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Domestication of Transposable Elements into MicroRNA Genes in Plants

Transposable elements (TE) usually take up a substantial portion of eukaryotic genome. Activities of TEs can cause genome instability or gene mutations that are harmful or even disastrous to the host. TEs also contribute to gene and genome evolution at many aspects. Part of miRNA genes in mammals ha...

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Autores principales: Li, Yang, Li, Chaoqun, Xia, Jie, Jin, Youxin
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086885/
https://www.ncbi.nlm.nih.gov/pubmed/21559273
http://dx.doi.org/10.1371/journal.pone.0019212
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author Li, Yang
Li, Chaoqun
Xia, Jie
Jin, Youxin
author_facet Li, Yang
Li, Chaoqun
Xia, Jie
Jin, Youxin
author_sort Li, Yang
collection PubMed
description Transposable elements (TE) usually take up a substantial portion of eukaryotic genome. Activities of TEs can cause genome instability or gene mutations that are harmful or even disastrous to the host. TEs also contribute to gene and genome evolution at many aspects. Part of miRNA genes in mammals have been found to derive from transposons while convincing evidences are absent for plants. We found that a considerable number of previously annotated plant miRNAs are identical or homologous to transposons (TE-MIR), which include a small number of bona fide miRNA genes that conform to generally accepted plant miRNA annotation rules, and hairpin derived siRNAs likely to be pre-evolved miRNAs. Analysis of these TE-MIRs indicate that transitions from the medium to high copy TEs into miRNA genes may undergo steps such as inverted repeat formation, sequence speciation and adaptation to miRNA biogenesis. We also identified initial target genes of the TE-MIRs, which contain homologous sequences in their CDS as consequence of cognate TE insertions. About one-third of the initial target mRNAs are supported by publicly available degradome sequencing data for TE-MIR sRNA induced cleavages. Targets of the TE-MIRs are biased to non-TE related genes indicating their penchant to acquire cellular functions during evolution. Interestingly, most of these TE insertions span boundaries between coding and non-coding sequences indicating their incorporation into CDS through alteration of splicing or translation start or stop signals. Taken together, our findings suggest that TEs in gene rich regions can form foldbacks in non-coding part of transcripts that may eventually evolve into miRNA genes or be integrated into protein coding sequences to form potential targets in a “temperate” manner. Thus, transposons may supply as resources for the evolution of miRNA-target interactions in plants.
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spelling pubmed-30868852011-05-10 Domestication of Transposable Elements into MicroRNA Genes in Plants Li, Yang Li, Chaoqun Xia, Jie Jin, Youxin PLoS One Research Article Transposable elements (TE) usually take up a substantial portion of eukaryotic genome. Activities of TEs can cause genome instability or gene mutations that are harmful or even disastrous to the host. TEs also contribute to gene and genome evolution at many aspects. Part of miRNA genes in mammals have been found to derive from transposons while convincing evidences are absent for plants. We found that a considerable number of previously annotated plant miRNAs are identical or homologous to transposons (TE-MIR), which include a small number of bona fide miRNA genes that conform to generally accepted plant miRNA annotation rules, and hairpin derived siRNAs likely to be pre-evolved miRNAs. Analysis of these TE-MIRs indicate that transitions from the medium to high copy TEs into miRNA genes may undergo steps such as inverted repeat formation, sequence speciation and adaptation to miRNA biogenesis. We also identified initial target genes of the TE-MIRs, which contain homologous sequences in their CDS as consequence of cognate TE insertions. About one-third of the initial target mRNAs are supported by publicly available degradome sequencing data for TE-MIR sRNA induced cleavages. Targets of the TE-MIRs are biased to non-TE related genes indicating their penchant to acquire cellular functions during evolution. Interestingly, most of these TE insertions span boundaries between coding and non-coding sequences indicating their incorporation into CDS through alteration of splicing or translation start or stop signals. Taken together, our findings suggest that TEs in gene rich regions can form foldbacks in non-coding part of transcripts that may eventually evolve into miRNA genes or be integrated into protein coding sequences to form potential targets in a “temperate” manner. Thus, transposons may supply as resources for the evolution of miRNA-target interactions in plants. Public Library of Science 2011-05-03 /pmc/articles/PMC3086885/ /pubmed/21559273 http://dx.doi.org/10.1371/journal.pone.0019212 Text en Li 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
Li, Yang
Li, Chaoqun
Xia, Jie
Jin, Youxin
Domestication of Transposable Elements into MicroRNA Genes in Plants
title Domestication of Transposable Elements into MicroRNA Genes in Plants
title_full Domestication of Transposable Elements into MicroRNA Genes in Plants
title_fullStr Domestication of Transposable Elements into MicroRNA Genes in Plants
title_full_unstemmed Domestication of Transposable Elements into MicroRNA Genes in Plants
title_short Domestication of Transposable Elements into MicroRNA Genes in Plants
title_sort domestication of transposable elements into microrna genes in plants
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3086885/
https://www.ncbi.nlm.nih.gov/pubmed/21559273
http://dx.doi.org/10.1371/journal.pone.0019212
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