Biology subjects

Aurelle, D.

Publications and source records attributed to Aurelle, D..

5 recordsLinked to original sources

bioRxiv2024

Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.

Reference 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 of C. 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. rubrum is 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 to C. rubrum.

genomics↗

bioRxiv2023

Temporal genomics help in deciphering neutral and adaptive patterns in the contemporary evolution of kelp populations

The long-term persistence of species in the face of climate change can be evaluated by examining the interplay between selection and genetic drift in the contemporary evolution of populations. In this study, we focused on spatial and temporal genetic variation in four populations of the cold-water kelp Laminaria digitata using thousands of SNPs (ddRAD-seq). These populations were sampled from the center to the south margin in the North Atlantic at two different time points, spanning at least two generations. By conducting genome scans for local adaptation from a single time point, we successfully identified candidate loci that exhibited clinal variation, closely aligned with the latitudinal changes in temperature. This finding suggests that temperature may drive the adaptive response of kelp populations, although other factors, such as the species demographic history should be considered. Furthermore, we provided compelling evidence of positive selection through the examination of allele frequency changes over time, offering additional insights into the impact of genetic drift. Specifically, we detected candidate loci exhibiting temporal differentiation that surpassed the levels typically attributed to genetic drift at the south margin, confirmed through simulations. This finding was in sharp contrast with the lack of detection of outlier loci based on temporal differentiation in a population from the North Sea, exhibiting low levels of genetic diversity, that further decreased over time. These contrasting evolutionary scenarios among populations can be primarily attributed to the differential prevalence of selection relative to genetic drift. In conclusion, our study highlights the potential of temporal genomics to gain deeper insights into the contemporary evolution of marine foundation species in response to rapid environmental changes.

evolutionary biology↗

bioRxiv2021

Population genomics of Pocillopora corals: insights from RAD-sequencing

Scleractinian corals are of great ecological interest as ecosystem engineer species. Accordingly, there is a wealth of studies on their adaptive abilities facing climate change. Such studies should rely on precise species and population delimitation. Nevertheless species delimitation in corals can be hindered by the lack of adequate genetic markers, by hybridization, and by morphological plasticity. Here we applied RAD sequencing to the study of species delimitation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia with the objectives to test primary species hypotheses based on mitochondrial DNA sequencing, and to study the genetic structure among sampling sites inside species. Regarding the varying levels of missing data observed among samples we tested different filtering strategy. The main genetic differentiation was observed between samples from Oman and French Polynesia, which also corresponded to different mitochondrial lineages and species hypotheses. In Oman, we did not observe any clear differentiation according to the main mitochondrial lineages considered here, nor between sampling sites. In French Polynesia where a single mitochondrial lineage was studied, we did not evidence any differentiation according to sampling sites. These results provide an additional example of the importance of using independent nuclear markers for the study of species delimitation. Our analyses also allowed the identification of clonal lineages in our samples, and to take them into account in our interpretations. We used simulations to study the impact of clonal reproduction on the distribution of statistics of genetic diversity and genetic structure among loci.

evolutionary biology↗

bioRxiv2018

Gene expression plasticity and frontloading promote thermotolerance in Pocilloporid corals

Ecosystems worldwide are suffering from climate change. Coral reef ecosystems are globally threatened by increasing sea surface temperatures. However, gene expression plasticity provides the potential for organisms to respond rapidly and effectively to environmental changes, and would be favored in variable environments. In this study, we investigated the thermal stress response in Pocillopora coral colonies from two contrasting environments by exposing them to heat stress. We compared the physiological state, bacterial and Symbionaceae communities (using 16S and ITS2 metabarcoding), and gene expression levels (using RNA-Seq) between control conditions and heat stress (the temperature just below the first signs of compromised health). Colonies from both thermal regimes remained apparently normal and presented open and colored polyps during heat stress, with no change in bacterial and Symbionaceae community composition. In contrast, they differed in their transcriptomic responses. The colonies from Oman displayed a more plastic transcriptome, but some genes had a higher basal expression level (frontloading) compared to the less thermotolerant colonies from New Caledonia. In terms of biological functions, we observed an increase in the expression of stress response genes (including induction of tumor necrosis factor receptors, heat shock proteins, and detoxification of reactive oxygen species), together with a decrease in the expression of genes involved in morpho-anatomical functions. Gene regulation (transcription factors, mobile elements, histone modifications and DNA methylation) appeared to be overrepresented in the Oman colonies, indicating possible epigenetic regulation. These results show that transcriptomic plasticity and frontloading can be co-occurring processes in corals confronted to highly variable thermal regimes.

evolutionary biology↗

bioRxiv2018

Separate the wheat from the chaff: genomic analysis of local adaptation in the red coral Corallium rubrum

Genomic data allow an in-depth and renewed study of local adaptation. The red coral (Corallium rubrum, Cnidaria) is a highly genetically structured species and a promising model for the study of adaptive processes along an environmental gradient. Here, we used RAD-Sequencing in order to study the vertical genetic structure of this species and to search for signals of local adaptation to depth and thermal regime in the red coral. Previous studies have shown different thermotolerance levels according to depth in this species which could correspond to genetic or environmental differences. We designed a sampling scheme with six pairs of shallow vs deep populations distributed in three geographical regions as replicates. Our results showed significant differentiation among locations and among sites separated by around 20 m depth. The tests of association between genetics and environment allowed the identification of candidate loci under selection but with a potentially high rate of false positive. We discuss the methodological obstacles and biases encountered for the detection of selected loci in such a strongly genetically structured species. On this basis, we also discuss the significance of the candidate loci for local adaptation detected in each geographical region and the evolution of red coral populations along environmental gradients.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC=\"FIGDIR/small/306456_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (110K):\norg.highwire.dtl.DTLVardef@11d6129org.highwire.dtl.DTLVardef@1d604c3org.highwire.dtl.DTLVardef@1d2bef2org.highwire.dtl.DTLVardef@f64160_HPS_FORMAT_FIGEXP M_FIG A colony of red coral, Corallium rubrum, near Marseille. Photo: F. Zuberer / OSU Pytheas / CNRS\n\nC_FIG

evolutionary biology↗