• Energy Research

Abstract The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e., varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes, including genetic factors, contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo genome assembly accounting for 607 Mb in 64,145 scaffolds. The contig and scaffold N50s are 19.15 Kb and 23.92 Kb, respectively. Despite of the low contiguity of the assembly, its gene completeness is relatively high, including 75.8% complete and 9.4% fragmented genes out of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 62,652 protein-coding genes have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, having the genome of P. clavata will facilitate studies of various aspects of its evolutionary ecology and elaboration of effective conservation plans such as active restoration to overcome the threats of global change.

This upload contains three datasets in CSV files and a PDF file with the specific description of the CSV files. These data was used for the analysis of the mass mortality events reported during the period 2015-2019 across the Mediterranean. The datasets are 1) a CSV file with the data used for the description of the spatial-temporal, depth and biological patterns of mortality observed in the Mediterranean Sea in the 2015-2019 period; 2) a CSV file with the data used to conduct the analyses on the relationship between marine heatwaves (MHW) days found on the surface (averaged per monitored area and year) and the corresponding mass mortality incidence of benthic organisms; 3) a CSV file with the data used to conduct the analyses on the relationship between in-situ MHW days (averaged per monitored area, depth and year) and the corresponding mass mortality incidence. Data were obtained through benthic community field surveys conducted by 33 research teams from 11 Mediterranean countries. Surveys covered thousands of kms of coastline, spanning 13º of latitude (32 °S to 45 °N) and 40º of longitude (-5°W to 35°E) in the Mediterranean Sea. The dataset provides the most updated inventory of mass mortality events records for benthic species between 2015-2019 in the region. The surveys were conducted in 142 monitoring areas. Monitoring areas were considered as geographic areas (10-25 km coastline, e.g., a marine protected area and the nearby coast) sharing common environmental features. In situ temperature conditions datasets base consists of high frequency (hourly) time series obtained using HOBO data loggers (accuracy ± 0.21°C) set-up at standard depths along rocky walls by divers, generally every 5 m from the surface to 40 m depth.This dataset as in the case of the mortality was assembled under the T-MEDNet initiative (www.t-mednet.org). Satellite derived sea surface temperature (SST) across the Mediterranean Sea was obtained from CMEMS (https://resources.marine.copernicus.eu/?option=com_csw&view=details&product_id=SST_MED_SST_L4_REP_OBSERVATIONS_010_021). The data consists of daily (night-time), gap free, optimally interpolated foundation SST at ~4 km resolution from AVHRR with improved accuracy and stability over the 1982-2019 period

AbstractClimate change is causing an increase in the frequency and intensity of marine heatwaves (MHWs) and mass mortality events (MMEs) of marine organisms are one of their main ecological impacts. Here, we show that during the 2015–2019 period, the Mediterranean Sea has experienced exceptional thermal conditions resulting in the onset of five consecutive years of widespread MMEs across the basin. These MMEs affected thousands of kilometers of coastline from the surface to 45 m, across a range of marine habitats and taxa (50 taxa across 8 phyla). Significant relationships were found between the incidence of MMEs and the heat exposure associated with MHWs observed both at the surface and across depths. Our findings reveal that the Mediterranean Sea is experiencing an acceleration of the ecological impacts of MHWs which poses an unprecedented threat to its ecosystems' health and functioning. Overall, we show that increasing the resolution of empirical observation is critical to enhancing our ability to more effectively understand and manage the consequences of climate change.

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AbstractReference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed in the tree of life questioning our true ability to enlighten conservation with genomic data. Good quality reference genomes remain scarce in octocorals while these species are highly relevant target for conservation. Here, we present the first annotated reference genome in the red coral,Corallium rubrum(Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 475 Mb (21 chromosomes, 326 scaffolds) with contig and scaffold N50 of 1.6 Mb and 16.2 Mb, respectively. Fifty percent of the sequence (L50) was contained in eight superscaffolds. The consensus quality (QV) of the final assembly was 42 and the gene completeness reported by BUSCO was 74% (metazoa_odb10 database). We annotated 39,114 protein-coding genes and 32,678 non-coding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals, is currently used in a project based on whole genome re-sequencing dedicated to the conservation and management ofC. rubrum.Significance StatementThe Mediterranean red coral,Corallium rubrum, is critically impacted by overharvesting and by mass mortality events linked to marine heat waves. Accordingly,C. rubrumis increasingly receiving conservation efforts. Previous population genetics studies based on microsatellites contributed to improving our knowledge of the species ecology. Yet, crucial questions regarding, admixture among lineages, demographic history, effective population sizes and local adaptation, are still open owing to a lack of genomic resources. Here, we present the first chromosome-level genome assembly for the species with high contiguity, good completeness and protein-coding genes and repeat sequence annotations. This genome, one of the first in octocorals, will pave the way for the integration of population genomics data into ongoing interdisciplinary conservation efforts dedicated toC. rubrum.