Warming induced mass mortality events induce strong demographic declines in different Mediterranean habitat-forming octocorals, such as Eunicella singularis and Eunicella cavolini. The main objective of the project was to improve the quality of existing genome references in the two species. Indeed, high quality genome references are a prerequisite to conduct population genomic studies which can fuel conservation policies and restoration efforts. 

 

The whole gorgonian, Eunicella singularis (c) Jordi Chias

We reached the objective of the project (i.e. reference genomes in E. singularis and E. cavolini) and went even further by producing a third reference genome a third Mediterranean habitat-forming octocoral, Corallium rubrum. As expected, we assembled and annotated the two high quality reference genomes for the two Eunicella species (annotation is on-going). Albeit with relatively good contiguity, the genome of Eunicella cavolini remains at scaffold level (scN50 > 500 kb; length=447 Mb; 1,918 scaffolds; BUSCO 89%; QV=38). However, we were able to reach chromosome level assembly for Eunicella singularis (scN50 = 16.5 Mb; length=504 Mb; 15K (72%); BUSCO 87.9%; QV = 39.8) and for the third species C. rubrum (scN50=18.5 Mb; length=532 Mb; 20k; BUSCO 86.4%; QV= 42). Noteworthily, those are some of the first chromosome level reference genome assembly in octocorals. 

Focusing on Eunicella species, these highly valuable genomic resources were presented in the Biodiversity Genomics congress in 2023 (see Reference-free analyses provide insights into the population genomics of six octocorals here: https://biodiversitygenomics.eu/5326-2/ ) and in the 1st BGE-ERGA Genome Applications Symposium in 2024 (see Genomics of Unconventional Species: Unravelling Earth's Hidden Biodiversity here https://biodiversitygenomics.eu/2024/08/27/1st-bge-erga-genome-applications-symposium/ ). Moreover, these resources are the foundation of an on-going project dedicated to species delimitation and evolution in Eunicella. Indeed, the two reference genomes were used to map sequencing reads obtained from a RAD sequencing approach to look for the occurrence of hybridization among the two species. This study entitled “Symbiosis, hybridization and speciation in Mediterranean octocorals (Octocorallia, Eunicellidae)” has been accepted last week in Biological Journal of the Linean Society. In parallel, we are working on a whole genome re-sequencing dataset to go further in the genomic landscape of differentiation among the two species. The first results of this whole genome study will be presented at the Portuguese national congress of evolutionary biology (https://enbe2024.rd.ciencias.ulisboa.pt) under the title “Comparative Population Genomics Illuminates Species Boundaries and Symbiotic Disruption in Eunicella Octocorals”.

 

Sampling of Corallium rubrum for population genomics analyses

Regarding the red coral, Corallium rubrum, a genome note entitled “Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.” is in press in Genome Biology and Evolution. Interestingly, this genomic resource will be used in a project funded by the Biodiversity Genomics Europe and dedicated to the population genomics of the red coral. Indeed, C. rubrum is an iconic species from the Mediterranean with high cultural and economic values. Yet, C. rubrum is under conservation concerns due to overharvesting and anthropogenic climate change. C. rubrum received conservation attentions both from the scientific and biodiversity managers communities and restoration actions were identified as a potential tool to preserve red coral populations. In this context, the project “RED-COR_Conservation genomics of the Mediterranean red coral, Corallium rubrum: a habitat-forming octocoral threatened by overharvesting and anthropogenic climate change.” aims to provide population genomics data to support the conservation of the species.