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Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa

MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play essential roles in eukaryotes. Although the influence of whole-genome triplication (WGT) on protein-coding genes has been well documented in Brassica rapa, little is known about its impacts on MIRNAs. In this study, throug...

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Autores principales: Sun, Chao, Wu, Jian, Liang, Jianli, Schnable, James C., Yang, Wencai, Cheng, Feng, Wang, Xiaowu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635596/
https://www.ncbi.nlm.nih.gov/pubmed/26527651
http://dx.doi.org/10.1093/gbe/evv206
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author Sun, Chao
Wu, Jian
Liang, Jianli
Schnable, James C.
Yang, Wencai
Cheng, Feng
Wang, Xiaowu
author_facet Sun, Chao
Wu, Jian
Liang, Jianli
Schnable, James C.
Yang, Wencai
Cheng, Feng
Wang, Xiaowu
author_sort Sun, Chao
collection PubMed
description MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play essential roles in eukaryotes. Although the influence of whole-genome triplication (WGT) on protein-coding genes has been well documented in Brassica rapa, little is known about its impacts on MIRNAs. In this study, through generating a comprehensive annotation of 680 MIRNAs for B. rapa, we analyzed the evolutionary characteristics of these MIRNAs from different aspects in B. rapa. First, while MIRNAs and genes show similar patterns of biased distribution among subgenomes of B. rapa, we found that MIRNAs are much more overretained than genes following fractionation after WGT. Second, multiple-copy MIRNAs show significant sequence conservation than that of single-copy MIRNAs, which is opposite to that of genes. This indicates that increased purifying selection is acting upon these highly retained multiple-copy MIRNAs and their functional importance over singleton MIRNAs. Furthermore, we found the extensive divergence between pairs of miRNAs and their target genes following the WGT in B. rapa. In summary, our study provides a valuable resource for exploring MIRNA in B. rapa and highlights the impacts of WGT on the evolution of MIRNA.
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spelling pubmed-56355962017-10-16 Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa Sun, Chao Wu, Jian Liang, Jianli Schnable, James C. Yang, Wencai Cheng, Feng Wang, Xiaowu Genome Biol Evol Research Article MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play essential roles in eukaryotes. Although the influence of whole-genome triplication (WGT) on protein-coding genes has been well documented in Brassica rapa, little is known about its impacts on MIRNAs. In this study, through generating a comprehensive annotation of 680 MIRNAs for B. rapa, we analyzed the evolutionary characteristics of these MIRNAs from different aspects in B. rapa. First, while MIRNAs and genes show similar patterns of biased distribution among subgenomes of B. rapa, we found that MIRNAs are much more overretained than genes following fractionation after WGT. Second, multiple-copy MIRNAs show significant sequence conservation than that of single-copy MIRNAs, which is opposite to that of genes. This indicates that increased purifying selection is acting upon these highly retained multiple-copy MIRNAs and their functional importance over singleton MIRNAs. Furthermore, we found the extensive divergence between pairs of miRNAs and their target genes following the WGT in B. rapa. In summary, our study provides a valuable resource for exploring MIRNA in B. rapa and highlights the impacts of WGT on the evolution of MIRNA. Oxford University Press 2015-11-01 /pmc/articles/PMC5635596/ /pubmed/26527651 http://dx.doi.org/10.1093/gbe/evv206 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Research Article
Sun, Chao
Wu, Jian
Liang, Jianli
Schnable, James C.
Yang, Wencai
Cheng, Feng
Wang, Xiaowu
Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa
title Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa
title_full Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa
title_fullStr Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa
title_full_unstemmed Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa
title_short Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa
title_sort impacts of whole-genome triplication on mirna evolution in brassica rapa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635596/
https://www.ncbi.nlm.nih.gov/pubmed/26527651
http://dx.doi.org/10.1093/gbe/evv206
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