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Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage

Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 spe...

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Autores principales: Song, Xiaoming, Hu, Jingjing, Wu, Tong, Yang, Qihang, Feng, Xuehuan, Lin, Hao, Feng, Shuyan, Cui, Chunlin, Yu, Ying, Zhou, Rong, Gong, Ke, Yu, Tong, Pei, Qiaoying, Li, Nan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7917108/
https://www.ncbi.nlm.nih.gov/pubmed/33642591
http://dx.doi.org/10.1038/s41438-021-00484-4
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author Song, Xiaoming
Hu, Jingjing
Wu, Tong
Yang, Qihang
Feng, Xuehuan
Lin, Hao
Feng, Shuyan
Cui, Chunlin
Yu, Ying
Zhou, Rong
Gong, Ke
Yu, Tong
Pei, Qiaoying
Li, Nan
author_facet Song, Xiaoming
Hu, Jingjing
Wu, Tong
Yang, Qihang
Feng, Xuehuan
Lin, Hao
Feng, Shuyan
Cui, Chunlin
Yu, Ying
Zhou, Rong
Gong, Ke
Yu, Tong
Pei, Qiaoying
Li, Nan
author_sort Song, Xiaoming
collection PubMed
description Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the “protein processing in endoplasmic reticulum” and “plant hormone signal transduction” pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.
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spelling pubmed-79171082021-03-12 Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage Song, Xiaoming Hu, Jingjing Wu, Tong Yang, Qihang Feng, Xuehuan Lin, Hao Feng, Shuyan Cui, Chunlin Yu, Ying Zhou, Rong Gong, Ke Yu, Tong Pei, Qiaoying Li, Nan Hortic Res Article Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the “protein processing in endoplasmic reticulum” and “plant hormone signal transduction” pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies. Nature Publishing Group UK 2021-03-01 /pmc/articles/PMC7917108/ /pubmed/33642591 http://dx.doi.org/10.1038/s41438-021-00484-4 Text en © The Author(s) 2021 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
Song, Xiaoming
Hu, Jingjing
Wu, Tong
Yang, Qihang
Feng, Xuehuan
Lin, Hao
Feng, Shuyan
Cui, Chunlin
Yu, Ying
Zhou, Rong
Gong, Ke
Yu, Tong
Pei, Qiaoying
Li, Nan
Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage
title Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage
title_full Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage
title_fullStr Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage
title_full_unstemmed Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage
title_short Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage
title_sort comparative analysis of long noncoding rnas in angiosperms and characterization of long noncoding rnas in response to heat stress in chinese cabbage
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7917108/
https://www.ncbi.nlm.nih.gov/pubmed/33642591
http://dx.doi.org/10.1038/s41438-021-00484-4
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