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Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress

BACKGROUND: Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thu...

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Autores principales: Chen, Liang, Shi, Shilai, Jiang, Ninfei, Khanzada, Hira, Wassan, Ghulam Mustafa, Zhu, Changlan, Peng, Xiaosong, Xu, Jie, Chen, Yujin, Yu, Qiuying, He, Xiaopeng, Fu, Junru, Chen, Xiaorong, Hu, Lifang, Ouyang, Linjuan, Sun, Xiaotang, He, Haohua, Bian, Jianmin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002989/
https://www.ncbi.nlm.nih.gov/pubmed/29902991
http://dx.doi.org/10.1186/s12864-018-4807-6
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author Chen, Liang
Shi, Shilai
Jiang, Ninfei
Khanzada, Hira
Wassan, Ghulam Mustafa
Zhu, Changlan
Peng, Xiaosong
Xu, Jie
Chen, Yujin
Yu, Qiuying
He, Xiaopeng
Fu, Junru
Chen, Xiaorong
Hu, Lifang
Ouyang, Linjuan
Sun, Xiaotang
He, Haohua
Bian, Jianmin
author_facet Chen, Liang
Shi, Shilai
Jiang, Ninfei
Khanzada, Hira
Wassan, Ghulam Mustafa
Zhu, Changlan
Peng, Xiaosong
Xu, Jie
Chen, Yujin
Yu, Qiuying
He, Xiaopeng
Fu, Junru
Chen, Xiaorong
Hu, Lifang
Ouyang, Linjuan
Sun, Xiaotang
He, Haohua
Bian, Jianmin
author_sort Chen, Liang
collection PubMed
description BACKGROUND: Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress. RESULTS: The lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd. CONCLUSION: The present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4807-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-60029892018-07-06 Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress Chen, Liang Shi, Shilai Jiang, Ninfei Khanzada, Hira Wassan, Ghulam Mustafa Zhu, Changlan Peng, Xiaosong Xu, Jie Chen, Yujin Yu, Qiuying He, Xiaopeng Fu, Junru Chen, Xiaorong Hu, Lifang Ouyang, Linjuan Sun, Xiaotang He, Haohua Bian, Jianmin BMC Genomics Research Article BACKGROUND: Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress. RESULTS: The lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd. CONCLUSION: The present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4807-6) contains supplementary material, which is available to authorized users. BioMed Central 2018-06-15 /pmc/articles/PMC6002989/ /pubmed/29902991 http://dx.doi.org/10.1186/s12864-018-4807-6 Text en © The Author(s). 2018 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
Chen, Liang
Shi, Shilai
Jiang, Ninfei
Khanzada, Hira
Wassan, Ghulam Mustafa
Zhu, Changlan
Peng, Xiaosong
Xu, Jie
Chen, Yujin
Yu, Qiuying
He, Xiaopeng
Fu, Junru
Chen, Xiaorong
Hu, Lifang
Ouyang, Linjuan
Sun, Xiaotang
He, Haohua
Bian, Jianmin
Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress
title Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress
title_full Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress
title_fullStr Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress
title_full_unstemmed Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress
title_short Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress
title_sort genome-wide analysis of long non-coding rnas affecting roots development at an early stage in the rice response to cadmium stress
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6002989/
https://www.ncbi.nlm.nih.gov/pubmed/29902991
http://dx.doi.org/10.1186/s12864-018-4807-6
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