Full-length chloroplast genome of Dongxiang wild rice reveals small single-copy region switching
文献类型： 外文期刊
作者： Liang, Jianguang 1 ; Chen, Rui 2 ; Zhang, Fantao 4 ; Wang, Qian 2 ; Yang, Yingxia 2 ; Lv, Mingjie 2 ; Yan, Shuangyong 3 ; Gao, Shan 5 ;
作者机构： 1.Changzhou Univ, Sch Pharm, Changzhou, Peoples R China
2.Tianjin Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Tianjin, Peoples R China
3.Tianjin Acad Agr Sci, Tianjin Inst Crop Res, Tianjin, Peoples R China
4.Jiangxi Normal Univ, Coll Life Sci, Nanchang, Peoples R China
5.Nankai Univ, Coll Life Sci, Tianjin, Peoples R China
关键词： structural variation; inverted repeat; asymmetric recombination; SDSA; transposon-like element
期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：6.627； 五年影响因子：7.255 ）
ISSN： 1664-462X
年卷期： 2022 年 13 卷
页码：
收录情况： SCI
摘要： BackgroundPlant chloroplast DNA (cpDNA) typically has a circular structure, including a large single-copy region (LSC), a small single-copy region (SSC) and two inverted repeats (IR1 and IR2). The organization of these four elementary regions LSC-IR1-SSC-IR2 is highly conserved across all plant cpDNAs. Very few structural variations (SVs) occurring at the elementary-region level have been reported. ResultsIn the present study, we assembled the full-length cpDNA of Dongxiang wild rice line 159 (DXWR159). Using the long PacBio subreads, we discovered a large inversion of SSC and a large duplication of IR in DXWR159 cpDNAs. Significantly, we reported for the first time forward and reverse SSCs of cpDNAs in similar proportions and named the frequent inversion of a whole SSC as SSC switching. ConclusionsOur study helps researchers to correctly assemble the chloroplast genomes. Our recombination model explained the formation of large SVs in cpDNAs and provided insights into a novel scientific question that if there are common mechanisms in the formation or translocation of all kinds of transposon-like elements (TLEs). We propose that: (1) large inversion is the most accepted mutation type of SVs in cpDNAs; (2) SSC switching ubiquitous occurs in plant cpDNAs; and (3) further investigation of molecular mechanism underlying SSC switching may reveal new driving forces for large SVs.
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