The draft genome of an octocoral, Dendronephthya gigantea

Jeon, Yeonsu; Park, Seung Gu; Lee, Nayun; Weber, Jessica A.; Kim, Hui-Su; Hwang, Sun‐Tak; Woo, Seonock; Kim, Hak-min; Bhak, Youngjune; Jeon, Sungwon; Lee, Nayoung; Jo, Yejin; Blažytė, Asta; Ryu, Taewoo; Cho, Yun Sung; Kim, Hyunho; Lee, Jung-Hyun; Yim, Hyung-Soon; Bhak, Jong; Yum, Seungshic

doi:10.1101/487058

Cited by 7 publications

(8 citation statements)

References 49 publications

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“…For all searches, Renilla reniformis luciferase was used as the query sequence (SwissProt accession: P27652). Genomic data of Renilla muelleri (Jiang et al 2019) and Dendronephthya gigantea (Jeon et al 2019) were downloaded from the websites indicated in their respective papers. Transcriptome data were used from Gorgonia ventalina (Burge et al 2013), Leptogorgia sarmentosa (Romiguier et al 2014), Corallium rubrum (Pratlong et al 2015), Heliopora coerulea (Hongo et al 2017), Tubipora musica, Sinularia cruciata, Pinnigorgia flava (Conci et al 2019), Anthomastus sp., Cerianthid sp., Keratoisid sp., Scleronephthya sp.…”

Section: Homology Search For Luciferase and Phylogenetic Analysismentioning

confidence: 99%

“…S2). However, two homologs were also found in the genome of the non-luminous soft coral Dendronephthya gigantea (Jeon et al 2019), and these also have the same conserved catalytic triad. Further BLAST searches against the publicly available octocoral genome and transcriptome data found genes similar to Renilla luciferase.…”

Section: Evolution Of Bioluminescence In Octocoralliamentioning

confidence: 99%

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Biochemical characterization of diverse deep-sea anthozoan bioluminescence systems

2020

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Bioluminescence, light produced by living organisms, is a common trait in the ocean. In benthic ecosystems in the deep-sea, octocorals are some of the most abundant luminous animals. Among luminous sessile organisms, the shallow-water sea pansy Renilla has been well studied for its chemistry and molecular biology. Aside from Renilla, however, little is known about the bioluminescent mechanisms of other anthozoans, especially deep-sea corals. In this study, we investigated the characteristics of bioluminescence in deep-sea anthozoans. The bioluminescent capabilities of Heteropolypus, Kophobelemnon, Paragorgia, and a hormathiid anemone are newly described. Coelenterazine, a substrate for bioluminescent reactions, was detected in extracts from octocorals. Coelenterazine-dependent luciferase activity was found in all the anthozoans. Moreover, immunoreactivity against Renilla luciferase was detected in protein extracts from the families Isididae, Alcyoniidae, Umbellulidae, Funiculinidae, Kophobelemnidae and Protoptilidae, suggesting that all luminous octocorals may share a common biochemical mechanism, which utilizes coelenterazine and Renilla-type luciferase. Our results support the hypothesis that the last common ancestor of all the octocorals was bioluminescent, and that bioluminescence evolved a minimum of six times in Cnidaria. Future studies with robust phylogenies, wide taxon sampling, and comparative transcriptome analyses could reveal the patterns of evolution of bioluminescence in octocorals and anthozoans. Our study provides fundamental observations of deep-sea corals and experimental evidence of their coelenterazine-dependent luciferase systems.

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Section: Homology Search For Luciferase and Phylogenetic Analysismentioning

confidence: 99%

Section: Evolution Of Bioluminescence In Octocoralliamentioning

confidence: 99%

Biochemical characterization of diverse deep-sea anthozoan bioluminescence systems

2020

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“…It was, therefore, unclear whether neuropeptides were present in all cnidarians and, if so, what the structures of these neuropeptides were. This question, however, can now be solved, because the genomes from many cnidarians have been sequenced and numerous cnidarian transcriptomes are also available [37][38][39][40][41][42][43][44][45][46][47][48][49][50][51]. Last year, we developed a bioinformatics tool that could analyze cnidarian genomes and transcriptomes for the presence of neuropeptide preprohormones genes [37].…”

Section: Introductionmentioning

confidence: 99%

A comparative genomics study of neuropeptide genes in the cnidarian subclasses Hexacorallia and Ceriantharia

