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Crocetta, F.

Publications and source records attributed to Crocetta, F..

3 recordsLinked to original sources

Under pressure: Evolutionary trade-offs shape the single visual opsin of deep-sea octopods

Octopods possess remarkable camera-type eyes and specialised image-forming vision that support orientation, prey detection, predator avoidance and visual communication. Unlike vertebrates and arthropods, however, octopod vision is thought to rely mainly on a single rhodopsin (r-opsin1), raising the question of how such a constrained system adapts across contrasting light environments from shallow coastal waters to deep-sea habitats. Using transcriptional profiling of the retina and optic lobe from seven native octopod species of the Gulf of Naples, we show that r-opsin1 is the predominant visual gene across all species and investigate how contrasting photic habitats have shaped its molecular and functional evolution. Although positive selection analyses revealed no general association between habitat depth and r-opsin1 evolution, twelve codons in the deep-mesopelagic Pteroctopus tetracirrhus r-opsin1 showed evidence of positive selection, including two residues located on opposing helices of the retinal-binding pocket. In vitro experiments demonstrated that substituting either I87V and F201N produced a marked bathochromatic shift from the wild-type blue-green spectrum towards red wavelengths, whereas their combination restored the wild-type spectral profile. Other deep-sea octopod r-opsin1 naturally bearing one of these substitutions retained blue-green sensitivity. Reconstructed ancestral proteins similarly maintained blue-green absorption, supporting conservation of this spectral phenotype throughout octopod r-opsin1 evolution. We further show that F201N reduces adiabatic compressibility within the retinal-binding pocket, by co-evolving compensatory sites offering a structural trade-off, favouring pressure adaptation while restraining spectral tuning. Together, our findings support that octopod visual rhodopsin evolution has been shaped by the multiple ecological pressures of contrasting marine environments, illustrated with lineage-specific and habitat-dependent trajectories on a single locus while preserving a conserved visual phenotype.

evolutionary biology↗

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

Patella caerulea (Linnaeus, 1758) is a molluscan limpet species of the class Gastropoda. Endemic to the Mediterranean Sea, it is considered to be a keystone species in tidal and subtidal habitats due to its primary role in structuring and regulating the ecological balance of these 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 used a single specimen collected in the field to generate [~]30 Gb of PacBio HiFi data. The final assembly is 749.8 Mb large and contains 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 is an important resource for future ecological and evolutionary studies. SignificanceReference genomes are essential resources for biodiversity conservation and management. Patella caerulea (Linnaeus, 1758) is a gastropod species occurring in the Mediterranean Sea that is currently used as a model to understand the impact of pollution and ocean acidification on marine biodiversity. Here we present a high-quality reference genome of P. caerulea, that almost reaches chromosome-level contiguity. We further provide a high-quality genome annotation supported by transcriptomic evidence. This reference genome will be of interest for researchers working on the ecology and evolution of marine biodiversity. All data is available on the public database NCBI for future use by researchers.

genomics↗

Duplication and losses of opsin genes in lophotrochozoan evolution

Opsins are G-coupled receptors playing a key role in metazoan visual processes. While many studies enriched our understanding of opsin diversity in several animal clades, the opsin evolution in Lophotrochozoa, one of the major metazoan groups, remains poorly understood. We investigated the opsin evolution in 74 translated lophotrochozoan genomes and capitalized on recently developed phylogenetic approaches. We found that the common ancestor of Lophotrochozoa possessed at least seven opsin paralog groups that underwent divergent evolutionary history in the different phyla. Furthermore, we showed for the first time placopsin-related molecules in Bilateria, that we named pseudopsins, which may prove critical in uncovering opsin evolution.

evolutionary biology↗