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

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.

Keywords: Biodiversity Genomics Europe; Catalan Initiative for the Earth BioGenome Project; Cnidaria; Hi-C; Oxford Nanopore; RNA-seq.

Fig. 1.

a) Coralligenous habitat dominated by the red coral, C. rubrum (picture by J. Garrabou). b) Phylogenetic relationships among different anthozoans species including five octocorals (Dendronephthya gigantea, Paramuricea clavata, Phenganax marumi, Xenia sp., and C. rubrum) and three hexacorals (Actinia tenebrosa, Plumapathes pennacea, and Acropora palmata) for which good-quality assemblies are available. The tree is based on 298 single-copy orthologous genes identified with BUSCO. c) BlobToolKit Snailplot showing different assembly metrics. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 532 Mb assembly. The distribution of scaffold lengths is shown in dark gray with the plot radius scaled to the longest scaffold present in the assembly (115,004,408 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (18,521,360 and 2,388,869 bp), respectively. The pale gray spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue areas around the outside of the plot show the distribution of GC, AT, and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated, and missing BUSCO genes in the metazoa_odb10 set is shown in the top right. d) Chromatin contact map generated from Arima2 Hi-C data shows the 20 chromosomes (2n = 40) that represent 89.3% of the assembled C. rubrum genome.