The genome sequence of the spiny starfish, Marthasterias glacialis (Linnaeus, 1758)

We present a genome assembly from an individual Marthasterias glacialis (the spiny starfish; Echinodermata; Asteroidea; Forcipulatida; Asteriidae). The genome sequence is 521 megabases in span. The majority of the assembly, 99.44%, is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, and is 16 kb in span.


Background
The spiny starfish, Marthasterias glacialis, is an opportunistic and generalist feeder distributed widely throughout Europe (https://www.sealifebase.ca/summary/Marthasterias). In England and Scotland, it is only found on the west coast, and the specimen sequenced here was captured on the Isle of Cumbrae in Scotland. It was found at a depth of about 4 metres on the northeast of the island, and processed in the lab of FSC Millport in August 2020. An image of the sequenced specimen just prior to processing is provided in Figure 1. Cytochrome Oxidase I studies of the species throughout Europe have shown that there are two divergent lineages in the Mediterranean (Pérez-Portela et al., 2010). This new reference genome will assist in better understanding population structure within the species across its full range.

Genome sequence report
The genome was sequenced from a single M. glacialis of unknown sex collected from Farland Point, Great Cumbrae, North Ayrshire, Scotland (latitude 55.746815, longitude -4.914907). A total of 49-fold coverage in Pacific Biosciences single-molecule long reads and 69-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 363 missing/misjoins and removed 42 haplotypic duplications, reducing the assembly size by 2.74% and scaffold number by 61.31%, and increasing the scaffold N50 by 37.41%.
The final assembly has a total length of 521 Mb in 106 sequence scaffolds with a scaffold N50 of 25 Mb (Table 1). Of the assembly sequence, 99.44% was assigned to 22 chromosomal-level scaffolds, representing 22 autosomes (numbered by sequence length) (Figure 2- Figure 5; Table 2). The assembly has a BUSCO (Simão et al., 2015) v5.1.2 completeness of 98.4% using the   metazoa_odb10 reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.  Leg tissue was cryogenically disrupted to a fine powder using a Covaris cryoPREP Automated Dry Pulveriser, receiving multiple impacts. Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. Low molecular weight DNA was removed from a 200-ng aliquot of extracted DNA using 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing. HMW DNA was sheared into an average fragment size between 12-20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the     et al., 2018) and Pretext. Regions of concern were identified and resolved using 10X longranger and genetic mapping data. The genome was analysed within the BlobToolKit environment (Challis et al., 2020). Table 3 contains a list of all software tool versions used, where appropriate.

Ethical/compliance issues
The materials that have contributed to this genome note were supplied by a Tree of Life collaborator. 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 undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Tree of Life collaborator, Genome Research

Shunsuke Yaguchi
Shimoda Marine Research Center, Tsukuba Daigaku, Tsukuba, Ibaraki Prefecture, Japan The manuscript describes the whole genome assembly of M. glacialis. The authors detail the sampling, reading, and assembly process of the genome. Thanks to recent advancements in sequencing and bioinformatics technologies, it has become much easier to read genomes of many non-model organisms compared to the previous decade. However, not many journals accept simple "read and assembled" genome papers like this manuscript. Therefore, I'm personally pleased to see this Data Note on genome reading in this journal.
Minor points; Why didn't the authors determine the specimen's sex? 1.
Which part of the leg (generally referred to as the arm by other reviewers) did the authors use for sampling? As the leg or arm is an organ and not a tissue, the authors need to indicate whether they used the whole leg (arm) or just a part of it.

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 In the legend of Figure 3 the authors state "Scaffolds labelled Chordata are spurious and assumed to reflect some confusion in the sequence databases from which data is pulled." I suggest that this issue should be resolved.
do not have expertise on the technical details of genome sequencing and 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, however I have significant reservations, as outlined above.