Unveiling the micronome of cassava (manihot esculenta crantz).

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dc.citation.doi10.1371/journal.pone.0147251en_ZA
dc.citation.issue1en_ZA
dc.contributor.authorRogans, S.J.
dc.contributor.authorRey, C.
dc.date.accessioned2016-09-16T09:45:37Z
dc.date.available2016-09-16T09:45:37Z
dc.date.issued2016-01-01
dc.description.abstractMicroRNAs (miRNAs) are an important class of endogenous non-coding single-stranded small RNAs (21-24 nt in length), which serve as post-transcriptional negative regulators of gene expression in plants. Despite the economic importance of Manihot esculenta Crantz (cassava) only 153 putative cassava miRNAs (from multiple germplasm) are available to date in miRBase (Version 21), and identification of a number of miRNAs from the cassava EST database have been limited to comparisons with Arabidopsis. In this study, mature sequences of all known plant miRNAs were used as a query for homologous searches against cassava EST and GSS databases, and additional identification of novel and conserved miRNAs were gleaned from next generation sequencing (NGS) of two cassava landraces (T200 from southern Africa and TME3 from West Africa) at three different stages post explant transplantation and acclimatization. EST and GSS derived data revealed 259 and 32 miRNAs in cassava, and one of the miRNA families (miR2118) from previous studies has not been reported in cassava. NGS data collectively displayed expression of 289 conserved miRNAs in leaf tissue, of which 230 had not been reported previously. Of the 289 conserved miRNAs identified in T200 and TME3, 208 were isomiRs. Thirty-nine novel cassava-specific miRNAs of low abundance, belonging to 29 families, were identified. Thirtyeight (98.6%) of the putative new miRNAs identified by NGS have not been previously reported in cassava. Several miRNA targets were identified in T200 and TME3, highlighting differential temporal miRNA expression between the two cassava landraces. This study contributes to the expanding knowledge base of the micronome of this important crop.en_ZA
dc.description.librarianNCS2016en_ZA
dc.description.sponsorshipThis work was supported by National Research Foundation (ZA) Grant number: 93467; National Research Foundation (ZA) Grant Number: 73895.en_ZA
dc.description.urlhttp://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147251en_ZA
dc.identifier.citationRogans, S.J. and Rey, C. 2016. Unveiling the micronome of cassava (manihot esculenta crantz). PLoS ONE 11(1) :e0147251.en_ZA
dc.identifier.issn1932-6203
dc.identifier.urihttp://hdl.handle.net/10539/21035
dc.journal.titlePLoS ONEen_ZA
dc.journal.volume11en_ZA
dc.language.isoenen_ZA
dc.publisherPublic Library of Science.en_ZA
dc.rights© 2016 Rogans, Rey. This 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_ZA
dc.subjectmicroRNA;en_ZA
dc.subjectmicroRNA 1435;en_ZA
dc.subjectmicroRNA 2118;en_ZA
dc.subjectmicroRNA 2275;en_ZA
dc.subjectmicroRNA 441;en_ZA
dc.subjectmicroRNA 582;en_ZA
dc.subjectmicroRNA 818;en_ZA
dc.subjectmicroRNA 821;en_ZA
dc.subjectribosome RNA;en_ZA
dc.subjectsmall nuclear RNA;en_ZA
dc.subjecttransfer RNA;en_ZA
dc.subjectunclassified drug;en_ZA
dc.subject3' untranslated region;en_ZA
dc.subject5' untranslated region;en_ZA
dc.subjectArticle;en_ZA
dc.subjectbase pairing;en_ZA
dc.subjectbinding affinity;en_ZA
dc.subjectcassava;en_ZA
dc.subjectcontrolled study;en_ZA
dc.subjectevolutionary adaptation;en_ZA
dc.subjectgene expression;en_ZA
dc.titleUnveiling the micronome of cassava (manihot esculenta crantz).en_ZA
dc.typeArticleen_ZA
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