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Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii

N6-methyladenosine modifications (m6A) is one of the most abundant and prevalent post-transcriptional RNA modifications in plants, playing the crucial role in plant growth and development and stress adaptation. However, the m6A regulatory machinery in Aegilops_tauschii, the D genome progenitor of co...

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Autores principales: Lin, Huiyuan, Shi, Tingrui, Zhang, Ying, He, Chuyang, Zhang, Qiying, Mo, Zhiping, Pan, Wenqiu, Nie, Xiaojun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10385245/
https://www.ncbi.nlm.nih.gov/pubmed/37514361
http://dx.doi.org/10.3390/plants12142747
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author Lin, Huiyuan
Shi, Tingrui
Zhang, Ying
He, Chuyang
Zhang, Qiying
Mo, Zhiping
Pan, Wenqiu
Nie, Xiaojun
author_facet Lin, Huiyuan
Shi, Tingrui
Zhang, Ying
He, Chuyang
Zhang, Qiying
Mo, Zhiping
Pan, Wenqiu
Nie, Xiaojun
author_sort Lin, Huiyuan
collection PubMed
description N6-methyladenosine modifications (m6A) is one of the most abundant and prevalent post-transcriptional RNA modifications in plants, playing the crucial role in plant growth and development and stress adaptation. However, the m6A regulatory machinery in Aegilops_tauschii, the D genome progenitor of common wheat, is not well understood at present. Here, we systematically identified the m6A-related genes in Aegilops with a genome-wide search approach. In total, 25 putative m6A genes composed of 5 writers, 13 readers and 7 erasers were obtained. A phylogenetic analysis clearly grouped them into three subfamilies with the same subfamily showing similar gene structures and conserved domains. These m6A genes were found to contain a large number of cis-acting elements associating with plant hormones, regulation of growth and development as well as stress response, suggesting their widespread regulation function. Furthermore, the expression profiling of them was investigated using RNA-seq data to obtain stress-responsive candidates, of which 5 were further validated with a qPCR analysis. Finally, the genetic variation of m6A-related genes was investigated between Aegilops and D subgenome of wheat based on re-sequencing data, and an obvious genetic bottleneck occurred on them during the wheat domestication process. The promising haplotype association with domestication and agronomic traits was also detected. This study provided some insights on the genomic organization and evolutionary features of m6A-related genes in Aegilops, which will facilitate the further functional study and also contribute to broaden the genetic basis for genetic improvement in wheat and other crops.
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spelling pubmed-103852452023-07-30 Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii Lin, Huiyuan Shi, Tingrui Zhang, Ying He, Chuyang Zhang, Qiying Mo, Zhiping Pan, Wenqiu Nie, Xiaojun Plants (Basel) Article N6-methyladenosine modifications (m6A) is one of the most abundant and prevalent post-transcriptional RNA modifications in plants, playing the crucial role in plant growth and development and stress adaptation. However, the m6A regulatory machinery in Aegilops_tauschii, the D genome progenitor of common wheat, is not well understood at present. Here, we systematically identified the m6A-related genes in Aegilops with a genome-wide search approach. In total, 25 putative m6A genes composed of 5 writers, 13 readers and 7 erasers were obtained. A phylogenetic analysis clearly grouped them into three subfamilies with the same subfamily showing similar gene structures and conserved domains. These m6A genes were found to contain a large number of cis-acting elements associating with plant hormones, regulation of growth and development as well as stress response, suggesting their widespread regulation function. Furthermore, the expression profiling of them was investigated using RNA-seq data to obtain stress-responsive candidates, of which 5 were further validated with a qPCR analysis. Finally, the genetic variation of m6A-related genes was investigated between Aegilops and D subgenome of wheat based on re-sequencing data, and an obvious genetic bottleneck occurred on them during the wheat domestication process. The promising haplotype association with domestication and agronomic traits was also detected. This study provided some insights on the genomic organization and evolutionary features of m6A-related genes in Aegilops, which will facilitate the further functional study and also contribute to broaden the genetic basis for genetic improvement in wheat and other crops. MDPI 2023-07-24 /pmc/articles/PMC10385245/ /pubmed/37514361 http://dx.doi.org/10.3390/plants12142747 Text en © 2023 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
Lin, Huiyuan
Shi, Tingrui
Zhang, Ying
He, Chuyang
Zhang, Qiying
Mo, Zhiping
Pan, Wenqiu
Nie, Xiaojun
Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii
title Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii
title_full Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii
title_fullStr Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii
title_full_unstemmed Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii
title_short Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers in Aegilops_tauschii
title_sort genome-wide identification, expression and evolution analysis of m6a writers, readers and erasers in aegilops_tauschii
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10385245/
https://www.ncbi.nlm.nih.gov/pubmed/37514361
http://dx.doi.org/10.3390/plants12142747
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