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.

中文翻译：

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新黄芪（豆科）质体结构进化和同质性倒转

经过数亿年的进化，光合绿色植物的质体基因组在很大程度上保持了保守的基因内容和顺序以及结构。然而，一些植物谱系已经脱离了这种保守性，并包含许多质体结构重排，这些重排与整体和附近重排端点的大量重复序列有关。我们对黄芪 (豆科) 25 个类群的质体组进行了测序，黄芪是豆科植物反向重复缺失进化支中的一个大属，以更好地了解重复序列与质体体倒位之间的联系。我们发现，在这些密切相关的类群中，质体重复结构具有很强的系统发育信号，这些类群主要位于黄芪的新大陆分支（称为新黄芪）中。没有倒转的分类群在整体重复结构上也与四个分类群各有一个大规模倒转没有显着差异。对于在同一对基因之间具有反转端点的两个分类群，其确切端点的差异表明反转是独立发生的。我们提出的倒转形成机制表明，现在在四个倒转端点附近发现的短倒转重复序列可能是这些倒转的结果，而不是其原因。现在端点附近较长的反向重复可能允许首先由较短的微同源序列介导的倒转传播，在解释任何质体重排如何变得固定时应考虑这一点，无论初始形成的机制如何。