Genome-wide investigation and functional analysis of RNA editing sites in wheat

Wheat is an important cereal and half of the world population consumed it. Wheat faces environmental stresses and different techniques (CRISPR, gene silencing, GWAS, etc.) were used to enhance its production but RNA editing (RESs) is not fully explored in wheat. RNA editing has a special role in con...

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Autores principales: Rasool, Fatima, Ishtiaq, Iqra, Uzair, Muhammad, Naz, Ali Ahmed, Léon, Jens, Khan, Muhammad Ramzan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8916659/
https://www.ncbi.nlm.nih.gov/pubmed/35275970
http://dx.doi.org/10.1371/journal.pone.0265270
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author Rasool, Fatima
Ishtiaq, Iqra
Uzair, Muhammad
Naz, Ali Ahmed
Léon, Jens
Khan, Muhammad Ramzan
author_facet Rasool, Fatima
Ishtiaq, Iqra
Uzair, Muhammad
Naz, Ali Ahmed
Léon, Jens
Khan, Muhammad Ramzan
author_sort Rasool, Fatima
collection PubMed
description Wheat is an important cereal and half of the world population consumed it. Wheat faces environmental stresses and different techniques (CRISPR, gene silencing, GWAS, etc.) were used to enhance its production but RNA editing (RESs) is not fully explored in wheat. RNA editing has a special role in controlling environmental stresses. The genome-wide identification and functional characterization of RESs in different types of wheat genotypes was done. We employed six wheat genotypes by RNA-seq analyses to achieve RESs. The findings revealed that RNA editing events occurred on all chromosomes equally. RNA editing sites were distributed randomly and 10–12 types of RESs were detected in wheat genotypes. Higher number of RESs were detected in drought-tolerant genotypes. A-to-I RNA editing (2952, 2977, 1916, 2576, 3422, and 3459) sites were also identified in six wheat genotypes. Most of the genes were found to be engaged in molecular processes after a Gene Ontology analysis. PPR (pentatricopeptide repeat), OZ1 (organelle zinc-finger), and MORF/RIP gene expression levels in wheat were also examined. Normal growth conditions diverge gene expression of these three different gene families, implying that normal growth conditions for various genotypes can modify RNA editing events and have an impact on gene expression levels. While the expression of PPR genes was not change. We used Variant Effect Predictor (VEP) to annotate RNA editing sites, and Local White had the highest RESs in the CDS region of the protein. These findings will be useful for prediction of RESs in other crops and will be helpful in drought tolerance development in wheat.
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spelling pubmed-89166592022-03-12 Genome-wide investigation and functional analysis of RNA editing sites in wheat Rasool, Fatima Ishtiaq, Iqra Uzair, Muhammad Naz, Ali Ahmed Léon, Jens Khan, Muhammad Ramzan PLoS One Research Article Wheat is an important cereal and half of the world population consumed it. Wheat faces environmental stresses and different techniques (CRISPR, gene silencing, GWAS, etc.) were used to enhance its production but RNA editing (RESs) is not fully explored in wheat. RNA editing has a special role in controlling environmental stresses. The genome-wide identification and functional characterization of RESs in different types of wheat genotypes was done. We employed six wheat genotypes by RNA-seq analyses to achieve RESs. The findings revealed that RNA editing events occurred on all chromosomes equally. RNA editing sites were distributed randomly and 10–12 types of RESs were detected in wheat genotypes. Higher number of RESs were detected in drought-tolerant genotypes. A-to-I RNA editing (2952, 2977, 1916, 2576, 3422, and 3459) sites were also identified in six wheat genotypes. Most of the genes were found to be engaged in molecular processes after a Gene Ontology analysis. PPR (pentatricopeptide repeat), OZ1 (organelle zinc-finger), and MORF/RIP gene expression levels in wheat were also examined. Normal growth conditions diverge gene expression of these three different gene families, implying that normal growth conditions for various genotypes can modify RNA editing events and have an impact on gene expression levels. While the expression of PPR genes was not change. We used Variant Effect Predictor (VEP) to annotate RNA editing sites, and Local White had the highest RESs in the CDS region of the protein. These findings will be useful for prediction of RESs in other crops and will be helpful in drought tolerance development in wheat. Public Library of Science 2022-03-11 /pmc/articles/PMC8916659/ /pubmed/35275970 http://dx.doi.org/10.1371/journal.pone.0265270 Text en © 2022 Rasool et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Rasool, Fatima
Ishtiaq, Iqra
Uzair, Muhammad
Naz, Ali Ahmed
Léon, Jens
Khan, Muhammad Ramzan
Genome-wide investigation and functional analysis of RNA editing sites in wheat
title Genome-wide investigation and functional analysis of RNA editing sites in wheat
title_full Genome-wide investigation and functional analysis of RNA editing sites in wheat
title_fullStr Genome-wide investigation and functional analysis of RNA editing sites in wheat
title_full_unstemmed Genome-wide investigation and functional analysis of RNA editing sites in wheat
title_short Genome-wide investigation and functional analysis of RNA editing sites in wheat
title_sort genome-wide investigation and functional analysis of rna editing sites in wheat
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8916659/
https://www.ncbi.nlm.nih.gov/pubmed/35275970
http://dx.doi.org/10.1371/journal.pone.0265270
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