The genome sequence of the Gelatinous Scale Worm, Alentia gelatinosa (Sars, 1835)

We present a genome assembly from an individual Alentia gelatinosa (Gelatinous Scale Worm); Annelida; Polychaeta; Phyllodocida; Polynoidae). The genome sequence is 1,237.5 megabases in span. Most of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.37 kilobases in length.


Background
The Gelatinous Scale Worm (Alentia gelatinosa) is a polynoid found under rocks and boulders in the intertidal shores of the north-east Atlantic, from Portugal to Norway.In the British Isles it is an abundant and recognisable worm, especially on western coasts.It is rare to absent in the south-east.As with other species in this family, it is typified by the presence of elytra attached to the dorsal surface.The elytra on A. gelatinosa are soft and overlap, covering the entire dorsum, with each scale being covered in cylindrical multifid micro-tubercles.When irritated, A. gelatinosa autotomise these scales and subsequently regrow them (Wilkie, 2011).The elytra give the worm a 'dirty white' colouration and distinctive gelatinous appearance.This genome contributes to the growing number of polynoid genomes sequenced as part of the Darwin Tree of Life Project, and provides the basis for comparative genomics and future work into the group's phylogeny (Lepidonotus clava (Darbyshire et al., 2022) Acholoe squamosa (Adkins et al., 2023a), Harmothoe impar (Adkins et al., 2023b) and Sthenelais limicola (Darbyshire et al., 2023)).

Genome sequence report
The genome was sequenced from one Alentia gelatinosa (Figure 1) collected from Hannafore Point, Looe, Cornwall, UK (50.34,.A total of 31-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 77 missing joins or mis-joins and removed 17 haplotypic duplications, reducing the assembly length by 0.79% and the scaffold number by 16.09%, and increasing the scaffold N50 by 0.39%.
The final assembly has a total length of 1237.5 Mb in 192 sequence scaffolds with a scaffold N50 of 79.0 Mb (Table 1).A summary of the assembly statistics is shown in Figure 2, 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 (99.33%) of the assembly sequence was assigned to 15 chromosomal-level scaffolds.Chromosomescale scaffolds confirmed by the Hi-C data are named in order of size (Figure 5; Table 2).Large heterozygous inversions were observed in the following regions: Chromosome 2: 34 Mb to 105 Mb; Chromosome 6: 2 Mb to 44 Mb; Chromosome 12: 21 Mb to 38.5 Mb.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/271774.

Genome assembly
Assembly accession GCA_950022655.1  RNA was extracted from mid-body tissue of wpAleGela1 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.NovaSeq 6000 (RNA-Seq) instruments.Hi-C data were also generated from tissue of wpAleGela1 using the Arima2 kit and sequenced 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    et al., 2023).The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021).Manual curation was performed using gEVAL, HiGlass (Kerpedjiev et al., 2018) and Pretext (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.
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

Software tool Version
This paper presents the genome sequence and chromosome-scale assembly of the annelid worm Alentia gelatinosa from a single specimen.The authors combined long-read DNA sequencing, Hi-C mapping and RNA sequencing to generate a high-quality resource for this species.The project is part of the Darwin Tree of Life Project and follows the protocols and best practices of the project.The data are presented clearly and raw data, assemblies and the analyses are available in open databases.The interested reader is encouraged to look at the very well presented interactive figures that make the analysis of the raw data accessible.An annotation of the genome will be presented through the Ensembl pipeline.The authors may consider posting an update or a comment linked to this paper once the annotation becomes available.
Is the rationale for creating the dataset(s) clearly described?

Stéphane Hourdez
Observatoire Océanologique de Banyuls, Sorbonne Université, Banyuls-sur-Mer, France This data paper reports the sequencing and assembly of the Polynoidae Alentia gelatinosa (Annelida, Polychaeta).The family Polynoidae is the most speciose (~1000 described species worldwide) of the scale worm families (Aphroditiformia).This genus is mono-specific and belongs to the subfamily Lepidonotinae, which also comprises Lepidonotus clava, already sequenced by the DToL initiative.This adds to the growing resources for the scale worm families.The methods used are proven and reliable.The resulting assembly is high quality and spans 1.24 Gbases, scaffolded into 15 chromosomal pseudomolecules (16-18 in other species).This will be a very valuable resource for the scientific community worldwide.In particular, 6 Polynoidae genomes are now available (4 shallow-water, 2 deep-sea hydrothermal vent), which allows comparative genomics studies.No major problem was found.A minor point is that with 4 sallow-water species (2 Lepidontinae, 1 Acholoinae and 1 Polynoinae), comparative studies could be carried out.In particular, genome size differences (ranging from 1 to 1.5 Gbases) could reflect partial genome duplications, or vast variations in transposable elements copies.He et al. 2023 have shown some important chromosomal translocations between Harmothoe impair and Branchipolynoe longqiensis.Can we find others compared to Alentia gelatinosa.

Methods
Sample acquisition and nucleic acid extraction An Alentia gelatinosa (specimen ID MBA-210330-010A, ToLID wpAleGela1) was collected by hand from Hannafore Point, Looe, Cornwall, UK (latitude 50.34, longitude -4.45) on 2021-03-30.The specimen was collected by Rob Mrowicki and Patrick Adkins (Marine Biological Association), identified by Patrick Adkins, and then preserved in liquid nitrogen.DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).The wpAleGela1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.

Figure 2 .
Figure 2. Genome assembly of Alentia gelatinosa, wpAleGela1.1: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 1,237,514,791 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 (180,793,948 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (79,000,438 and 50,631,370 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/Alentia%20gelatinosa/dataset/CATLOP01/snail.

Figure 5 .
Figure 5. Genome assembly of Alentia gelatinosa, wpAleGela1.1:Hi-C contact map of the wpAleGela1.1 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=Bvl6OQAaSkGkm3Niwl1GGQ.

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
Reviewer Expertise: annelid molecular biology, transcriptomics, neurobiology 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.
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