Identification of MicroRNAs in the Coral Stylophora pistillata

• Published in: PloS one Vol. 9; no. 3; p. e91101
• Main Authors: Liew, Yi Jin, Aranda, Manuel, Carr, Adrian, Baumgarten, Sebastian, Zoccola, Didier, Tambutté, Sylvie, Allemand, Denis, Micklem, Gos, Voolstra, Christian R.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 21.03.2014; Public Library of Science (PLoS)
• Subjects: Acidification; Analysis; Animals; Anthozoa - genetics; Anthozoa - physiology; Biodiversity; Biology; Biology and life sciences; Calcification; Cell cycle; Conservation; Conserved sequence; Coral reefs; Corals; Core protein; Ecology and Environmental Sciences; Environmental changes; Evolution; Gene expression; Gene Expression Regulation; Gene sequencing; Genome; Genomes; Genomics; Homology; Hydrolases; Immunity; Laboratory animals; Likelihood Functions; Machinery; Machinery and equipment; Macroevolution; Marine pollution; Metabolism; MicroRNA; MicroRNAs; MicroRNAs - genetics; MicroRNAs - physiology; miRNA; Molecular Sequence Data; Ocean acidification; Phylogeny; Physiological aspects; Plants (botany); Proteins; Ribonucleic acid; RNA; RNA sequencing; RNA-mediated interference; Sea surface temperature; Sequence Analysis, RNA; Stylophora pistillata; Surface temperature; Symbiodinium microadriaticum; Symbiosis; Transcription; Transcription (Genetics); Transcriptome; Monaco
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0091101

Coral reefs are major contributors to marine biodiversity. However, they are in rapid decline due to global environmental changes such as rising sea surface temperatures, ocean acidification, and pollution. Genomic and transcriptomic analyses have broadened our understanding of coral biology, but a study of the microRNA (miRNA) repertoire of corals is missing. miRNAs constitute a class of small non-coding RNAs of ∼22 nt in size that play crucial roles in development, metabolism, and stress response in plants and animals alike. In this study, we examined the coral Stylophora pistillata for the presence of miRNAs and the corresponding core protein machinery required for their processing and function. Based on small RNA sequencing, we present evidence for 31 bona fide microRNAs, 5 of which (miR-100, miR-2022, miR-2023, miR-2030, and miR-2036) are conserved in other metazoans. Homologues of Argonaute, Piwi, Dicer, Drosha, Pasha, and HEN1 were identified in the transcriptome of S. pistillata based on strong sequence conservation with known RNAi proteins, with additional support derived from phylogenetic trees. Examination of putative miRNA gene targets indicates potential roles in development, metabolism, immunity, and biomineralisation for several of the microRNAs. Here, we present first evidence of a functional RNAi machinery and five conserved miRNAs in S. pistillata, implying that miRNAs play a role in organismal biology of scleractinian corals. Analysis of predicted miRNA target genes in S. pistillata suggests potential roles of miRNAs in symbiosis and coral calcification. Given the importance of miRNAs in regulating gene expression in other metazoans, further expression analyses of small non-coding RNAs in transcriptional studies of corals should be informative about miRNA-affected processes and pathways.