Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals

• Published in: BMC genomics Vol. 14; no. 1; p. 704
• Main Authors: Baumgarten, Sebastian, Bayer, Till, Aranda, Manuel, Liew, Yi Jin, Carr, Adrian, Micklem, Gos, Voolstra, Christian R
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 12.10.2013; BioMed Central
• Subjects: 3' Untranslated regions; Algae; Analysis; Animals; Anthozoa - parasitology; Coral reef ecology; Coral Reefs; Coral reefs and islands; Dinoflagellates; Dinoflagellida - genetics; DNA binding proteins; DNA methylation; Epigenetic inheritance; Gene expression; Gene Expression Profiling; Gene Expression Regulation; Gene Ontology; Genetic aspects; Genetic transcription; Genomes; Genomics; Heat tolerance; Messenger RNA; MicroRNAs - genetics; MicroRNAs - metabolism; Photosynthesis; Photosynthesis - genetics; Phytochemistry; RNA sequencing; RNA, Messenger - genetics; RNA, Messenger - metabolism; Scleractinia; Studies; Symbiosis - genetics; Transcriptome - genetics; United Kingdom
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-14-704

Animal 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. We 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. Integration 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.