Chromosome-Level Genome Assembly and Annotation of <i>Corallium rubrum</i>: A Mediterranean Coral Threatened by Overharvesting and Climate Change

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed across the tree of life raising concerns over our ability to enlighten conservation with genomic data. Good-quality reference genomes remain scarce in octocorals while these species are highly relevant targets 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 532 Mb (20 chromosomes, 309 scaffolds) with contig and scaffold N50 of 1.6 and 18.5 Mb, respectively. Fifty percent of the sequence (L50) was contained in seven superscaffolds. The consensus quality value of the final assembly was 42, and the single and duplicated gene completeness reported by BUSCO was 86.4% and 1%, respectively (metazoa_odb10 database). We annotated 26,348 protein-coding genes and 34,548 noncoding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals and the first in Scleralcyonacea order, is currently used in a project based on whole-genome resequencing dedicated to the conservation and management of C. rubrum.

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Publication Details

Journal
Genome Biology and Evolution
Published
2025-02-01
DOI
https://doi.org/10.1093/gbe/evae253
Citations
2
Primary Topic
Coral and Marine Ecosystems Studies
Type
article
Field-Weighted Citation Impact
3.43

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article

Chromosome-Level Genome Assembly and Annotation of Corallium rubrum: A Mediterranean Coral Threatened by Overharvesting and Climate Change

Tyler Alioto, Francisco Câmara Ferreira, Agostinho Antunes, Jean‐Baptiste Ledoux et al.
2 citations
Genome Biology and Evolution
Coral and Marine Ecosystems Studies
3.43
article

Chromosome-Level Genome Assembly and Annotation of Corallium rubrum: A Mediterranean Coral Threatened by Overharvesting and Climate Change

Tyler Alioto, Francisco Câmara Ferreira, Agostinho Antunes, Jean‐Baptiste Ledoux, Xenia Sarropoulou, Judit Salces-Ortiz, Ana Matos, Natalie E Grayson, Bradley S. Moore, Cristina Linares, Paula López‐Sendino, Sandra Ramirez‐Calero, Joaquim Garrabou, Didier Aurelle, Rosa Fernández, Fernando Cruz, Laura Aguilera, Jèssica Gómez‐Garrido, Marta Ortova Gut
article en
2 citations

Abstract

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed across the tree of life raising concerns over our ability to enlighten conservation with genomic data. Good-quality reference genomes remain scarce in octocorals while these species are highly relevant targets 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 532 Mb (20 chromosomes, 309 scaffolds) with contig and scaffold N50 of 1.6 and 18.5 Mb, respectively. Fifty percent of the sequence (L50) was contained in seven superscaffolds. The consensus quality value of the final assembly was 42, and the single and duplicated gene completeness reported by BUSCO was 86.4% and 1%, respectively (metazoa_odb10 database). We annotated 26,348 protein-coding genes and 34,548 noncoding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals and the first in Scleralcyonacea order, is currently used in a project based on whole-genome resequencing dedicated to the conservation and management of C. rubrum.

Genome Biology and EvolutionVol. 17(2)
Centre National de la Recherche Scientifique (FR), University of Crete (GR), Université de Toulon (FR), Scripps Institution of Oceanography (US), Universidade do Porto (PT), Aix-Marseille Université (FR), University of California San Diego (US), Sorbonne Université (FR), Institut de Systématique, Évolution, Biodiversité (FR), Institut Català de Ciències del Clima (ES), Hellenic Centre for Marine Research (GR), Institut de Biologia Evolutiva (ES), Centro Nacional de Análisis Genómico (ES), Institut de Ciències del Mar (ES), Université des Antilles (GP), University of Montana (US), Universitat de Barcelona (ES)
Esperantic Studies Foundation, Aix-Marseille Université, National Estuarine Research Reserve System, Generalitat de Catalunya, Institució Catalana de Recerca i Estudis Avançats, Ministerio de Ciencia e Innovación, European Research Council, Fundação para a Ciência e a Tecnologia, Agència de Gestió d'Ajuts Universitaris i de Recerca, Instituto de Salud Carlos III, Agencia Estatal de Investigación, European Social Fund
Life below water
Openalex Percentile: Top 11%
Coral and Marine Ecosystems Studies
3.43
DOIOpen Access PDFOpenAlex
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