title: Identification of microRNAs in the coral Stylophora pistillata.
abstract: 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.
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Cambridge Systems Biology Centre & Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Yi Jin
authors.initials: YJ
authors.lastname: Liew
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Manuel
authors.initials: M
authors.lastname: Aranda
authors.affiliation: Cambridge Systems Biology Centre & Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Adrian
authors.initials: A
authors.lastname: Carr
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Baumgarten
authors.affiliation: Centre Scientifique de Monaco, Monaco, Monaco.
authors.forename: Didier
authors.initials: D
authors.lastname: Zoccola
authors.affiliation: Centre Scientifique de Monaco, Monaco, Monaco.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Tambutté
authors.affiliation: Centre Scientifique de Monaco, Monaco, Monaco.
authors.forename: Denis
authors.initials: D
authors.lastname: Allemand
authors.affiliation: Cambridge Systems Biology Centre & Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Gos
authors.initials: G
authors.lastname: Micklem
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Christian R
authors.initials: CR
authors.lastname: Voolstra
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000235:genetics* / Q000502:physiology; D005786:Gene Expression Regulation; D016678:Genome; D016013:Likelihood Functions; D035683:MicroRNAs / Q000235:genetics* / Q000502:physiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D035683:MicroRNAs