The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery

doi:10.1111/tpj.15851

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	The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery
	Xiang, Qiao-Ping ; Tang, Jun-Yong ; Yu, Ji-Gao ; Smith, David Roy 3; Zhu, Yan-Mei ; Wang, Ya-Rong ; Kang, Jong-Soo ; Yang, Jie 2; Zhang, Xian-Chun
刊名	PLANT JOURNAL
	2022
卷号	111 期号:3 页码:768-784
关键词	Selaginella sinensis network plastome perfect repeats dynamic mitogenome GC content RNA editing
ISSN号	0960-7412
DOI	10.1111/tpj.15851
文献子类	Article
英文摘要	Two factors are proposed to account for the unusual features of organellar genomes: the disruptions of organelle-targeted DNA replication, repair, and recombination (DNA-RRR) systems in the nuclear genome and repetitive elements in organellar genomes. Little is known about how these factors affect organellar genome evolution. The deep-branching vascular plant family Selaginellaceae is known to have a deficient DNA-RRR system and convergently evolved organellar genomes. However, we found that the plastid genome (plastome) of Selaginella sinensis has extremely accelerated substitution rates, a low GC content, pervasive repeat elements, a dynamic network structure, and it lacks direct or inverted repeats. Unexpectedly, its organelle DNA-RRR system is short of a plastid-targeted Recombinase A1 (RecA1) and a mitochondrion-targeted RecA3, in line with other explored Selaginella species. The plastome contains a large collection of short- and medium-sized repeats. Given the absence of RecA1 surveillance, we propose that these repeats trigger illegitimate recombination, accelerated mutation rates, and structural instability. The correlations between repeat quantity and architectural complexity in the Selaginella plastomes support these conclusions. We, therefore, hypothesize that the interplay of the deficient DNA-RRR system and the high repeat content has led to the extraordinary divergence of the S. sinensis plastome. Our study not only sheds new light on the mechanism of plastome divergence by emphasizing the power of cytonuclear integration, but it also reconciles the longstanding contradiction on the effects of DNA-RRR system disruption on genome structure evolution.
学科主题	Plant Sciences
电子版国际标准刊号	1365-313X
出版地	HOBOKEN
WOS关键词	TRANSFER-RNA GENES ; MITOCHONDRIAL-DNA ; CHLOROPLAST DNA ; PLASTID GENOME ; PHYLOGENETIC-RELATIONSHIPS ; SUBSTITUTION RATES ; LINEAR-MOLECULES ; INVERTED REPEAT ; EDITING SITES ; RECA PROTEIN
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
语种	英语
出版者	WILEY
WOS记录号	WOS:000815649400001
资助机构	National Natural Science Foundation of China [31770237, 32170233] ; Beijing Municipal Natural Science Foundation [5202019]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/28661]
专题	系统与进化植物学国家重点实验室
作者单位	1.Univ Western Ontario, Dept Biol, London, ON N6A 5B7, Canada 2.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Xiang, Qiao-Ping,Tang, Jun-Yong,Yu, Ji-Gao,et al. The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery[J]. PLANT JOURNAL,2022,111(3):768-784.
APA	Xiang, Qiao-Ping.,Tang, Jun-Yong.,Yu, Ji-Gao.,Smith, David Roy.,Zhu, Yan-Mei.,...&Zhang, Xian-Chun.(2022).The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery.PLANT JOURNAL,111(3),768-784.
MLA	Xiang, Qiao-Ping,et al."The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery".PLANT JOURNAL 111.3(2022):768-784.