Full-length chloroplast genome of Dongxiang wild rice reveals single-copy region switching in cpDNAs

Abstract Background: Plant 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. Only very a few structural variations (SVs) occurring at the elementary-region level have been reported. Results: In 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. The large inversion of SSC results in a reverse orientation of SSC. According to the orientation of SSC, the structures of rice cpDNAs can be classified into the forward SSC (SSC-F) and reverse SSC (SSC-R) types. As the most significant finding, both SSC-F and SSC-R type cpDNAs were detected in several seedlings of DXWR159. The inversion of SSC was named as SSC switching. Conclusions: The frequencies of short tandem repeats (STRs) and large SVs were under-estimated in plant cpDNAs. STRs may not be useful as molecular markers in phylogenetic studies, particularly at low taxonomic levels. SSC switching is not a rarely occurring event and is active in cell growth. We propose that SSC switching ubiquitous occurs in plant cpDNAs and further investigation may reveal novel and important functions associated with SSC switching.