Article Dans Une Revue Genome Biology and Evolution Année : 2025

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

Jean-Baptiste Ledoux
Jessica Gomez-Garrido
Fernando Cruz
Francisco Camara Ferreira
Ana Matos
Xenia Sarropoulou
Sandra Ramirez-Calero
Paula Lopez-Sendino
Natalie Grayson
Bradley Moore
Agostinho Antunes
Laura Aguilera
Marta Gut
Judit Salces-Ortiz
Rosa Fernández
Cristina Linares
Joaquim Garrabou
Tyler Alioto

Résumé

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.

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hal-04935559 , version 1 (13-08-2025)

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Jean-Baptiste Ledoux, Jessica Gomez-Garrido, Fernando Cruz, Francisco Camara Ferreira, Ana Matos, et al.. Chromosome-Level Genome Assembly and Annotation of Corallium rubrum : A Mediterranean Coral Threatened by Overharvesting and Climate Change. Genome Biology and Evolution, 2025, 17 (2), ⟨10.1093/gbe/evae253⟩. ⟨hal-04935559⟩
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