Open Access Highly Accessed Research article

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

Sebastian Baumgarten1, Till Bayer1, Manuel Aranda1, Yi Jin Liew12, Adrian Carr2, Gos Micklem2 and Christian R Voolstra1*

Author Affiliations

1 Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia

2 Cambridge Systems Biology Centre & Department of Genetics, University of Cambridge, Cambridge, UK

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BMC Genomics 2013, 14:704  doi:10.1186/1471-2164-14-704

Published: 12 October 2013

Abstract

Background

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.

Results

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.

Conclusions

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.

Keywords:
Symbiodinium; Dinoflagellates; Scleractinian corals; Symbiont; Coral reef; Small RNA (smRNA); microRNA (miRNA); Small interfering RNA (siRNA); mRNA; Expression profiling; RNAseq