The genome of the rayed Mediterranean limpet Patella caerulea (Linnaeus, 1758)

Abstract

Patella caerulea (Linnaeus, 1758) is a mollusc limpet species of the class Gastropoda. Endemic to the Mediterranean Sea, it is considered a keystone species due to its primary role in structuring and regulating the ecological balance of tidal and subtidal habitats. It is currently being used as a bioindicator to assess the environmental quality of coastal marine waters and as a model species to understand adaptation to ocean acidification. Here, we provide a high-quality reference genome assembly and annotation for P. caerulea. We generated ∼30 Gb of Pacific Biosciences high-fidelity data from a single individual and provide a final 749.8 Mb assembly containing 62 contigs, including the mitochondrial genome (14,938 bp). With an N50 of 48.8 Mb and 98% of the assembly contained in the 18 largest contigs, this assembly is near chromosome-scale. Benchmarking Universal Single-Copy Orthologs scores were high (Mollusca, 87.8% complete; Metazoa, 97.2% complete) and similar to metrics observed for other chromosome-level Patella genomes, highlighting a possible bias in the Mollusca database for Patellids. We generated transcriptomic Illumina data from a second individual collected at the same locality and used it together with protein evidence to annotate the genome. A total of 23,938 protein-coding gene models were found. By comparing this annotation with other published Patella annotations, we found that the distribution and median values of exon and gene lengths was comparable with other Patella species despite different annotation approaches. The present high-quality P. caerulea reference genome, available on GenBank (BioProject: PRJNA1045377; assembly: GCA_036850965.1), is an important resource for future ecological and evolutionary studies.

Keywords: ERGA; PacBio HiFi; RNAseq; annotation; assembly; mollusc.

Fig. 1.

P. caerulea reference specimens and reference genome. A) Ventral view of a typical specimen of P. caerulea. B) Dorsal view of P. caerulea specimens collected in San Pietro, Italy. This is the same locality where the P. caerulea individuals used for genome and transcriptome sequencing were collected. C) Cumulative sum of contig length (bp), ordered by contig length. D) Annotation feature comparison with other Patella annotations available on NCBI. Distribution and median values for gene and exon length are similar between species.