Generally, it is believed that the contraction of IRs is related to the deletion/loss of DNA in one IR copy. For instance, small single-copy (SSC) of Lamprocapnos spectabilis and some Ericaceae species are quite short and only contain part of a gene or one gene. If the expansion of IRs is caused by genes shift between IRs and SC, it will be accompanied by a decrease in SC. However, some extreme cases exist, such as Pelargonium x hortorum (~76 kb), Monsonia speciosa (7 kb), or the loss of IRs of Pinaceae and some other species. For example, the size of the IRs in angiosperms is generally between 20 and 30 kb, while in most non-seed plants, the size only ranges from 10 to 15 kb. Even within closely related taxa, the changes in IR border genes can vary, a process referred to as “ebb and flow”, and this process is often linked to genome size change. However, cp genomes also exhibit some structural variation, such as uneven expansion and contraction of inverted repeat (IR), which is a dynamic process where genes are transferred from single-copy (SC) to IRs or sequences are inserted into IRs, leading to IR expansion inversely, if genes are transferred from IRs to SC, or if sequences are deleted in IRs, this will cause IR contraction. Cp genome structure is generally conserved in terms of gene structure, gene content and gene order. They usually contain about 120 genes, including protein-coding genes, ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs). Typical cp genomes of terrestrial plants are 120–160 kb in size, and their structures are mostly quadripartite. They consist of a double-stranded genome with a genetic system that is independent of the nuclear genome. In future research, we can expand the sample to Pteridaceae to test whether this phenomenon is universal in Pteridaceae.Ĭhloroplasts (cp) are important sites for plant photosynthesis and play an important role in the biosynthesis of carbohydrates, proteins and lipids in plants. Moreover, this study also provides useful data for dissecting the evolution of cp genomes of Adiantum. Then, the study provides a model to explain how the rpoB-trnD-GUC IGS in LSC affects A. malesianum cp genome size change, rather than ebb and flow events. This study provides evidence showing that it is the large rpoB-trnD-GUC IGS that leads to A. Consequently, this leads to changes of the IR/SC boundaries and may even destroy the integrity of trnT-UGU, which is located in IRs. ![]() This IGS may create topological tension towards the LSC/IRb boundary in the cp genome, resulting in a sequential movement of the LSC genes. malesianum caused by a 6876 bp long rpoB-trnD-GUC intergenic spacer (IGS) in the LSC. ![]() The results revealed differences in the IR/SC boundaries of A. ![]() malesianum cp genomes using the Illumina NovaSeq6000 platform, and we performed a comparative genome analysis of six Adiantum species. We sequenced, assembled and corrected the A. Nonetheless, the Adiantum malesianum cp genome does not seem to follow this pattern. 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.
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