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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\u2005Mb (20 chromosomes, 309 scaffolds) with contig and scaffold N50 of 1.6 and 18.5\u2005Mb, 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.<\/jats:p>","DOI":"10.1093\/gbe\/evae253","type":"journal-article","created":{"date-parts":[[2025,2,7]],"date-time":"2025-02-07T09:51:41Z","timestamp":1738921901000},"source":"Crossref","is-referenced-by-count":3,"title":["Chromosome-Level Genome Assembly and Annotation of <i>Corallium rubrum<\/i>: A Mediterranean Coral Threatened by Overharvesting and Climate Change"],"prefix":"10.1093","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8796-6163","authenticated-orcid":false,"given":"Jean-Baptiste","family":"Ledoux","sequence":"first","affiliation":[{"name":"CIIMAR\/CIMAR, Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental, Universidade do Porto , Porto ,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6409-8009","authenticated-orcid":false,"given":"Jessica","family":"Gomez-Garrido","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG) , Barcelona 08028 ,","place":["Spain"]},{"name":"Universitat de Barcelona (UB) , Barcelona ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4098-8829","authenticated-orcid":false,"given":"Fernando","family":"Cruz","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG) , Barcelona 08028 ,","place":["Spain"]},{"name":"Universitat de Barcelona (UB) , Barcelona ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1971-5466","authenticated-orcid":false,"given":"Francisco","family":"Camara Ferreira","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG) , Barcelona 08028 ,","place":["Spain"]},{"name":"Universitat de Barcelona (UB) , Barcelona ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5331-2660","authenticated-orcid":false,"given":"Ana","family":"Matos","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental, Universidade do Porto , Porto ,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3671-9693","authenticated-orcid":false,"given":"Xenia","family":"Sarropoulou","sequence":"additional","affiliation":[{"name":"Department of Biology, School of Sciences and Engineering, University of Crete , Heraklion, Crete ,","place":["Greece"]},{"name":"Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR) , Heraklion, Crete ,","place":["Greece"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5153-1042","authenticated-orcid":false,"given":"Sandra","family":"Ramirez-Calero","sequence":"additional","affiliation":[{"name":"Departament de Biologia Marina, Institut de Ci\u00e8ncies del Mar (CSIC) , Barcelona ,","place":["Spain"]},{"name":"Departament de Biologia Evolutiva, Ecologia i Ci\u00e8ncies Ambientals, Universitat de Barcelona (UB) , Barcelona 08028 ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3922-7291","authenticated-orcid":false,"given":"Didier","family":"Aurelle","sequence":"additional","affiliation":[{"name":"Aix Marseille Universit\u00e9, Universit\u00e9 de Toulon, CNRS, IRD, MIO , Marseille ,","place":["France"]},{"name":"Institut Syst\u00e9matique Evolution Biodiversit\u00e9 (ISYEB), Mus\u00e9um national d'Histoire naturelle, CNRS, Sorbonne Universit\u00e9, EPHE, Universit\u00e9 des Antilles , CP 26, 75005 Paris ,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9786-8006","authenticated-orcid":false,"given":"Paula","family":"Lopez-Sendino","sequence":"additional","affiliation":[{"name":"Departament de Biologia Marina, Institut de Ci\u00e8ncies del Mar (CSIC) , Barcelona ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-0162-4938","authenticated-orcid":false,"given":"Natalie E","family":"Grayson","sequence":"additional","affiliation":[{"name":"Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , La Jolla, CA ,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4652-1253","authenticated-orcid":false,"given":"Bradley S","family":"Moore","sequence":"additional","affiliation":[{"name":"Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego , La Jolla, CA ,","place":["USA"]},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, CA ,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1328-1732","authenticated-orcid":false,"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Centro Interdisciplinar de Investiga\u00e7\u00e3o Marinha e Ambiental, Universidade do Porto , Porto ,","place":["Portugal"]},{"name":"Department of Biology, Faculty of Sciences, University of Porto , Porto 4169-007 ,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8631-8778","authenticated-orcid":false,"given":"Laura","family":"Aguilera","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG) , Barcelona 08028 ,","place":["Spain"]},{"name":"Universitat de Barcelona (UB) , Barcelona ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4063-7159","authenticated-orcid":false,"given":"Marta","family":"Gut","sequence":"additional","affiliation":[{"name":"Centro Nacional de An\u00e1lisis Gen\u00f3mico (CNAG) , Barcelona 08028 ,","place":["Spain"]},{"name":"Universitat de Barcelona (UB) , Barcelona ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3572-4020","authenticated-orcid":false,"given":"Judit","family":"Salces-Ortiz","sequence":"additional","affiliation":[{"name":"Metazoa Phylogenomics Lab, Institute of Evolutionary Biology (CSIC-University Pompeu Fabra) , Barcelona ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4719-6640","authenticated-orcid":false,"given":"Rosa","family":"Fern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Metazoa Phylogenomics Lab, Institute of Evolutionary Biology (CSIC-University Pompeu Fabra) , Barcelona ,","place":["Spain"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3855-2743","authenticated-orcid":false,"given":"Cristina","family":"Linares","sequence":"additional","affiliation":[{"name":"Departament de Biologia Evolutiva, Ecologia i Ci\u00e8ncies Ambientals, Universitat de Barcelona (UB) , Barcelona 08028 ,","place":["Spain"]},{"name":"Institut de Recerca de la Biodiversitat (IRBio), Universitat de 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