Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA.
Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, USA.
Genome Biol Evol. 2021 Oct 1;13(10). doi: 10.1093/gbe/evab215.
The plastid genomes of photosynthetic green plants have largely maintained conserved gene content and order as well as structure over hundreds of millions of years of evolution. Several plant lineages, however, have departed from this conservation and contain many plastome structural rearrangements, which have been associated with an abundance of repeated sequences both overall and near rearrangement endpoints. We sequenced the plastomes of 25 taxa of Astragalus L. (Fabaceae), a large genus in the inverted repeat-lacking clade of legumes, to gain a greater understanding of the connection between repeats and plastome inversions. We found plastome repeat structure has a strong phylogenetic signal among these closely related taxa mostly in the New World clade of Astragalus called Neo-Astragalus. Taxa without inversions also do not differ substantially in their overall repeat structure from four taxa each with one large-scale inversion. For two taxa with inversion endpoints between the same pairs of genes, differences in their exact endpoints indicate the inversions occurred independently. Our proposed mechanism for inversion formation suggests the short inverted repeats now found near the endpoints of the four inversions may be there as a result of these inversions rather than their cause. The longer inverted repeats now near endpoints may have allowed the inversions first mediated by shorter microhomologous sequences to propagate, something that should be considered in explaining how any plastome rearrangement becomes fixed regardless of the mechanism of initial formation.
光合绿色植物的质体基因组在数亿年的进化过程中，在基因内容和顺序以及结构上都保持着很大的保守性。然而，有几个植物谱系偏离了这种保守性，包含许多质体结构重排，这些重排与大量重复序列有关，无论是整体上还是在重排终点附近。我们对 25 种黄芪属（豆科）植物的质体基因组进行了测序，以更好地了解重复序列和质体倒位之间的联系。我们发现，在这些密切相关的新世界黄芪属（称为新黄芪属）植物中，质体重复结构具有很强的系统发育信号。没有倒位的类群在其整体重复结构上也与每个类群各有一个大规模倒位的四个类群没有显著差异。对于两个具有相同基因对之间的倒位终点的类群，其确切终点的差异表明这些倒位是独立发生的。我们提出的倒位形成机制表明，现在在四个倒位的终点附近发现的短倒置重复可能是这些倒位的结果，而不是它们的原因。现在在终点附近的较长的倒置重复可能允许首先通过较短的微同源序列介导的倒位传播，这在解释任何质体重排如何固定，无论初始形成的机制如何，都应该被考虑。
