Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida)
Directed Repeats Co-occur with Few Short-Dispersed Repeats in Plastid Genome of a Spikemoss, Selaginella vardei (Selaginellaceae, Lycopodiopsida)
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定向重复与少量短分散重复在穗苔、卷柏 (Selaginellaceae, Lycopodiopsida) 的质体基因组中同时出现
DOI：
10.1186/s12864-019-5843-6
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发表时间：
2019-06
期刊：
影响因子：
4.4
通讯作者：
Xiang Qiao-Ping
中科院分区：
文献类型：
--
作者：
Zhang Hong-Rui;Zhang Xian-Chun;Xiang Qiao-Ping
背景：陆地植物质体基因组（plastomes）中高度保守的反向重复序列（inverted repeats，IR）结构被认为有利于质体的稳定组织，而最近报道的直接重复序列（direct repeats，DR）结构的发生和稳定维持机制尚待进一步探讨。本文描述了卷柏质体的DR结构，以阐明DR发生和稳定性维持的机制。vardei基因全长121，254 bp，编码76个基因，其中62个编码蛋白质，10个编码tRNA，4个编码rRNA。出乎意料的是，两个相同的rRNA基因区域（13，893 bp）以直接方向（DR）排列，而不是倒置。与松叶水韭（Isoetaceae，Lycopodiopsida）质体的IR结构相比，松叶水韭（Isoetraceae，Lycopodiopsida）质体的IR结构有明显的差异.在S. vardei，这可能会导致方向的变化。此外，我们还发现在S. vardei及其近缘种S.结论：我们认为，ca. indica。50-kb的倒位导致了DR结构，而SDR的减少通过避免潜在的二次重组在维持具有DR结构的质体的稳定性方面起着关键作用。我们进一步证实了DR区域之间存在同源重组，这能够产生亚基因组并形成不同的多聚体。我们的研究加深了对卷柏质体的理解，并为陆地植物质体结构的多样性提供了新的见解。
Background:It 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.Results:The 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.Conclusions:We 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.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
石松科石杉 (Huperzia javanica (sw.) C. Y. Yang) 叶绿体基因组全序列
DOI：
10.1080/23802359.2017.1310603
发表时间：
2017-04-09
期刊：
Mitochondrial DNA. Part B, Resources
影响因子：
--
作者：
Zhang HR;Kang JS;Viane RLL;Zhang XC
通讯作者：
Zhang XC
影响因子：
3.3
作者：
Wu CS;Wang YN;Hsu CY;Lin CP;Chaw SM
通讯作者：
Chaw SM
影响因子：
3.6
作者：
Guo ZY;Zhang HR;Shrestha N;Zhang XC
通讯作者：
Zhang XC
影响因子：
10.7
作者：
Guisinger, Mary M.;Kuehl, Jennifer V.;Jansen, Robert K.
通讯作者：
Jansen, Robert K.