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

• Type: Article in International Scientific Journal
• Date: 2025

Authors

Ledoux, JB (Author) Other; Gomez-Garrido, J (Author) Other; Cruz, F (Author) Other; Ferreira, FC (Author) Other; Matos, A (Author) Other; Sarropoulou, X (Author) Other; Ramirez-Calero, S (Author) Other; Aurelle, D (Author) Other; Lopez-Sendino, P (Author) Other; Grayson, NE (Author) Other; Moore, BS (Author) Other; Agostinho Antunes (Author) FCUP; Aguilera, L (Author) Other; Gut, M (Author) Other; Salces-Ortiz, J (Author) Other; Fernández, R (Author) Other; Linares, C (Author) Other; Garrabou, J (Author) Other; Alioto, T (Author) Other

Journal

Title: Genome Biology and Evolution

Vol. 17

ISSN: 1759-6653

Publisher: Oxford University Press

Indexing

ISI Web of Knowledge - 0 Citations

Scopus - 0 Citations

Other information

Authenticus ID: P-018-4AB

DOI: 10.1093/gbe/evae253

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 8