Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida)

doi:10.1186/s12864-019-5843-6

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	Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida)
	Zhang, Hong-Rui ; Zhang, Xian-Chun ; Xiang, Qiao-Ping
刊名	BMC GENOMICS
	2019
卷号	20
关键词	direct repeat inversion inverted repeat plastome evolution short dispersed repeats
ISSN号	1471-2164
DOI	10.1186/s12864-019-5843-6
文献子类	Article
英文摘要	BackgroundIt is hypothesized that the highly conserved inverted repeats (IR) structure of land plant plastid genomes (plastomes) is beneficial for stabilizing plastome organization, whereas the mechanism of the occurrence and stability maintenance of the recently reported direct repeats (DR) structure is yet awaiting further exploration. Here we describe the DR structure of the Selaginella vardei (Selaginellaceae) plastome, to elucidate the mechanism of DR occurrence and stability maintenance.ResultsThe plastome of S. vardei is 121,254 bp in length and encodes 76 genes, of which 62 encode proteins, 10 encode tRNAs, and four encode rRNAs. Unexpectedly, the two identical rRNA gene regions (13,893 bp) are arranged in a direct orientation (DR), rather than inverted. Comparing to the IR organization in Isoetes flaccida (Isoetaceae, Lycopodiopsida) plastome, a ca. 50-kb trnN-trnF inversion that spans one DR copy was found in the plastome of S. vardei, which might cause the orientation change. In addition, we find extremely rare short dispersed repeats (SDRs) in the plastomes of S. vardei and its closely related species S. indica.ConclusionsWe suggest that the ca. 50-kb inversion resulted in the DR structure, and the reduction in SDRs plays a key role in maintaining the stability of plastomes with DR structure by avoiding potential secondary recombination. We further confirmed the presence of homologous recombination between DR regions, which are able to generate subgenomes and form diverse multimers. Our study deepens the understanding of Selaginella plastomes and provides new insights into the diverse plastome structures in land plants.
学科主题	Biotechnology & Applied Microbiology ; Genetics & Heredity
出版地	LONDON
WOS关键词	TRANSFER-RNA GENES ; CHLOROPLAST GENOME ; INVERTED REPEAT ; SEQUENCE ; DNA ; REARRANGEMENTS ; RECOMBINATION ; LYCOPHYTE ; ORGANIZATION ; ARCHITECTURE
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
语种	英语
出版者	BMC
WOS记录号	WOS:000472091700006
资助机构	National Natural Science Foundation of China (NSFC)National Natural Science Foundation of China (NSFC) [31670205, 31770237]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/19856]
专题	系统与进化植物学国家重点实验室
作者单位	1.[Zhang, Hong-Rui 2.Zhang, Xian-Chun 3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Hong-Rui,Zhang, Xian-Chun,Xiang, Qiao-Ping. Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida)[J]. BMC GENOMICS,2019,20.
APA	Zhang, Hong-Rui,Zhang, Xian-Chun,&Xiang, Qiao-Ping.(2019).Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida).BMC GENOMICS,20.
MLA	Zhang, Hong-Rui,et al."Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida)".BMC GENOMICS 20(2019).