Identification and Analysis of Red Sea Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and Their Association with Stress Responses

Handle URI:
http://hdl.handle.net/10754/325314
Title:
Identification and Analysis of Red Sea Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and Their Association with Stress Responses
Authors:
Khraiwesh, Basel; Pugalenthi, Ganesan; Fedoroff, Nina V.
Abstract:
Although RNA silencing has been studied primarily in model plants, advances in high-throughput sequencing technologies have enabled profiling of the small RNA components of many more plant species, providing insights into the ubiquity and conservatism of some miRNA-based regulatory mechanisms. Small RNAs of 20 to 24 nucleotides (nt) are important regulators of gene transcript levels by either transcriptional or by posttranscriptional gene silencing, contributing to genome maintenance and controlling a variety of developmental and physiological processes. Here, we used deep sequencing and molecular methods to create an inventory of the small RNAs in the mangrove species, Avicennia marina. We identified 26 novel mangrove miRNAs and 193 conserved miRNAs belonging to 36 families. We determined that 2 of the novel miRNAs were produced from known miRNA precursors and 4 were likely to be species-specific by the criterion that we found no homologs in other plant species. We used qRT-PCR to analyze the expression of miRNAs and their target genes in different tissue sets and some demonstrated tissue-specific expression. Furthermore, we predicted potential targets of these putative miRNAs based on a sequence homology and experimentally validated through endonucleolytic cleavage assays. Our results suggested that expression profiles of miRNAs and their predicted targets could be useful in exploring the significance of the conservation patterns of plants, particularly in response to abiotic stress. Because of their well-developed abilities in this regard, mangroves and other extremophiles are excellent models for such exploration. © 2013 Khraiwesh et al.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Center for Desert Agriculture; Biosciences Core Lab
Citation:
Khraiwesh B, Pugalenthi G, Fedoroff NV (2013) Identification and Analysis of Red Sea Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and Their Association with Stress Responses. PLoS ONE 8: e60774. doi:10.1371/journal.pone.0060774.
Publisher:
Public Library of Science
Journal:
PLoS ONE
Issue Date:
8-Apr-2013
DOI:
10.1371/journal.pone.0060774
PubMed ID:
23593307
PubMed Central ID:
PMC3620391
Type:
Article
ISSN:
19326203
Appears in Collections:
Articles; Biosciences Core Lab; Center for Desert Agriculture; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorKhraiwesh, Baselen
dc.contributor.authorPugalenthi, Ganesanen
dc.contributor.authorFedoroff, Nina V.en
dc.date.accessioned2014-08-27T09:46:32Zen
dc.date.available2014-08-27T09:46:32Zen
dc.date.issued2013-04-08en
dc.identifier.citationKhraiwesh B, Pugalenthi G, Fedoroff NV (2013) Identification and Analysis of Red Sea Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and Their Association with Stress Responses. PLoS ONE 8: e60774. doi:10.1371/journal.pone.0060774.en
dc.identifier.issn19326203en
dc.identifier.pmid23593307en
dc.identifier.doi10.1371/journal.pone.0060774en
dc.identifier.urihttp://hdl.handle.net/10754/325314en
dc.description.abstractAlthough RNA silencing has been studied primarily in model plants, advances in high-throughput sequencing technologies have enabled profiling of the small RNA components of many more plant species, providing insights into the ubiquity and conservatism of some miRNA-based regulatory mechanisms. Small RNAs of 20 to 24 nucleotides (nt) are important regulators of gene transcript levels by either transcriptional or by posttranscriptional gene silencing, contributing to genome maintenance and controlling a variety of developmental and physiological processes. Here, we used deep sequencing and molecular methods to create an inventory of the small RNAs in the mangrove species, Avicennia marina. We identified 26 novel mangrove miRNAs and 193 conserved miRNAs belonging to 36 families. We determined that 2 of the novel miRNAs were produced from known miRNA precursors and 4 were likely to be species-specific by the criterion that we found no homologs in other plant species. We used qRT-PCR to analyze the expression of miRNAs and their target genes in different tissue sets and some demonstrated tissue-specific expression. Furthermore, we predicted potential targets of these putative miRNAs based on a sequence homology and experimentally validated through endonucleolytic cleavage assays. Our results suggested that expression profiles of miRNAs and their predicted targets could be useful in exploring the significance of the conservation patterns of plants, particularly in response to abiotic stress. Because of their well-developed abilities in this regard, mangroves and other extremophiles are excellent models for such exploration. © 2013 Khraiwesh et al.en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.rightsArchived with thanks to PLoS ONEen
dc.subjectmicroRNAen
dc.subjectabiotic stressen
dc.subjectAvicenniaen
dc.subjectAvicennia marinaen
dc.subjectgene expression profilingen
dc.subjectgenetic conservationen
dc.subjecthigh throughput sequencingen
dc.subjectmangroveen
dc.subjectmultigene familyen
dc.subjectnucleotide sequenceen
dc.subjectreverse transcription polymerase chain reactionen
dc.subjectRNA analysisen
dc.subjectRNA cleavageen
dc.subjectsequence homologyen
dc.subjectspecies differenceen
dc.subjecttissue specificityen
dc.subjectAvicenniaen
dc.subjectBase Sequenceen
dc.subjectConserved Sequenceen
dc.subjectHigh-Throughput Nucleotide Sequencingen
dc.subjectMicroRNAsen
dc.subjectMolecular Sequence Annotationen
dc.subjectMolecular Sequence Dataen
dc.subjectRNA Cleavageen
dc.subjectRNA, Planten
dc.subjectRNA, Small Interferingen
dc.subjectSequence Analysis, RNAen
dc.subjectStress, Physiologicalen
dc.subjectTranscriptomeen
dc.subjectAvicennia marinaen
dc.subjectRhizophoraceaeen
dc.titleIdentification and Analysis of Red Sea Mangrove (Avicennia marina) microRNAs by High-Throughput Sequencing and Their Association with Stress Responsesen
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentCenter for Desert Agricultureen
dc.contributor.departmentBiosciences Core Laben
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3620391en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionEvan Pugh Professor, Huck Institutes of the Life Sciences, Penn State University, University Park, PA, United Statesen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorKhraiwesh, Baselen
kaust.authorGanesan, Pugalenthien
kaust.authorFedoroff, Nina V.en

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