title: Integrating microRNA and mRNA expression profiling in Symbiodinium microadriaticum, a dinoflagellate symbiont of reef-building corals.
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.
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, Thuwal 23955, Saudi Arabia. christian.voolstra@kaust.edu.sa.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Baumgarten
authors.forename: Till
authors.initials: T
authors.lastname: Bayer
authors.forename: Manuel
authors.initials: M
authors.lastname: Aranda
authors.forename: Yi Jin
authors.initials: YJ
authors.lastname: Liew
authors.forename: Adrian
authors.initials: A
authors.lastname: Carr
authors.forename: Gos
authors.initials: G
authors.lastname: Micklem
authors.forename: Christian R
authors.initials: CR
authors.lastname: Voolstra
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000469:parasitology*; D057894:Coral Reefs; D004141:Dinoflagellida / Q000235:genetics*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D063990:Gene Ontology; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010788:Photosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D013559:Symbiosis / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger