
The data availability section states the Project webpage, but the actual genome sequence is not download-able?Also, the genome is not annotated.I suppose this comes at a later stage, or there is an automated EMBL pipeline?but something to this regard should be stated to inform the interested researcher.

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: cnidarian/bacterial genome/transcriptome 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, however I have significant reservations, as outlined above.

Steinar Daae Johansen
Nord University, Bodø, Norway The current data note is well presented.The introduction gives an overview of taxonomic issues, and explains well the current status of Metridium senile sub-species.The DNA sequencing, assembly, and feature analyses follow the current practice at the "Darwin Tree of Life" consortium. 1.
The ca 391 Mb genome was found to be assigned to 16 chromosomal-like scaffolds.The total number of scaffolds (250) could have been significantly reduced if the authors, in addition to PacBio and Hi-C, also have applied Oxford Nanopore long-reads and ultra longreads.Great technical improvements have been made on ON sequencing the last couple of years.Anyway, ON is in my view not mandatory for this data note, but hopefully the consortium will consider this technology in future genome reports.

2.
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: Eukaryote genome sequencing, mitogenomics, RNA biology 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.Photographs of the Metridium senile (jaMetSeni4) specimen used for genome sequencing showing dorsal views of the retracted animal (A and B), and a lateral view of the column of the retracted animal (C).

Figure 2 .
Figure 2. Genome assembly of Metridium senile, jaMetSeni4.1: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 390,902,175 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 (66,427,095 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (20,827,098 and 16,127,631 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 metazoa_odb10 set is shown in the top right.An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Metridium%20senile/dataset/CATKSA01/snail.

Figure 3 .
Figure 3. Genome assembly of Metridium senile, jaMetSeni4.1: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/Metridium%20senile/dataset/CATKSA01/blob.

Figure 4 .
Figure 4. Genome assembly of Metridium senile, jaMetSeni4.1: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/Metridium%20senile/dataset/CATKSA01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Metridium senile, jaMetSeni4.1:Hi-C contact map of the jaMetSeni4.1 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=VIzq4JJXTx-ZKC8jiLPHTw.

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.

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