Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, 68588, USA.
Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, 68583, USA.
New Phytol. 2019 Apr;222(2):1061-1075. doi: 10.1111/nph.15650. Epub 2019 Jan 24.
Lycophytes are a key group for understanding vascular plant evolution. Lycophyte plastomes are highly distinct, indicating a dynamic evolutionary history, but detailed evaluation is hindered by the limited availability of sequences. Eight diverse plastomes were sequenced to assess variation in structure and functional content across lycophytes. Lycopodiaceae plastomes have remained largely unchanged compared with the common ancestor of land plants, whereas plastome evolution in Isoetes and especially Selaginella is highly dynamic. Selaginella plastomes have the highest GC content and fewest genes and introns of any photosynthetic land plant. Uniquely, the canonical inverted repeat was converted into a direct repeat (DR) via large-scale inversion in some Selaginella species. Ancestral reconstruction identified additional putative transitions between an inverted and DR orientation in Selaginella and Isoetes plastomes. A DR orientation does not disrupt the activity of copy-dependent repair to suppress substitution rates within repeats. Lycophyte plastomes include the most archaic examples among vascular plants and the most reconfigured among land plants. These evolutionary trends correlate with the mitochondrial genome, suggesting shared underlying mechanisms. Copy-dependent repair for DR-localized genes indicates that recombination and gene conversion are not inhibited by the DR orientation. Gene relocation in lycophyte plastomes occurs via overlapping inversions rather than transposase/recombinase-mediated processes.
石松类植物是理解维管植物进化的关键类群。石松类植物的质体基因组高度独特，表明其进化历史具有动态性，但由于序列的有限可用性，详细的评估受到阻碍。我们对 8 个不同的质体基因组进行了测序，以评估石松类植物中结构和功能内容的变异。与陆生植物的共同祖先相比，石松科的质体基因组基本没有变化，而石松目和特别是卷柏目的质体进化则非常活跃。卷柏目的质体基因组具有最高的 GC 含量、最少的基因和内含子，是所有光合陆生植物中最少的。独特的是，在一些卷柏目中，通过大规模反转，规范的反向重复通过大规模反转转化为直接重复（DR）。祖先重建确定了石松目和石松目中的另外一些潜在的反向和 DR 取向之间的转变。DR 取向不会破坏依赖于复制的修复活动，从而抑制重复内的替代率。石松类植物的质体基因组包含了在维管植物中最古老的例子，以及在陆生植物中最重新配置的例子。这些进化趋势与线粒体基因组相关，表明存在共同的潜在机制。DR 定位基因的依赖复制修复表明，重组和基因转换不受 DR 取向的抑制。石松类植物的质体基因组中基因的重定位是通过重叠反转而不是转座酶/重组酶介导的过程发生的。
