College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
Int J Mol Sci. 2022 Dec 9;23(24):15616. doi: 10.3390/ijms232415616.
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.
重复序列（IR）边界的扩展和收缩（潮涨潮落事件）发生，通常被认为是影响叶绿体（cp）基因组大小变化的主要因素。尽管如此，cp 基因组似乎并不遵循这种模式。我们使用 Illumina NovaSeq6000 平台对 和 进行测序、组装和纠错，并对六个 物种进行了比较基因组分析。结果表明，由于 LSC 中 6876bp 长的基因间间隔（IGS），导致 中 IR/SC 边界的差异。这个 IGS 可能会在 cp 基因组中对 LSC/IRb 边界产生拓扑张力，导致 LSC 基因的顺序移动。因此，这会导致 IR/SC 边界的变化，甚至可能破坏位于 IRs 中的 的完整性。本研究提供了证据表明，导致 cp 基因组大小变化的是大的 IGS，而不是潮涨潮落事件。然后，该研究提供了一个模型来解释 LSC 中的 IGS 如何影响 IR/SC 边界。此外，本研究还为解析 科 cp 基因组的进化提供了有用的数据。在未来的研究中，我们可以扩大样本范围，包括凤尾蕨科，以测试这种现象是否在凤尾蕨科中普遍存在。
