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 Patella caerulea. We generated ∼30 Gb of PacBio HiFi 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. BUSCO 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. 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 to other Patella species despite different annotation approaches. The present high-quality Patella caerulea reference genome, available on GenBank (BioProject: PRJNA1045377; Assembly: GCA_036850965.1), is an important resource for future ecological and evolutionary studies.

The genome of the rayed Mediterranean limpet Patella caerulea (Linnaeus, 1758) / G. Halstead-Nussloch, S.G. Signorini, M. Giulio, F. Crocetta, M. Munari, C. Della Torre, A.A. Weber. - In: GENOME BIOLOGY AND EVOLUTION. - ISSN 1759-6653. - 16:4(2024 Mar 28), pp. evae070.1-evae070.8. [10.1093/gbe/evae070]

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

S.G. Signorini
Secondo
;
C. Della Torre
Penultimo
;
2024

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 Patella caerulea. We generated ∼30 Gb of PacBio HiFi 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. BUSCO 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. 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 to other Patella species despite different annotation approaches. The present high-quality Patella caerulea reference genome, available on GenBank (BioProject: PRJNA1045377; Assembly: GCA_036850965.1), is an important resource for future ecological and evolutionary studies.
ERGA; PacBio HiFi; RNAseq; annotation; assembly; mollusc;
Settore BIO/07 - Ecologia
28-mar-2024
Article (author)
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/1042889
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