ArticleBMC genomics2013
Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 119 citations in OpenAlex.
- Coral-associated microbiome dynamics under thermal and pollution stress.Conservation biology : the journal of the Society for Conservation Biology · 2026Article
- RNA-Binding Proteins in Dinoflagellates.International journal of molecular sciences · 2026Review
- Characterization of long noncoding RNAs, microRNAs, and piwiRNAs in reef-building corals.Environmental epigenetics · 2026Article
- Octadecanoids as emerging lipid mediators in cnidarian-dinoflagellate symbiosis.Communications biology · 2025Article
- Widespread Presence of SPX and Its Potential Role as a Phosphorus Nutrient Regulator in Dinoflagellates.Microorganisms · 2025Article
- Living Coral Displays, Research Laboratories, and Biobanks as Important Reservoirs of Chemodiversity with Potential for Biodiscovery.Marine drugs · 2025Review
- Review
- The genome of a giant clam zooxanthella (Cladocopium infistulum) offers few clues to adaptation as an extracellular symbiont with high thermotolerance.BMC genomics · 2024Article
- Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.Nucleic acids research · 2024Article
- Intersection of coral molecular responses to a localized mortality event and ex situ deoxygenation.Ecology and evolution · 2024Article
- Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates.NAR genomics and bioinformatics · 2024Article
- Molecular Insights into the Synergistic Effects of Putrescine and Ammonium on Dinoflagellates.International journal of molecular sciences · 2024Article
- Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.Communications biology · 2023Article
- Temporal gene expression patterns in the coralScience advances · 2022Article
- A Strategy for Gene Knockdown in Dinoflagellates.Microorganisms · 2022Article
- Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum.Nature genetics · 2021Article
- Longevity strategies in response to light in the reef coral Stylophora pistillata.Scientific reports · 2020Article
- De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis.BMC genomics · 2020Article
- Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate.BMC biology · 2020Article
- Competitive traits of coral symbionts may alter the structure and function of the microbiome.The ISME journal · 2020Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAnimal and plant genomes produce numerous small RNAs (smRNAs) that regulate gene expression post-transcriptionally affecting metabolism, development, and epigenetic inheritance. In order to characterize the repertoire of endogenous smRNAs and potential gene targets in dinoflagellates, we conducted smRNA and mRNA expression profiling over 9 experimental treatments of cultures from Symbiodinium microadriaticum, a photosynthetic symbiont of scleractinian corals.
resultsWe identified a set of 21 novel smRNAs that share stringent key features with functional microRNAs from other model organisms. smRNAs were predicted independently over all 9 treatments and their putative gene targets were identified. We found 1,720 animal-like target sites in the 3'UTRs of 12,858 mRNAs and 19 plant-like target sites in 51,917 genes. We assembled a transcriptome of 58,649 genes and determined differentially expressed genes (DEGs) between treatments. Heat stress was found to produce a much larger number of DEGs than other treatments that yielded only few DEGs. Analysis of DEGs also revealed that minicircle-encoded photosynthesis proteins seem to be common targets of transcriptional regulation. Furthermore, we identified the core RNAi protein machinery in Symbiodinium.
conclusionsIntegration of smRNA and mRNA expression profiling identified a variety of processes that could be under microRNA control, e.g. protein modification, signaling, gene expression, and response to DNA damage. Given that Symbiodinium seems to have a paucity of transcription factors and differentially expressed genes, identification and characterization of its smRNA repertoire establishes the possibility of a range of gene regulatory mechanisms in dinoflagellates acting post-transcriptionally.
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