The associated evolution among the extensive RNA editing, GC-biased mutation, and PPR family expansion in the organelle genomes of Selaginellaceae

doi:10.1111/jse.12927

	The associated evolution among the extensive RNA editing, GC-biased mutation, and PPR family expansion in the organelle genomes of Selaginellaceae
	Kang, Jong-Soo ; Yu, Jigao 1; Zhang, Xian-Chun; Xiang, Qiao-Ping
	2022
发表期刊	JOURNAL OF SYSTEMATICS AND EVOLUTION
ISSN	1674-4918
摘要	Extensive C-to-U editing has been reported from plastid genomes (plastomes) and mitochondrial genomes (mitogenomes) of spikemoss. While reverse U-to-C editing was recorded in other seed-free plants such as hornworts, quillworts, and ferns, it was not observed in spikemosses. However, no comprehensive study on the association between RNA editing and other genomic features was conducted for the organelle genomes of spikemosses. Here, we report thousands of C-to-U editing sites from plastomes and mitogenomes of two species: 1767 and 2394 edits in Selaginella remotifolia, and 4091 and 2786 edits in Selaginella nipponica, respectively. Comparative analyses revealed two different editing frequencies among plastomes, but one similar frequency in mitogenomes. The different editing frequency in the Selaginella organelle genomes is related to the nonsynonymous substitution rate and the genome structural complexity. The high guanine and cytosine (GC) content caused by GC-biased mutations in organelle genomes might be related to the absence of U-to-C editing in Selaginellaceae. Using RNA-seq and whole-genome data, we screened the pentatricopeptide repeat (PPR) family and discovered that the number of aspartic acid-tyrosine-tryptophan (DYW) domain-containing PPR proteins corresponded roughly to the editing abundance in the Selaginella organelle genomes. Consequently, we hypothesize that associated evolution among RNA editing, GC-biased mutation in organelle genomes, and the PPR protein family encoded in the nuclear genome, is probably triggered by the aberrant DNA repair system in Selaginellaceae. Our study provides new insights into the association between organelle and nuclear genomes in Selaginellaceae, which would contribute to understanding the evolution of post-transcriptional modifications of organelle genomes in land plants.
关键词	GC-biased mutation mitochondrial genome (mitogenome) pentatricopeptide repeat (PPR) protein plastid genome (plastome) RNA editing Selaginellaceae
学科领域	Plant Sciences
DOI	10.1111/jse.12927
收录类别	SCI
语种	英语
WOS关键词	PENTATRICOPEPTIDE REPEAT PROTEINS ; MITOCHONDRIAL GENOMES ; CHLOROPLAST GENOME ; NUCLEOTIDE SUBSTITUTION ; DEAMINASE DOMAIN ; PLASTID GENOME ; DYW DOMAIN ; GENE ; LYCOPHYTE ; EXTREME
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000896029900001
出版者	WILEY
文献子类	Article; Early Access
出版地	HOBOKEN
EISSN	1759-6831
资助机构	National Natural Science Foundation of China ; [31770237] ; [32170233]
作者邮箱	qpxiang@ibcas.ac.cn
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/28759
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Kang, Jong-Soo,Yu, Jigao,Zhang, Xian-Chun,et al. The associated evolution among the extensive RNA editing, GC-biased mutation, and PPR family expansion in the organelle genomes of Selaginellaceae[J]. JOURNAL OF SYSTEMATICS AND EVOLUTION,2022.
APA	Kang, Jong-Soo,Yu, Jigao,Zhang, Xian-Chun,&Xiang, Qiao-Ping.(2022).The associated evolution among the extensive RNA editing, GC-biased mutation, and PPR family expansion in the organelle genomes of Selaginellaceae.JOURNAL OF SYSTEMATICS AND EVOLUTION.
MLA	Kang, Jong-Soo,et al."The associated evolution among the extensive RNA editing, GC-biased mutation, and PPR family expansion in the organelle genomes of Selaginellaceae".JOURNAL OF SYSTEMATICS AND EVOLUTION (2022).

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