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.

A stony coral cell atlas illuminates the molecular and cellular basis of coral symbiosis, calcification, and immunity

“…In order the infer orthologous pairs between S. pistillata, N. vectensis, Xenia sp and H. vulgaris we applied the Broccoli algorithm ( Derelle et al, 2020 ) to the predicted proteomes of 35 species, with parameters -nb_hits 6-ratio_ortho 0.5 and based on reciprocal DIAMOND ( Buchfink et al, 2015 ) searches with default parameters. Our taxon sampling includes 13 cnidarian genomes ( Baumgarten et al, 2015 ; Bhattacharya et al, 2016 ; Jeon et al, 2019 ; Liew et al, 2016 ; Voolstra et al, 2015 , 2017 ; Ying et al, 2018 ), 20 noncnidarian metazoan genomes and 2 unicellular outgroups (Table S2).…”

Cnidarian Pattern Recognition Receptor Repertoires Reflect Both Phylogeny and Life History Traits

“…The proteomes of Acropora millepora ( 54 ), Actinia tenebrosa ( 53 ), Aurelia sp. ( 50 ), Calavadosia cruxmelitensis ( 51 ), Cassiopea xamachana ( 55 ), Clytia hemisphaerica ( 49 ), Dendronephyta gigantea ( 56 ), Exaiptasia daiphana (previously Exaiptaisa pallida ) ( 57 ), Hydra vulgaris ( 14 ), Montipora capitata ( 58 ), Morbakka virulenta ( 59 ), Nematostella vectensis ( 60 ), Orbicella faveolata ( 61 ), Pocillopora damicornis ( 62 ), Xenia sp. ( 52 ), and sponge Amphimedon queenslandica ( 63 ) were surveyed for TLRs, RLRs, NLRs, and CTLs using HMMR ( 64 ).…”

A myxozoan genome reveals mosaic evolution in a parasitic cnidarian

“…The protein data of representative cnidarian species, including T. kitauei (NCBI: GCA_000827895.1, [ 23 ]), K. iwatai (NCBI: GCA_001407235.2, [ 22 ]), H. salminicola (NCBI: GCA_009887335.1, [ 25 ]), M. squamalis (NCBI: GCA_010108815.1, [ 25 ]), H. vulgaris (NCBI: GCF_000004095.1, [ 72 ]), Morbakka virulenta (NCBI: GCA_003991215.1, [ 65 ]), Clytia hemisphaerica (NCBI: GCA_902728285.1, [ 137 ]), Aurelia aurita (NCBI: GCA_004194415.1, [ 65 ]), Calvadosia cruxmelitensis (NCBI: GCA_900245855.1, [ 138 ]), Cassiopea xamachana (NCBI: GCA_900291935.1, [ 138 ]), A. digitifera (NCBI: GCF_000222465.1, [ 126 ]), N. vectensis (NCBI: GCF_000209225.1, [ 73 ]), Dendronephthya gigantea (NCBI: GCA_004324835.1, [ 139 ]), Renilla reniformis (NCBI: GCA_900177555.1, [ 140 ]), and Amplexidiscus fenestrafer (NCBI: PRJNA354436, [ 141 ]), were used for gene family clustering (Additional file 1 : Table S23). The 16 cnidarians were chosen because they have relatively good genome quality and gene models.…”