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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
2019
发表期刊BMC GENOMICS
ISSN1471-2164
卷号20
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.
关键词direct repeat inversion inverted repeat plastome evolution short dispersed repeats
学科领域Biotechnology & Applied Microbiology ; Genetics & Heredity
DOI10.1186/s12864-019-5843-6
收录类别SCI
语种英语
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
WOS记录号WOS:000472091700006
出版者BMC
文献子类Article
出版地LONDON
资助机构National Natural Science Foundation of China (NSFC)National Natural Science Foundation of China (NSFC) [31670205, 31770237]
作者邮箱zhanghr@ibcas.ac.cn ; qpxiang@ibcas.ac.cn
作品OA属性gold, Green Published
引用统计
被引频次:11[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/2S10CLM1/19856
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
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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).
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