The genome sequence of a scale worm, Harmothoe impar (Johnston, 1839)

We present a genome assembly from an individual scale worm, Harmothoe impar; Annelida; Polychaeta; Phyllodocida; Polynoidae). The genome sequence is 1,512.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.37 kilobases in length.


Background
A scale worm found across the north-east Atlantic and into the Mediterranean, Harmothoe impar is often found under stones and inside kelp holdfasts, both intertidally and down to depths of 45 m.As with other polynoids, it is predatory, consuming small crustaceans and other small invertebrates, as well as being aggressive to the extent of cannibalisation to other members of the same species (Bentley & Serries, 1992;Wolff, 1973).H. impar is found in the gut contents of several commercially important, mostly bottom-feeding fish species (Pinnegar, 2014).
Polynoids are typified by the presence of scales called elytra across their dorsum.H. impar is distinguished from other UK Harmothoe species primarily by these elytra, which are strongly spined and papillated, covering the worm dorsally almost in its entirety (Figure 1C).The elytra have been shown in other members of the genus to be used by females to hold eggs, whilst ciliated tracks carry sperm towards them allowing direct fertilisation.The fertilised eggs are then brooded until released into the plankton as trochophores (Daly, 1972).Bioluminescence has also been recorded across the family and members of the genus (Livermore et al., 2018;Moraes et al., 2021), although it has yet to be described in this species.
The genome of Harmothoe impar was sequenced as part of the Darwin Tree of Life Project, a collaborative effort to sequence all named eukaryotic species in the Atlantic Archipelago of Britain and Ireland.This high-quality reference genome will provide the tools for further work with a variety of applications relating to this species.

Genome sequence report
The genome was sequenced from one Harmothoe impar specimen (Figure 1) collected from Batten Bay South, Devon, UK (50.36, -4.13).A total of 30-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 638 missing joins or mis-joins and removed 266 haplotypic duplications, reducing the assembly length by 9.71% and the scaffold number by 22.97%, and increasing the scaffold N50 by 12.34%.
The final assembly has a total length of 1,512.3Mb in 861 sequence scaffolds with a scaffold N50 of 83.4 Mb (Table 1).Most (96.89%) of the assembly sequence was assigned to 18 chromosomal-level scaffolds.Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2-Figure 5; Table 2).It appears that there are inversions between sister chromatids in the following approximate locations: Chromosome 1: 54-69 Mb, Chromosome 2: 14-80 Mb, Chromosome 12: 22-64 Mb, and Chromosome 14: 20-60 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/46595.

Sample acquisition and nucleic acid extraction
Harmothoe impar specimens were collected from Batten Bay South, Mount Batten, Devon, UK (latitude 50.36, longitude -4.13) on 2021-03-03.The specimens were taken by hand from underneath cobbles by Patrick Adkins and Rob Mrowicki   (Marine Biological Association).Patrick Adkins and Joanna Harley (Marine Biological Association) identified the specimens, which were then preserved in liquid nitrogen.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI).A sample of anterior body taken from specimen number wpHarImpa5 was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing.Anterior body 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 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 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 anterior body tissue of wpHarImpa6 in the Tree of Life Laboratory at the WSI using TRIzol, according to the manufacturer's instructions.RNA was 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 specimen wpHarImpa3 using the Arimav2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Figure 2 .
Figure 2. Genome assembly of Harmothoe impar, wpHarImpa5.1: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 1,512,319,410 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 (124,100,948 bp, shown in red). .Orange and pale-orange arcs show the N50 and N90 scaffold lengths (83,397,641 and 65,536,652 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/wpHarImpa5.1/dataset/CANHQG01/snail.

Figure 5 .
Figure 5. Genome assembly of Harmothoe impar, wpHarImpa5.1:Hi-C contact map of the wpHarImpa5.1 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=UxszSefoSW-pQuBgl6frig.

Table 3
contains a list of relevant software tool versions and sources.

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.

Table 3 . Software tools: versions and sources. Software tool Version 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.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
Reviewer Report 17 August 2023