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Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut
Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8745729/ https://www.ncbi.nlm.nih.gov/pubmed/35008672 http://dx.doi.org/10.3390/ijms23010246 |
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author | Tong, Bin Shi, Yusun Ntambiyukuri, Aaron Li, Xia Zhan, Jie Wang, Aiqin Xiao, Dong He, Longfei |
author_facet | Tong, Bin Shi, Yusun Ntambiyukuri, Aaron Li, Xia Zhan, Jie Wang, Aiqin Xiao, Dong He, Longfei |
author_sort | Tong, Bin |
collection | PubMed |
description | Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies have been found related to aluminum (Al)-induced programmed cell death (PCD). In the present study, transcriptomics, sRNAs, and degradome analysis in the root tips of two peanut cultivars ZH2 (Al-sensitive, S) and 99-1507 (Al-tolerant, T) were carried out. Here, we generated a comprehensive resource focused on identifying key regulatory miRNA-target circuits that regulate PCD under Al stress. Through deep sequencing, 2284 miRNAs were identified and 147 miRNAs were differentially expressed under Al stress. Furthermore, 19237 target genes of 749 miRNAs were validated by degradome sequencing. GO and KEGG analyses of differential miRNA targets showed that the pathways of synthesis and degradation of ketone bodies, citrate cycle (TCA cycle), and peroxisome were responded to Al stress. The combined analysis of the degradome data sets revealed 89 miRNA-mRNA interactions that may regulate PCD under Al stress. Ubiquitination may be involved in Al-induced PCD in peanut. The regulatory networks were constructed based on the differentially expressed miRNAs and their targets related to PCD. Our results will provide a useful platform to research on PCD induced by Al and new insights into the genetic engineering for plant stress response. |
format | Online Article Text |
id | pubmed-8745729 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-87457292022-01-11 Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut Tong, Bin Shi, Yusun Ntambiyukuri, Aaron Li, Xia Zhan, Jie Wang, Aiqin Xiao, Dong He, Longfei Int J Mol Sci Article Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies have been found related to aluminum (Al)-induced programmed cell death (PCD). In the present study, transcriptomics, sRNAs, and degradome analysis in the root tips of two peanut cultivars ZH2 (Al-sensitive, S) and 99-1507 (Al-tolerant, T) were carried out. Here, we generated a comprehensive resource focused on identifying key regulatory miRNA-target circuits that regulate PCD under Al stress. Through deep sequencing, 2284 miRNAs were identified and 147 miRNAs were differentially expressed under Al stress. Furthermore, 19237 target genes of 749 miRNAs were validated by degradome sequencing. GO and KEGG analyses of differential miRNA targets showed that the pathways of synthesis and degradation of ketone bodies, citrate cycle (TCA cycle), and peroxisome were responded to Al stress. The combined analysis of the degradome data sets revealed 89 miRNA-mRNA interactions that may regulate PCD under Al stress. Ubiquitination may be involved in Al-induced PCD in peanut. The regulatory networks were constructed based on the differentially expressed miRNAs and their targets related to PCD. Our results will provide a useful platform to research on PCD induced by Al and new insights into the genetic engineering for plant stress response. MDPI 2021-12-27 /pmc/articles/PMC8745729/ /pubmed/35008672 http://dx.doi.org/10.3390/ijms23010246 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Tong, Bin Shi, Yusun Ntambiyukuri, Aaron Li, Xia Zhan, Jie Wang, Aiqin Xiao, Dong He, Longfei Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut |
title | Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut |
title_full | Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut |
title_fullStr | Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut |
title_full_unstemmed | Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut |
title_short | Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut |
title_sort | integration of small rna and degradome sequencing reveals the regulatory network of al-induced programmed cell death in peanut |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8745729/ https://www.ncbi.nlm.nih.gov/pubmed/35008672 http://dx.doi.org/10.3390/ijms23010246 |
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