Genome of elegance coral Catalaphyllia jardinei (Euphylliidae)

Abstract

Coral reefs are under stress throughout the world. To better understand the molecular mechanisms underlying coral biology and their genomic evolution, here we sequenced the genome and transcriptomes of elegance coral Catalaphyllia jardinei (Euphylliidae). This monotypic genus stony coral is widespread but rare, being found across the Indo-West Pacific, from the northern Indian Ocean, Australia, Philippines, to the South China Sea. Due to its popularity among aquarium hobbyists, it is an overexploited species collected in large quantities from the wild for aquarium trade. The assembled genome is ~ 651.3 Mb in total length and of high physical contiguity with a scaffold N50 size of 28.9 Mb. The gene copy numbers of abiotic stress regulator (heat shock protein family genes) and neuropeptides (GLWamide, GRFamide, PRGamide and HIRamide) are similar to other sequenced anthozoans, and we have also identified the first set of sesquiterpenoid biosynthetic pathway genes in coral. Sequencing of small RNAs allows us to identify 35 microRNAs in C. jardinei and update the number of conserved microRNAs in cnidarians. This study established a foundation for further investigation into the roles of sesquiterpenoids and microRNAs in development of coral and understand their responses to climate change. Due to the easiness to culture C. jardinei in reef tanks and the established resources in this study, we propose this species be adopted as a new laboratory model in environmental and ecological experiments aiming to understand coral biology and responses to environmental stressors.

The genome of the deep-sea anemone Actinernus sp. contains a mega-array of ANTP-class homeobox genes

“…Bilaterians tend to have a similar split of their ANTP-class gene families across approximately four distinct chromosomes, consisting of the Hox cluster genes with a handful of HoxL genes on one chromosome, the NK cluster genes and a few NKL genes on another, with the ParaHox cluster and the NK2 genes on two further distinct chromosomes [18,19,[31][32][33]. In contrast, some cnidarians have been found to have mixtures of a small number of Hox, HoxL, NK and NKL genes dispersed around their respective genomes [34,35] (figure 2). To our surprise, we found the first case of the existence of the previously hypothetical mega-homeobox array of Hox cluster, HoxL, NK cluster and NKL genes in an extant species, on Actinernus chr 1 (figure 2; electronic supplementary material, S6 and figures S7-S10).…”

“…Potential homeobox genes were identified by searching with homeodomain sequences from N. vectensis [66], Branchiostoma floridae, Drosophila melanogaster (retrieved from HomeoDB2 [67] in the Actinernus sp. genome and previous published high-quality cnidarian genomes [14,31,32,34,35,57,[68][69][70][71][72][73]) using tBLASTN (electronic supplementary material, S4). NCBI CD-Search [74] was then used to validate the presence of homeodomains in the retrieved sequences.…”

Deciphering omics atlases to aid stony corals in response to global change

“…Coral reefs face severe environmental threats: global warming, ocean acidi cation, Crown-of-thorns star sh (COTS), algae blooms, over shing, and pollution. The protection of stony corals and their habitats is crucial for marine ecosystem health and diversity [1][2][3][4][5]7,[12][13][14]17 . As the climate changes, without gene regulation technologies, stony corals may undergo bleaching and disappear 7,[12][13][14] .…”

“…The protection of stony corals and their habitats is crucial for marine ecosystem health and diversity [1][2][3][4][5]7,[12][13][14]17 . As the climate changes, without gene regulation technologies, stony corals may undergo bleaching and disappear 7,[12][13][14] . A signi cant number of stony coral transcriptomes and genomes were previously sequenced [2][3][4][5]14 , and the scRNA-seq remains in progress 5 .…”

Genome assemblies and genetic maps highlight chromosome-scale macrosynteny in Atlantic acroporids

“…In Anthozoa, the Hexacorallia are represented by dozens of genomes from genera such as Acropora (Shinzato et al 2020; Fuller et al 2020, Lopez-Natam et al 2023), Astrangia (Stankiewicz et al 2023), Exaiptasia (Baumgarten et al 2015) , Nematostella (Putnam et al 2007) and the Octocorallia by at least eight genomes from taxa such as Renilla (Jiang et al 2019), Dendronephthya (Jeon et al 2019) , Xenia (Hu et al 2020), and Heliopora (Ip et al 2023). Seven chromosome-resolved assemblies are published for scleractinian corals (Fuller et al 2020, McKenna et al 2021, Yu et al 2022, Thomas et al 2022, López-Nandam et al 2023). While most coral species are diploid, other ploidies exist (e.g.…”