A Large Intergenic Spacer Leads to the Increase in Genome Size and Sequential Gene Movement around IR/SC Boundaries in the Chloroplast Genome of (Pteridaceae).

Expansion and contraction (ebb and flow events) of inverted repeat (IR) boundaries occur and are generally considered to be major factors affecting chloroplast (cp) genome size changes. Nonetheless, the cp genome does not seem to follow this pattern. We sequenced, assembled and corrected the and cp genomes using the Illumina NovaSeq6000 platform, and we performed a comparative genome analysis of six species. The results revealed differences in the IR/SC boundaries of caused by a 6876 bp long intergenic spacer (IGS) in the LSC. This IGS may create topological tension towards the LSC/IRb boundary in the cp genome, resulting in a sequential movement of the LSC genes. Consequently, this leads to changes of the IR/SC boundaries and may even destroy the integrity of , which is located in IRs. This study provides evidence showing that it is the large IGS that leads to cp genome size change, rather than ebb and flow events. Then, the study provides a model to explain how the IGS in LSC affects IR/SC boundaries. Moreover, this study also provides useful data for dissecting the evolution of cp genomes of . In future research, we can expand the sample to Pteridaceae to test whether this phenomenon is universal in Pteridaceae.