Identification of microRNAs in the coral Stylophora pistillata.

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...

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Autores principales:	Yi Jin Liew, Manuel Aranda, Adrian Carr, Sebastian Baumgarten, Didier Zoccola, Sylvie Tambutté, Denis Allemand, Gos Micklem, Christian R Voolstra
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8ee4750ff34e48d89a9410b7305fd804
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spelling	oai:doaj.org-article:8ee4750ff34e48d89a9410b7305fd8042021-11-18T08:26:42ZIdentification of microRNAs in the coral Stylophora pistillata.1932-620310.1371/journal.pone.0091101https://doaj.org/article/8ee4750ff34e48d89a9410b7305fd8042014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24658574/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Coral 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.Yi Jin LiewManuel ArandaAdrian CarrSebastian BaumgartenDidier ZoccolaSylvie TambuttéDenis AllemandGos MicklemChristian R VoolstraPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e91101 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Yi Jin Liew Manuel Aranda Adrian Carr Sebastian Baumgarten Didier Zoccola Sylvie Tambutté Denis Allemand Gos Micklem Christian R Voolstra Identification of microRNAs in the coral Stylophora pistillata.
description	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.
format	article
author	Yi Jin Liew Manuel Aranda Adrian Carr Sebastian Baumgarten Didier Zoccola Sylvie Tambutté Denis Allemand Gos Micklem Christian R Voolstra
author_facet	Yi Jin Liew Manuel Aranda Adrian Carr Sebastian Baumgarten Didier Zoccola Sylvie Tambutté Denis Allemand Gos Micklem Christian R Voolstra
author_sort	Yi Jin Liew
title	Identification of microRNAs in the coral Stylophora pistillata.
title_short	Identification of microRNAs in the coral Stylophora pistillata.
title_full	Identification of microRNAs in the coral Stylophora pistillata.
title_fullStr	Identification of microRNAs in the coral Stylophora pistillata.
title_full_unstemmed	Identification of microRNAs in the coral Stylophora pistillata.
title_sort	identification of micrornas in the coral stylophora pistillata.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/8ee4750ff34e48d89a9410b7305fd804
work_keys_str_mv	AT yijinliew identificationofmicrornasinthecoralstylophorapistillata AT manuelaranda identificationofmicrornasinthecoralstylophorapistillata AT adriancarr identificationofmicrornasinthecoralstylophorapistillata AT sebastianbaumgarten identificationofmicrornasinthecoralstylophorapistillata AT didierzoccola identificationofmicrornasinthecoralstylophorapistillata AT sylvietambutte identificationofmicrornasinthecoralstylophorapistillata AT denisallemand identificationofmicrornasinthecoralstylophorapistillata AT gosmicklem identificationofmicrornasinthecoralstylophorapistillata AT christianrvoolstra identificationofmicrornasinthecoralstylophorapistillata
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Identification of microRNAs in the coral Stylophora pistillata.

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