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.
Highlights
Corals that belong to the phylum Cnidaria, class Anthozoa, provide habitats for a diversity of marine organisms (Friedlander and Parrish 1998) and are foundational members of the benthic community playing a major role in energy transfer between plankton and the benthos (van de Water et al 2018)
Corals can be classified into hexacorals and octocorals
We found that D. gigantea has diverged the earliest among the anthozoans based on our calculations
Summary
Corals that belong to the phylum Cnidaria, class Anthozoa, provide habitats for a diversity of marine organisms (Friedlander and Parrish 1998) and are foundational members of the benthic community playing a major role in energy transfer between plankton and the benthos (van de Water et al 2018). The D. gigantea gene set was of high quality among the cnidarians and covered $94% of the complete BUSCO ortholog benchmark genes We identified that D. gigantea contains 12,597 orthologous gene families, excluding singletons, and 3,656 of them are shared with stony corals (Orbicella faveolata, Stylophora pistillata, and Acropora digitifera) and hydra (Hydra magnipapillata) Divergence time estimation analysis suggested the divergence of the octocoral (D. gigantea) from the other three stony corals (O. faveolata, S. pistillata, and A. digitifera) happened 544 MYA Our analyses show the octocoral is the earliest diverged group among anthozoans with an estimated divergence time of 544 MYA from the hexacorals It adds a new octocoral assembly for cnidarians, in addition to hexacoral and hydra genomes, it facilitates in depth comparative analyses of stony and soft corals that are either symbiotic and/or nonsymbiotic. The D. gigantea genome will support future experiments aimed at determining differences in the genetic
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