The genome sequence of the King Ragworm, Alitta virens (Sars, 1835)

We present a genome assembly from an individual Alitta virens (the King Ragworm; Annelida; Polychaeta; Phyllodocida; Nereididae). The genome sequence is 671.2 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.83 kilobases in length.


Background
Alitta virens, commonly known as the King Ragworm, is a polychaete species from the family Nereididae. It is one of the larger intertidal polychaetes, reported by Chambers and Garwood (1992) as reaching up to 320 mm long with 160 chaetigers. It is common in sheltered muddy and sandy intertidal zones and estuaries throughout the UK and Europe (Chambers & Garwood, 1992;Kristensen, 1984). A. virens burrows into the sediment, feeding using a combination of deposit feeding and suspension feeding, the latter by using mucus nets (Herringshaw et al., 2010).
Reproduction most likely occurs in the same way as other ragworms such as Hediste diversicolor, where females release oocytes from their burrows to be fertilised by males. Larvae will settle in the upper intertidal zone and migrate to lower intertidal zone after approximately 3 years, but this may vary depending on habitat and size of the individual (Desrosiers et al., 1994;Kristensen, 1984).
A .virens preys on other invertebrate species but is also an important prey species for birds, fish and other crustaceans. Along with other species of large intertidal polychaete, it is also widely commercially and recreationally exploited worldwide, owing to its popularity as bait for recreational fishing. (Devon & Severn IFCA, 2019;Olive, 1994;Watson et al., 2017) Here we present the chromosomally complete genome sequence for A. virens, sequenced as part of the Darwin Tree of Life Project. It is hoped that this will provide further insight into the biology, ecology and evolution of A. virens and other nereid worms.

Genome sequence report
The genome was sequenced from one Alitta virens (Figure 1) collected from Newtown Quay Lagoon, England (50.72, -1.41). A total of 49-fold coverage in Pacific Biosciences singlemolecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 143 missing joins or mis-joins and removed 7 haplotypic duplications, reducing the assembly length by 0.23% and the scaffold number by 73.03%, and increasing the scaffold N50 by 6.68%.
The final assembly has a total length of 671.2 Mb in 24 sequence scaffolds with a scaffold N50 of 42.3 Mb (Table 1). Most (99.97%) of the assembly sequence was assigned to 14 chromosomal-level scaffolds. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size (Figure 2- Figure 5; Table 2). Repetitive scaffolds have been inserted into a repeat region of chromosome 4, but their order and orientation is uncertain. 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/880429.

Sample acquisition and nucleic acid extraction
An Alitta virens specimen (wpAliVire1) was collected from Newtown Quay Lagoon, UK (latitude 50.72, longitude -1.41) on 2020-10-11 using a pond net. The specimen was collected by Chris Fletcher (Natural History Museum) and Lyndall Pereira Da Conceicoa (Wellcome Sanger Institute) and identified by Chris Fletcher. Body tissue extracted from the specimen was preserved in liquid nitrogen. The remainder of the specimen was preserved in 80% ethanol and stored at the Natural History Museum, London.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute (WSI). The wpAliVire1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Posterior body tissue was disrupted using a Nippi Powermasher fitted with a BioMasher pestle. 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     Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from tissue of wpAliVire1 using the Arimav2 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 purge_dups (Guan et al., 2020). The assembly was scaffolded with Hi-C data (Rao et al., 2014) using YaHS (Zhou et al., 2023). The assembly was checked for contamination and corrected 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.
A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019)    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 • Legality of collection, transfer and use (national and international)  The genome sequence is released openly for reuse. The Alitta virens 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.

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