Koch

Grimmelikhuijzen

2020

BMC Genomics

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Background Nervous systems originated before the split of Proto- and Deuterostomia, more than 600 million years ago. Four animal phyla (Cnidaria, Placozoa, Ctenophora, Porifera) diverged before this split and studying these phyla could give us important information on the evolution of the nervous system. Here, we have annotated the neuropeptide preprohormone genes of twenty species belonging to the subclass Hexacorallia or Ceriantharia (Anthozoa: Cnidaria), using thirty-seven publicly accessible genome or transcriptome databases. Studying hexacorals is important, because they are versatile laboratory models for development (e.g., Nematostella vectensis) and symbiosis (e.g., Exaiptasia diaphana) and also are prominent reef-builders. Results We found that each hexacoral or ceriantharian species contains five to ten neuropeptide preprohormone genes. Many of these preprohormones contain multiple copies of immature neuropeptides, which can be up to 50 copies of identical or similar neuropeptide sequences. We also discovered preprohormones that only contained one neuropeptide sequence positioned directly after the signal sequence. Examples of them are neuropeptides that terminate with the sequence RWamide (the Antho-RWamides). Most neuropeptide sequences are N-terminally protected by pyroglutamyl (pQ) or one or more prolyl residues, while they are C-terminally protected by an amide group. Previously, we isolated and sequenced small neuropeptides from hexacorals that were N-terminally protected by an unusual L-3-phenyllactyl group. In our current analysis, we found that these N-phenyllactyl-peptides are derived from N-phenylalanyl-peptides located directly after the signal sequence of the preprohormone. The N-phenyllactyl- peptides appear to be confined to the hexacorallian order Actiniaria and do not occur in other cnidarians. On the other hand, (1) the neuropeptide Antho-RFamide (pQGRFamide); (2) peptides with the C-terminal sequence GLWamide; and (3) tetrapeptides with the X1PRX2amide consensus sequence (most frequently GPRGamide) are ubiquitous in Hexacorallia. Conclusions We found GRFamide, GLWamide, and X1PRX2amide peptides in all tested Hexacorallia. Previously, we discovered these three neuropeptide classes also in Cubozoa, Scyphozoa, and Staurozoa, indicating that these neuropeptides originated in the common cnidarian ancestor and are evolutionarily ancient. In addition to these ubiquitous neuropeptides, other neuropeptides appear to be confined to specific cnidarian orders or subclasses.

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“…cut off e-value: 1e -10 ) against the NCBI non-redundant database. Distribution of homologs (S.Mat 1) of octocoral and M. digitataSOMPs was subsequently assessed within a set of cnidarian genomes and transcriptomes(Voolstra et al 2015;Shinzato et al 2011;Voolstra et al 2017;Pratlong et al 2015;Jeon et al;Liew et al 2016) with Blastp applying the same search criteria described above.Presence of signal peptide, transmembrane regions, GPI-anchor was predicted with SignalP 4.0 (Petersen et al 2011) , TMHMM 2.0 (Krogh et al 2001) and PredGPI (Pierleoni et al 2008) respectively. Protein isoelectric point was determined with ProtParam (Gasteiger et al 2005) .…”

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confidence: 99%

Comparative proteomics of octocoral and scleractinian skeletomes and the evolution of coral calcification

Conci

Lehmann

Vargas

et al. 2019

Preprint

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Corals are ecosystem engineers of the coral reefs, one of the most biodiverse but severely threatened marine ecosystems. The ability of corals to form the three dimensional structure of reefs depends on the precipitation of calcium carbonate under biologically control. However, the exact mechanisms underlying this biologically controlled biomineralization remain to be fully unelucidated, for example whether corals employ a different molecular machinery for the deposition of different calcium carbonate (CaCO 3 ) polymorphs (i.e., aragonite or calcite). Here we used tandem mass spectrometry (MS/MS) to compare skeletogenic proteins, i.e., the proteins occluded in the skeleton of three octocoral and one scleractinian species: Tubipora musica and Sinularia cf. cruciata , both forming calcite sclerites, the blue coral Heliopora coerulea with an aragonitic rigid skeleton, and the scleractinian aragonitic Montipora digitata . We observed extremely low overlap between aragonitic and calcitic species, while a core set of proteins is shared between octocorals producing calcite sclerites.However, the same carbonic anhydrase (CruCA4) is employed for the formation of skeletons of both polymorphs. Similarities could also be observed between octocorals and scleractinians, including the presence of a galaxin-like protein.Additionally, as in scleractinians, some octocoral skeletogenic proteins, such as acidic proteins and scleritin, appear to have been secondarily co-opted for calcification and likely derive from proteins playing different extracellular functions. In H. coerulea, co-option was characterized by aspartic acid-enrichment of proteins. This work represents the first attempt to identify the molecular basis underlying coral skeleton polymorph diversity, providing several new research targets and enabling both future functional and evolutionary studies aimed at elucidating the origin and evolution of biomineralization in corals.

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The draft genome of an octocoral, Dendronephthya gigantea

Cited by 7 publications

References 49 publications

Biochemical characterization of diverse deep-sea anthozoan bioluminescence systems

Biochemical characterization of diverse deep-sea anthozoan bioluminescence systems

A comparative genomics study of neuropeptide genes in the cnidarian subclasses Hexacorallia and Ceriantharia

Comparative proteomics of octocoral and scleractinian skeletomes and the evolution of coral calcification

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