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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 Roy2; Zhu, Yan-Mei; Wang, Ya-Rong; Kang, Jong-Soo; Yang, Jie1; Zhang, Xian-Chun
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| 2022 | |
| Source Publication | PLANT JOURNAL
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| ISSN | 0960-7412 |
| Volume | 111Issue:3Pages:768-784 |
| Abstract | 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. |
| Keyword | Selaginella sinensis network plastome perfect repeats dynamic mitogenome GC content RNA editing |
| Subject Area | Plant Sciences |
| DOI | 10.1111/tpj.15851 |
| Indexed By | SCI |
| Language | 英语 |
| WOS Keyword | TRANSFER-RNA GENES ; MITOCHONDRIAL-DNA ; CHLOROPLAST DNA ; PLASTID GENOME ; PHYLOGENETIC-RELATIONSHIPS ; SUBSTITUTION RATES ; LINEAR-MOLECULES ; INVERTED REPEAT ; EDITING SITES ; RECA PROTEIN |
| WOS Research Area | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS ID | WOS:000815649400001 |
| Publisher | WILEY |
| Subtype | Article |
| Publication Place | HOBOKEN |
| EISSN | 1365-313X |
| Funding Organization | National Natural Science Foundation of China [31770237, 32170233] ; Beijing Municipal Natural Science Foundation [5202019] |
| Corresponding Author Email | zhangxc@ibcas.ac.cn |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.ibcas.ac.cn/handle/2S10CLM1/28661 |
| Collection | 系统与进化植物学国家重点实验室 |
| Affiliation | 1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Univ Western Ontario, Dept Biol, London, ON N6A 5B7, Canada |
| Recommended Citation 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. |
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| 1705286124_de96e198d（1628KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | View Application Full Text | |
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