Name:
Article - PLoS ONE - Identification of microRNAs in the coral Stylophora pistillata - 2014.pdf
Size:
1.084Mb
Format:
PDF
Description:
Article - Full Text
Name:
journal.pone.0091101.s001.zip
Size:
15.64Mb
Format:
Unknown
Description:
Supporting Information S1 - Stylophora pistillata transcriptome (43,493 genes/loci ≥250 bp, DDBJ/EMBL/GenBank accession GARY00000000). doi:10.1371/journal.pone.0091101.s001
Name:
journal.pone.0091101.s002.zip
Size:
3.288Mb
Format:
Unknown
Description:
Supporting Information S2 - Stylophora pistillata transcriptome BLASTX and GO annotation (43,493 genes/loci ≥250 bp). doi:10.1371/journal.pone.0091101.s002
Name:
journal.pone.0091101.s003.docx
Size:
17.55Kb
Format:
Microsoft Word 2007
Description:
Supporting Information S3 - Candidate RNAi proteins in Stylophora pistillata. doi:10.1371/journal.pone.0091101.s003
Name:
journal.pone.0091101.s004.fa
Size:
51.60Kb
Format:
Unknown
Description:
Supporting Information S4 - Alignment of sequences used to construct maximum-likelihood phylogenetic trees (FASTA format). doi:10.1371/journal.pone.0091101.s004
Name:
journal.pone.0091101.s005.eps
Size:
2.730Mb
Format:
Postscript
Description:
Supporting Information S5 - Graphical alignment of the PAZ domains in Argonaute and Piwi proteins. Of note are the strong conservation of glutamate (E) at position 137 (mutants produce insoluble protein) and phenylalanine (F) at position 72 (required for RNA binding). However, the phenylalanine at position 48 in D. melanogaster AGO2 (also required for RNA binding) was not conserved at all. Key residue positions are marked with red asterisks. doi:10.1371/journal.pone.0091101.s005
Name:
journal.pone.0091101.s006.eps
Size:
3.541Mb
Format:
Postscript
Description:
Supporting Information S6 - Graphical alignment of the Piwi domains in Argonaute and Piwi proteins. The catalytic DDX triad, which contributes to the slicing activity of the ribonuclease (marked in red asterisks), is located at positions 46, 140 and 284 or positions 46, 140 and 155. This triad is present in one S. pistillata candidate, but not in two others, most likely due to the transcript sequences being incomplete. doi:10.1371/journal.pone.0091101.s006
Name:
journal.pone.0091101.s007.eps
Size:
1.822Mb
Format:
Postscript
Description:
Supporting Information S7 - Graphical alignment of the first RNase III domain in Dicer and Drosha proteins. Remarkably, all of the key acidic aspartate (D) and glutamate (E) residues, which are involved in the coordination of a divalent metal cation, are conserved across the candidate homologues and known sequences. doi:10.1371/journal.pone.0091101.s007
Name:
journal.pone.0091101.s008.eps
Size:
1.485Mb
Format:
Postscript
Description:
Supporting Information S8 - Graphical alignment of the second RNase III domain in Dicer and Drosha proteins. Similarly, most of the aspartate (D) and glutamate (E) residues involved in the coordination of a divalent metal cation are conserved - perfectly conserved for the Drosha candidate (“Locus_18820”), while the Dicer candidate (“Locus_10081”) only has the first two key residues. Both sequences however align well to known Dicer and Drosha proteins. doi:10.1371/journal.pone.0091101.s008
Name:
journal.pone.0091101.s009.eps
Size:
753.9Kb
Format:
Postscript
Description:
Supporting Information S9 - Graphical alignment of the dsRNA-binding domain in Pasha. The key alanine/alanine pair (AA, positions 21 and 22) and alanine/serine pair (AS, positions 139 and 140) involved in the binding of dsRNA are also present in the S. pistillata candidate Pasha. As Pasha is an essential cofactor of Drosha, it lends support to the positive discovery of Drosha in S. pistillata. doi:10.1371/journal.pone.0091101.s009
Name:
journal.pone.0091101.s010.eps
Size:
888.9Kb
Format:
Postscript
Description:
Supporting Information S10 - Graphical alignment of the methyltransferase domain in HEN1. The residues involved in Mg2+ coordination (positions 118, 121, 122 and 123) are well-conserved across the aligned sequences; residues associated with the cofactor AdoHcy and 3′ terminus (other positions marked by a red asterisk) are also well conserved. doi:10.1371/journal.pone.0091101.s010
Name:
journal.pone.0091101.s011.xlsx
Size:
29.38Kb
Format:
Microsoft Excel 2007
Description:
Supporting Information S11 - List of additional criteria used to select bona fide miRNAs in S. pistillata from miRDeep2 results. doi:10.1371/journal.pone.0091101.s011
Name:
journal.pone.0091101.s012.xlsx
Size:
42.76Kb
Format:
Microsoft Excel 2007
Description:
Supporting Information S12 - Enriched GO terms (P<0.01) associated with the set of 31 bona fide miRNAs identified in Stylophora pistillata. doi:10.1371/journal.pone.0091101.s012
Type
ArticleAuthors
Liew, Yi Jin
Aranda, Manuel

Carr, Adrian
Baumgarten, Sebastian

Zoccola, Didier

Tambutté, Sylvie
Allemand, Denis
Micklem, Gos
Voolstra, Christian R.

KAUST Department
Biological and Environmental Sciences and Engineering (BESE) DivisionMarine Science Program
Red Sea Research Center (RSRC)
Reef Genomics Lab
Date
2014-03-21Permanent link to this record
http://hdl.handle.net/10754/323560
Metadata
Show full item recordAbstract
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.Citation
Liew YJ, Aranda M, Carr A, Baumgarten S, Zoccola D, et al. (2014) Identification of MicroRNAs in the Coral Stylophora pistillata. PLoS ONE 9: e91101. doi:10.1371/journal.pone.0091101.Sponsors
This project was partially funded by bursaries from Cambridge Commonwealth Trust and Trinity Hall to YJL, and an Academic Excellence Alliance (AEA) Award (Award Number 1000000533) to CRV and GM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Publisher
Public Library of Science (PLoS)Journal
PLoS ONEPubMed ID
24658574PubMed Central ID
PMC3962355Additional Links
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0091101http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962355/
ae974a485f413a2113503eed53cd6c53
10.1371/journal.pone.0091101
Scopus Count
Related articles
- A microRNA regulates the response of corals to thermal stress.
- Authors: Gajigan AP, Conaco C
- Issue date: 2017 Jul
- Intracellular pH regulation: characterization and functional investigation of H(+) transporters in Stylophora pistillata.
- Authors: Capasso L, Ganot P, Planas-Bielsa V, Tambutté S, Zoccola D
- Issue date: 2021 Mar 8
- Transcriptome analysis of the scleractinian coral Stylophora pistillata.
- Authors: Karako-Lampert S, Zoccola D, Salmon-Divon M, Katzenellenbogen M, Tambutté S, Bertucci A, Hoegh-Guldberg O, Deleury E, Allemand D, Levy O
- Issue date: 2014
- Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals.
- Authors: Voolstra CR, Li Y, Liew YJ, Baumgarten S, Zoccola D, Flot JF, Tambutté S, Allemand D, Aranda M
- Issue date: 2017 Dec 14
- Eutrophication may compromise the resilience of the Red Sea coral Stylophora pistillata to global change.
- Authors: Hall ER, Muller EM, Goulet T, Bellworthy J, Ritchie KB, Fine M
- Issue date: 2018 Jun