The Draft Genome of an Octocoral, Dendronephthya gigantea

Abstract

Coral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities of octocorallian species, appear more resilient. The genomes of several cnidarians species have been published, including from stony corals, sea anemones, and hydra. To fill the phylogenetic gap for octocoral species of cnidarians, we sequenced the octocoral, Dendronephthya gigantea, a nonsymbiotic soft coral, commonly known as the carnation coral. The D. gigantea genome size is ∼276 Mb. A high-quality genome assembly was constructed from PacBio long reads (29.85 Gb with 108× coverage) and Illumina short paired-end reads (35.54 Gb with 128× coverage) resulting in the highest N50 value (1.4 Mb) reported thus far among cnidarian genomes. About 12% of the genome is repetitive elements and contained 28,879 predicted protein-coding genes. This gene set is composed of 94% complete BUSCO ortholog benchmark genes, which is the second highest value among the cnidarians, indicating high quality. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence times were estimated at 544 MYA. There is a clear difference in Hox gene composition between these species: unlike hexacorals, the Antp superclass Evx gene was absent in D. gigantea. Here, we present the first genome assembly of a nonsymbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including stony and soft corals, both symbiotic and nonsymbiotic. The D. gigantea genome may also provide clues to mechanisms of differential coping between the soft and stony corals in response to scenarios of global warming.

Keywords: Dendronephthya gigantea; cnidarian; genome; nonsymbiotic coral; octocoral; soft coral.

Fig. 1.

—Phylogenetic relationship and Hox gene clusters of Dendronephthya gigantea and other species. (A) Tree shows the phylogeny with divergence time among 15 species. Numbers in each branch denote the estimated divergence time (MYA). (B) Green dashed-line box denotes Hox gene cluster (HoxA, HoxB, HoxC, HoxDa, HoxDb, HoxE, and HoxF), yellow dashed-line box denotes EGF gene cluster (Evex and Gbx), and blue dashed-line box denotes ParaHox gene cluster (CDX and GSX). The number of boxes shows the number of each gene copies in the genome.