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Bioinformatic Identification and Expression Analysis of Banana MicroRNAs and Their Targets

MicroRNAs (miRNAs) represent a class of endogenous non-coding small RNAs that play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. Thousands of miRNAs have been identified in many plant species, whereas only a limited number of miRNAs have...

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Autores principales: Chai, Juan, Feng, Renjun, Shi, Hourui, Ren, Mengyun, Zhang, Yindong, Wang, Jingyi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391839/
https://www.ncbi.nlm.nih.gov/pubmed/25856313
http://dx.doi.org/10.1371/journal.pone.0123083
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author Chai, Juan
Feng, Renjun
Shi, Hourui
Ren, Mengyun
Zhang, Yindong
Wang, Jingyi
author_facet Chai, Juan
Feng, Renjun
Shi, Hourui
Ren, Mengyun
Zhang, Yindong
Wang, Jingyi
author_sort Chai, Juan
collection PubMed
description MicroRNAs (miRNAs) represent a class of endogenous non-coding small RNAs that play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. Thousands of miRNAs have been identified in many plant species, whereas only a limited number of miRNAs have been predicted in M. acuminata (A genome) and M. balbisiana (B genome). Here, previously known plant miRNAs were BLASTed against the Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS), a database of banana genes. A total of 32 potential miRNAs belonging to 13 miRNAs families were detected using a range of filtering criteria. 244 miRNA:target pairs were subsequently predicted, most of which encode transcription factors or enzymes that participate in the regulation of development, growth, metabolism, and other physiological processes. In order to validate the predicted miRNAs and the mutual relationship between miRNAs and their target genes, qRT-PCR was applied to detect the tissue-specific expression levels of 12 putative miRNAs and 6 target genes in roots, leaves, flowers, and fruits. This study provides some important information about banana pre-miRNAs, mature miRNAs, and miRNA target genes and these findings can be applied to future research of miRNA functions.
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spelling pubmed-43918392015-04-21 Bioinformatic Identification and Expression Analysis of Banana MicroRNAs and Their Targets Chai, Juan Feng, Renjun Shi, Hourui Ren, Mengyun Zhang, Yindong Wang, Jingyi PLoS One Research Article MicroRNAs (miRNAs) represent a class of endogenous non-coding small RNAs that play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. Thousands of miRNAs have been identified in many plant species, whereas only a limited number of miRNAs have been predicted in M. acuminata (A genome) and M. balbisiana (B genome). Here, previously known plant miRNAs were BLASTed against the Expressed Sequence Tag (EST) and Genomic Survey Sequence (GSS), a database of banana genes. A total of 32 potential miRNAs belonging to 13 miRNAs families were detected using a range of filtering criteria. 244 miRNA:target pairs were subsequently predicted, most of which encode transcription factors or enzymes that participate in the regulation of development, growth, metabolism, and other physiological processes. In order to validate the predicted miRNAs and the mutual relationship between miRNAs and their target genes, qRT-PCR was applied to detect the tissue-specific expression levels of 12 putative miRNAs and 6 target genes in roots, leaves, flowers, and fruits. This study provides some important information about banana pre-miRNAs, mature miRNAs, and miRNA target genes and these findings can be applied to future research of miRNA functions. Public Library of Science 2015-04-09 /pmc/articles/PMC4391839/ /pubmed/25856313 http://dx.doi.org/10.1371/journal.pone.0123083 Text en © 2015 Chai et al http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
spellingShingle Research Article
Chai, Juan
Feng, Renjun
Shi, Hourui
Ren, Mengyun
Zhang, Yindong
Wang, Jingyi
Bioinformatic Identification and Expression Analysis of Banana MicroRNAs and Their Targets
title Bioinformatic Identification and Expression Analysis of Banana MicroRNAs and Their Targets
title_full Bioinformatic Identification and Expression Analysis of Banana MicroRNAs and Their Targets
title_fullStr Bioinformatic Identification and Expression Analysis of Banana MicroRNAs and Their Targets
title_full_unstemmed Bioinformatic Identification and Expression Analysis of Banana MicroRNAs and Their Targets
title_short Bioinformatic Identification and Expression Analysis of Banana MicroRNAs and Their Targets
title_sort bioinformatic identification and expression analysis of banana micrornas and their targets
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391839/
https://www.ncbi.nlm.nih.gov/pubmed/25856313
http://dx.doi.org/10.1371/journal.pone.0123083
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