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A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms

Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern o...

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Autores principales: Huang, Kai-Yuan, Kan, Sheng-Long, Shen, Ting-Ting, Gong, Pin, Feng, Yuan-Yuan, Du, Hong, Zhao, Yun-Peng, Wan, Tao, Wang, Xiao-Quan, Ran, Jin-Hua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505161/
https://www.ncbi.nlm.nih.gov/pubmed/36142757
http://dx.doi.org/10.3390/ijms231810844
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author Huang, Kai-Yuan
Kan, Sheng-Long
Shen, Ting-Ting
Gong, Pin
Feng, Yuan-Yuan
Du, Hong
Zhao, Yun-Peng
Wan, Tao
Wang, Xiao-Quan
Ran, Jin-Hua
author_facet Huang, Kai-Yuan
Kan, Sheng-Long
Shen, Ting-Ting
Gong, Pin
Feng, Yuan-Yuan
Du, Hong
Zhao, Yun-Peng
Wan, Tao
Wang, Xiao-Quan
Ran, Jin-Hua
author_sort Huang, Kai-Yuan
collection PubMed
description Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms.
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spelling pubmed-95051612022-09-24 A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms Huang, Kai-Yuan Kan, Sheng-Long Shen, Ting-Ting Gong, Pin Feng, Yuan-Yuan Du, Hong Zhao, Yun-Peng Wan, Tao Wang, Xiao-Quan Ran, Jin-Hua Int J Mol Sci Article Although more than 9100 plant plastomes have been sequenced, RNA editing sites of the whole plastome have been experimentally verified in only approximately 21 species, which seriously hampers the comprehensive evolutionary study of chloroplast RNA editing. We investigated the evolutionary pattern of chloroplast RNA editing sites in 19 species from all 13 families of gymnosperms based on a combination of genomic and transcriptomic data. We found that the chloroplast C-to-U RNA editing sites of gymnosperms shared many common characteristics with those of other land plants, but also exhibited many unique characteristics. In contrast to that noted in angiosperms, the density of RNA editing sites in ndh genes was not the highest in the sampled gymnosperms, and both loss and gain events at editing sites occurred frequently during the evolution of gymnosperms. In addition, GC content and plastomic size were positively correlated with the number of chloroplast RNA editing sites in gymnosperms, suggesting that the increase in GC content could provide more materials for RNA editing and facilitate the evolution of RNA editing in land plants or vice versa. Interestingly, novel G-to-A RNA editing events were commonly found in all sampled gymnosperm species, and G-to-A RNA editing exhibits many different characteristics from C-to-U RNA editing in gymnosperms. This study revealed a comprehensive evolutionary scenario for chloroplast RNA editing sites in gymnosperms, and reported that a novel type of G-to-A RNA editing is prevalent in gymnosperms. MDPI 2022-09-16 /pmc/articles/PMC9505161/ /pubmed/36142757 http://dx.doi.org/10.3390/ijms231810844 Text en © 2022 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
Huang, Kai-Yuan
Kan, Sheng-Long
Shen, Ting-Ting
Gong, Pin
Feng, Yuan-Yuan
Du, Hong
Zhao, Yun-Peng
Wan, Tao
Wang, Xiao-Quan
Ran, Jin-Hua
A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms
title A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms
title_full A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms
title_fullStr A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms
title_full_unstemmed A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms
title_short A Comprehensive Evolutionary Study of Chloroplast RNA Editing in Gymnosperms: A Novel Type of G-to-A RNA Editing Is Common in Gymnosperms
title_sort comprehensive evolutionary study of chloroplast rna editing in gymnosperms: a novel type of g-to-a rna editing is common in gymnosperms
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9505161/
https://www.ncbi.nlm.nih.gov/pubmed/36142757
http://dx.doi.org/10.3390/ijms231810844
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