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High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs

BACKGROUND: Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential expression and regulate gene expression mainly through direct cleavage...

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Autores principales: Khatabi, Behnam, Arikit, Siwaret, Xia, Rui, Winter, Stephan, Oumar, Doungous, Mongomake, Kone, Meyers, Blake C., Fondong, Vincent N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730657/
https://www.ncbi.nlm.nih.gov/pubmed/26822616
http://dx.doi.org/10.1186/s12864-016-2391-1
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author Khatabi, Behnam
Arikit, Siwaret
Xia, Rui
Winter, Stephan
Oumar, Doungous
Mongomake, Kone
Meyers, Blake C.
Fondong, Vincent N.
author_facet Khatabi, Behnam
Arikit, Siwaret
Xia, Rui
Winter, Stephan
Oumar, Doungous
Mongomake, Kone
Meyers, Blake C.
Fondong, Vincent N.
author_sort Khatabi, Behnam
collection PubMed
description BACKGROUND: Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential expression and regulate gene expression mainly through direct cleavage of mRNA or indirectly via production of secondary phased siRNAs (phasiRNAs) that silence cognate target transcripts in trans. RESULTS: Here, we have identified cassava (Manihot esculenta Crantz) miRNAs using high resolution sequencing of sRNA libraries from leaf, stem, callus, male and female flower tissues. To analyze the data, we built a cassava genome database and, via sequence analysis and secondary structure prediction, 38 miRNAs not previously reported in cassava were identified. These new cassava miRNAs included two miRNAs not previously been reported in any plant species. The miRNAs exhibited tissue-differential accumulation as confirmed by quantitative RT-PCR and Northern blot analysis, largely reflecting levels observed in sequencing data. Some of the miRNAs identified were predicted to trigger production of secondary phased siRNAs (phasiRNAs) from 80 PHAS loci. CONCLUSIONS: Cassava is a woody perennial shrub, grown principally for its starch-rich storage roots, which are rich in calories. In this study, new miRNAs were identified and their expression was validated using qRT-PCR of RNA from five different tissues. The data obtained expand the list of annotated miRNAs and provide additional new resources for cassava improvement research. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2391-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-47306572016-01-29 High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs Khatabi, Behnam Arikit, Siwaret Xia, Rui Winter, Stephan Oumar, Doungous Mongomake, Kone Meyers, Blake C. Fondong, Vincent N. BMC Genomics Research Article BACKGROUND: Small RNAs (sRNAs) are endogenous sRNAs that play regulatory roles in plant growth, development, and biotic and abiotic stress responses. In plants, one subset of sRNAs, microRNAs (miRNAs) exhibit tissue-differential expression and regulate gene expression mainly through direct cleavage of mRNA or indirectly via production of secondary phased siRNAs (phasiRNAs) that silence cognate target transcripts in trans. RESULTS: Here, we have identified cassava (Manihot esculenta Crantz) miRNAs using high resolution sequencing of sRNA libraries from leaf, stem, callus, male and female flower tissues. To analyze the data, we built a cassava genome database and, via sequence analysis and secondary structure prediction, 38 miRNAs not previously reported in cassava were identified. These new cassava miRNAs included two miRNAs not previously been reported in any plant species. The miRNAs exhibited tissue-differential accumulation as confirmed by quantitative RT-PCR and Northern blot analysis, largely reflecting levels observed in sequencing data. Some of the miRNAs identified were predicted to trigger production of secondary phased siRNAs (phasiRNAs) from 80 PHAS loci. CONCLUSIONS: Cassava is a woody perennial shrub, grown principally for its starch-rich storage roots, which are rich in calories. In this study, new miRNAs were identified and their expression was validated using qRT-PCR of RNA from five different tissues. The data obtained expand the list of annotated miRNAs and provide additional new resources for cassava improvement research. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2391-1) contains supplementary material, which is available to authorized users. BioMed Central 2016-01-28 /pmc/articles/PMC4730657/ /pubmed/26822616 http://dx.doi.org/10.1186/s12864-016-2391-1 Text en © Khatabi et al. 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Khatabi, Behnam
Arikit, Siwaret
Xia, Rui
Winter, Stephan
Oumar, Doungous
Mongomake, Kone
Meyers, Blake C.
Fondong, Vincent N.
High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs
title High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs
title_full High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs
title_fullStr High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs
title_full_unstemmed High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs
title_short High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs
title_sort high-resolution identification and abundance profiling of cassava (manihot esculenta crantz) micrornas
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4730657/
https://www.ncbi.nlm.nih.gov/pubmed/26822616
http://dx.doi.org/10.1186/s12864-016-2391-1
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