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Identification of cucumber circular RNAs responsive to salt stress
BACKGROUND: Circular RNAs (circRNAs) are 3′-5′ head-to-tail covalently closed non-coding RNA that have been proved to play essential roles in many cellular and developmental processes. However, no information relate to cucumber circRNAs is available currently, especially under salt stress condition....
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486992/ https://www.ncbi.nlm.nih.gov/pubmed/31029105 http://dx.doi.org/10.1186/s12870-019-1712-3 |
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author | Zhu, Yong-Xing Jia, Jian-Hua Yang, Lei Xia, Yu-Chen Zhang, Hui-Li Jia, Jin-Bu Zhou, Ran Nie, Pei-Yao Yin, Jun-Liang Ma, Dong-Fang Liu, Le-Cheng |
author_facet | Zhu, Yong-Xing Jia, Jian-Hua Yang, Lei Xia, Yu-Chen Zhang, Hui-Li Jia, Jin-Bu Zhou, Ran Nie, Pei-Yao Yin, Jun-Liang Ma, Dong-Fang Liu, Le-Cheng |
author_sort | Zhu, Yong-Xing |
collection | PubMed |
description | BACKGROUND: Circular RNAs (circRNAs) are 3′-5′ head-to-tail covalently closed non-coding RNA that have been proved to play essential roles in many cellular and developmental processes. However, no information relate to cucumber circRNAs is available currently, especially under salt stress condition. RESULTS: In this study, we sequenced circRNAs in cucumber and a total of 2787 were identified, with 1934 in root and 44 in leaf being differentially regulated under salt stress. Characteristics analysis of these circRNAs revealed following features: most of them are exon circRNAs (79.51%) and they prefer to arise from middle exon(s) of parent genes (2035/2516); moreover, most of circularization events (88.3%) use non-canonical-GT/AG splicing signals; last but not least, pairing-driven circularization is not the major way to generate cucumber circRNAs since very few circRNAs (18) contain sufficient flanking complementary sequences. Annotation and enrichment analysis of both parental genes and target mRNAs were launched to uncover the functions of differentially expressed circRNAs induced by salt stress. The results showed that circRNAs may be paly roles in salt stress response by mediating transcription, signal transcription, cell cycle, metabolism adaptation, and ion homeostasis related pathways. Moreover, circRNAs may function to regulate proline metabolisms through regulating associated biosynthesis and degradation genes. CONCLUSIONS: The present study identified large number of cucumber circRNAs and function annotation revealed their possible biological roles in response to salt stress. Our findings will lay a solid foundation for further structure and function studies of cucumber circRNAs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1712-3) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6486992 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-64869922019-05-06 Identification of cucumber circular RNAs responsive to salt stress Zhu, Yong-Xing Jia, Jian-Hua Yang, Lei Xia, Yu-Chen Zhang, Hui-Li Jia, Jin-Bu Zhou, Ran Nie, Pei-Yao Yin, Jun-Liang Ma, Dong-Fang Liu, Le-Cheng BMC Plant Biol Research Article BACKGROUND: Circular RNAs (circRNAs) are 3′-5′ head-to-tail covalently closed non-coding RNA that have been proved to play essential roles in many cellular and developmental processes. However, no information relate to cucumber circRNAs is available currently, especially under salt stress condition. RESULTS: In this study, we sequenced circRNAs in cucumber and a total of 2787 were identified, with 1934 in root and 44 in leaf being differentially regulated under salt stress. Characteristics analysis of these circRNAs revealed following features: most of them are exon circRNAs (79.51%) and they prefer to arise from middle exon(s) of parent genes (2035/2516); moreover, most of circularization events (88.3%) use non-canonical-GT/AG splicing signals; last but not least, pairing-driven circularization is not the major way to generate cucumber circRNAs since very few circRNAs (18) contain sufficient flanking complementary sequences. Annotation and enrichment analysis of both parental genes and target mRNAs were launched to uncover the functions of differentially expressed circRNAs induced by salt stress. The results showed that circRNAs may be paly roles in salt stress response by mediating transcription, signal transcription, cell cycle, metabolism adaptation, and ion homeostasis related pathways. Moreover, circRNAs may function to regulate proline metabolisms through regulating associated biosynthesis and degradation genes. CONCLUSIONS: The present study identified large number of cucumber circRNAs and function annotation revealed their possible biological roles in response to salt stress. Our findings will lay a solid foundation for further structure and function studies of cucumber circRNAs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1712-3) contains supplementary material, which is available to authorized users. BioMed Central 2019-04-27 /pmc/articles/PMC6486992/ /pubmed/31029105 http://dx.doi.org/10.1186/s12870-019-1712-3 Text en © The Author(s). 2019 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 Zhu, Yong-Xing Jia, Jian-Hua Yang, Lei Xia, Yu-Chen Zhang, Hui-Li Jia, Jin-Bu Zhou, Ran Nie, Pei-Yao Yin, Jun-Liang Ma, Dong-Fang Liu, Le-Cheng Identification of cucumber circular RNAs responsive to salt stress |
title | Identification of cucumber circular RNAs responsive to salt stress |
title_full | Identification of cucumber circular RNAs responsive to salt stress |
title_fullStr | Identification of cucumber circular RNAs responsive to salt stress |
title_full_unstemmed | Identification of cucumber circular RNAs responsive to salt stress |
title_short | Identification of cucumber circular RNAs responsive to salt stress |
title_sort | identification of cucumber circular rnas responsive to salt stress |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486992/ https://www.ncbi.nlm.nih.gov/pubmed/31029105 http://dx.doi.org/10.1186/s12870-019-1712-3 |
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