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Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress

Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Resu...

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Autores principales: Huang, Xing, Liang, Yongsheng, Zhang, Baoqing, Song, Xiupeng, Li, Yangrui, Qin, Zhengqiang, Li, Dewei, Chen, Rongfa, Zhou, Zhongfeng, Deng, Yuchi, Wei, Jiguang, Wu, Jianming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7868625/
https://www.ncbi.nlm.nih.gov/pubmed/33569078
http://dx.doi.org/10.3389/fgene.2020.581993
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author Huang, Xing
Liang, Yongsheng
Zhang, Baoqing
Song, Xiupeng
Li, Yangrui
Qin, Zhengqiang
Li, Dewei
Chen, Rongfa
Zhou, Zhongfeng
Deng, Yuchi
Wei, Jiguang
Wu, Jianming
author_facet Huang, Xing
Liang, Yongsheng
Zhang, Baoqing
Song, Xiupeng
Li, Yangrui
Qin, Zhengqiang
Li, Dewei
Chen, Rongfa
Zhou, Zhongfeng
Deng, Yuchi
Wei, Jiguang
Wu, Jianming
author_sort Huang, Xing
collection PubMed
description Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress.
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spelling pubmed-78686252021-02-09 Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress Huang, Xing Liang, Yongsheng Zhang, Baoqing Song, Xiupeng Li, Yangrui Qin, Zhengqiang Li, Dewei Chen, Rongfa Zhou, Zhongfeng Deng, Yuchi Wei, Jiguang Wu, Jianming Front Genet Genetics Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress. Frontiers Media S.A. 2021-01-25 /pmc/articles/PMC7868625/ /pubmed/33569078 http://dx.doi.org/10.3389/fgene.2020.581993 Text en Copyright © 2021 Huang, Liang, Zhang, Song, Li, Qin, Li, Chen, Zhou, Deng, Wei and Wu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Huang, Xing
Liang, Yongsheng
Zhang, Baoqing
Song, Xiupeng
Li, Yangrui
Qin, Zhengqiang
Li, Dewei
Chen, Rongfa
Zhou, Zhongfeng
Deng, Yuchi
Wei, Jiguang
Wu, Jianming
Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress
title Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress
title_full Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress
title_fullStr Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress
title_full_unstemmed Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress
title_short Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress
title_sort integration of transcriptional and post-transcriptional analysis revealed the early response mechanism of sugarcane to cold stress
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7868625/
https://www.ncbi.nlm.nih.gov/pubmed/33569078
http://dx.doi.org/10.3389/fgene.2020.581993
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