Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species

Non-coding RNA (ncRNA) is abundant in plant genomes, but is poorly described with unknown functionality in most species. Using whole genome RNA sequencing, we identified 1885, 1910 and 1299 lncRNAs and 186, 157 and 161 miRNAs at the whole genome level in the three Brassica species B. napus, B. olera...

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Autores principales: Zhang, Jinfang, Wei, Lijuan, Jiang, Jun, Mason, Annaliese S., Li, Haojie, Cui, Cheng, Chai, Liang, Zheng, Benchuan, Zhu, Yongqing, Xia, Qing, Jiang, Liangcai, Fu, Donghui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
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Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862966/
https://www.ncbi.nlm.nih.gov/pubmed/29563515
http://dx.doi.org/10.1038/s41598-018-23334-1
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author Zhang, Jinfang
Wei, Lijuan
Jiang, Jun
Mason, Annaliese S.
Li, Haojie
Cui, Cheng
Chai, Liang
Zheng, Benchuan
Zhu, Yongqing
Xia, Qing
Jiang, Liangcai
Fu, Donghui
author_facet Zhang, Jinfang
Wei, Lijuan
Jiang, Jun
Mason, Annaliese S.
Li, Haojie
Cui, Cheng
Chai, Liang
Zheng, Benchuan
Zhu, Yongqing
Xia, Qing
Jiang, Liangcai
Fu, Donghui
author_sort Zhang, Jinfang
collection PubMed
description Non-coding RNA (ncRNA) is abundant in plant genomes, but is poorly described with unknown functionality in most species. Using whole genome RNA sequencing, we identified 1885, 1910 and 1299 lncRNAs and 186, 157 and 161 miRNAs at the whole genome level in the three Brassica species B. napus, B. oleracea and B. rapa, respectively. The lncRNA sequences were divergent between the three Brassica species. One quarter of lncRNAs were located in tandem repeat (TR) region. The expression of both lncRNAs and miRNAs was strongly biased towards the A rather than the C subgenome in B. napus, unlike mRNA expression. miRNAs in genic regions had higher average expression than miRNAs in non-genic regions in B. napus and B. oleracea. We provide a comprehensive reference for the distribution, functionality and interactions of lncRNAs and miRNAs in Brassica.
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spelling pubmed-58629662018-03-27 Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species Zhang, Jinfang Wei, Lijuan Jiang, Jun Mason, Annaliese S. Li, Haojie Cui, Cheng Chai, Liang Zheng, Benchuan Zhu, Yongqing Xia, Qing Jiang, Liangcai Fu, Donghui Sci Rep Article Non-coding RNA (ncRNA) is abundant in plant genomes, but is poorly described with unknown functionality in most species. Using whole genome RNA sequencing, we identified 1885, 1910 and 1299 lncRNAs and 186, 157 and 161 miRNAs at the whole genome level in the three Brassica species B. napus, B. oleracea and B. rapa, respectively. The lncRNA sequences were divergent between the three Brassica species. One quarter of lncRNAs were located in tandem repeat (TR) region. The expression of both lncRNAs and miRNAs was strongly biased towards the A rather than the C subgenome in B. napus, unlike mRNA expression. miRNAs in genic regions had higher average expression than miRNAs in non-genic regions in B. napus and B. oleracea. We provide a comprehensive reference for the distribution, functionality and interactions of lncRNAs and miRNAs in Brassica. Nature Publishing Group UK 2018-03-21 /pmc/articles/PMC5862966/ /pubmed/29563515 http://dx.doi.org/10.1038/s41598-018-23334-1 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Zhang, Jinfang
Wei, Lijuan
Jiang, Jun
Mason, Annaliese S.
Li, Haojie
Cui, Cheng
Chai, Liang
Zheng, Benchuan
Zhu, Yongqing
Xia, Qing
Jiang, Liangcai
Fu, Donghui
Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
title Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
title_full Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
title_fullStr Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
title_full_unstemmed Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
title_short Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species
title_sort genome-wide identification, putative functionality and interactions between lncrnas and mirnas in brassica species
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862966/
https://www.ncbi.nlm.nih.gov/pubmed/29563515
http://dx.doi.org/10.1038/s41598-018-23334-1
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