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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
Source PublicationBMC GENOMICS
ISSN1471-2164
Volume20
AbstractBackgroundIt 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.
Keyworddirect repeat inversion inverted repeat plastome evolution short dispersed repeats
Subject AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
DOI10.1186/s12864-019-5843-6
Indexed BySCI
Language英语
WOS KeywordTRANSFER-RNA GENES ; CHLOROPLAST GENOME ; INVERTED REPEAT ; SEQUENCE ; DNA ; REARRANGEMENTS ; RECOMBINATION ; LYCOPHYTE ; ORGANIZATION ; ARCHITECTURE
WOS Research AreaBiotechnology & Applied Microbiology ; Genetics & Heredity
WOS IDWOS:000472091700006
PublisherBMC
SubtypeArticle
Publication PlaceLONDON
Funding OrganizationNational Natural Science Foundation of China (NSFC)National Natural Science Foundation of China (NSFC) [31670205, 31770237]
Corresponding Author Emailzhanghr@ibcas.ac.cn ; qpxiang@ibcas.ac.cn
OAgold, Green Published
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Cited Times:4[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ibcas.ac.cn/handle/2S10CLM1/19856
Collection系统与进化植物学国家重点实验室
Affiliation1.[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
Recommended Citation
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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