The genome sequence of the blue-rayed limpet, Patella pellucida Linnaeus, 1758

We present a genome assembly from an individual Patella pellucida (the blue-rayed limpet; Mollusca; Gastropoda; Patellidae). The genome sequence is 712 megabases in span. The majority of the assembly (99.85%) is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial genome was assembled and is 14.9 kilobases in length.


Background
The blue-rayed limpet is a subtidal species, typically found on macroalgae (Sá-Pinto et al., 2005). Its range extends from Norway to Portugal ("Handbook of the Marine Fauna of North-West Europe", 2017). The scientific name reflects the dish-like shape (Patella) of the translucent (pellucida) shell and the common name describes the striking dashed stripes of iridescent blue down its shell. The underlying features that result in these iridescent blue rays have recently been described (Li et al., 2015). These authors speculate that the stripes are present to mimic toxic gastropods and ward off predators though this does not appear to have been tested yet. The blue-rayed limpet is a broadcast spawner, releasing one egg at a time that is externally fertilised. Individuals are thought to have a typical lifespan of about a year, with only a small portion of individuals continuing on into a second year ("Blue-Rayed Limpet (Patella Pellucida)", 2019).

Genome sequence report
The genome was sequenced from a single P. pellucida ( Figure 1) collected from Farland Point, Great Cumbrae, North Ayrshire, UK (latitude 55.74629, longitude -4.911721). A total of 31-fold coverage in Pacific Biosciences single-molecule long reads and 55-fold coverage in 10X Genomics read clouds were generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 309 missing/misjoins and removed 29 haplotypic duplications, reducing the assembly size by 1.72% and the scaffold number by 71.56%, and increasing the scaffold N50 by 162.71%.
The final assembly has a total length of 712 Mb in 62 sequence scaffolds with a scaffold N50 of 87.2 Mb (Table 1). Of the assembly sequence, 99.85% was assigned to 9 chromosomal-level scaffolds (numbered by sequence length) (Figure 2- Figure 5; Table 2). Chromosome 2 contains a large inversion between sister chromatids at approximately 15.43-87.97 Mb. The inversion spans the majority of the 91.75 Mb chromosome. The assembly has a BUSCO v5.1. 2 (Manni et al., 2021) completeness of 87.6% (single 86.7%, duplicated 0.8%) using the mollusca_odb10 reference set (n=5295). However, we believe that this relatively low BUSCO score is a result of limitations with the current mollusca_odb10 geneset. Using the metazoa_odb10 reference set (n=954), the assembly has a completeness of 97.5% (single 96.9%, duplicated 0.6%), which we believe is evidence of high completeness. This value also compares favourably with the 91.5% completeness value obtained by (Kang et al., 2020) for the transcriptome of related limpet, Patella vulgata, using the metazoa_odb reference set. While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited.

Sample acquisition and nucleic acid extraction
A total of three P. pellucida specimens (xgPatPell1, xgPatPell2, xgPatPell3) were collected from Farland Point, Great Cumbrae, North Ayrshire, UK (latitude 55.74629, longitude -4.911721) by Mara Lawniczak, Wellcome Sanger Institute, by hand from a sheltered rocky shore and boulder cove (old red sandstone bedrock; boulders sandstone and diorite from local dykes). The samples were identified by the same individual and snap-frozen on dry ice.
DNA was extracted at the Tree of Life laboratory, Wellcome Sanger Institute. The xgPatPell1 sample was weighed and dissected on dry ice with the shell removed. Whole organism 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 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.   (Allio et al., 2020). The assembly was checked for contamination and corrected using the gEVAL  and Pretext. 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.   Institute. Raw data and assembly accession identifiers are reported in Table 1.

Yes Yes
Are the datasets clearly presented in a useable and accessible format? Partly can be verified.

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