The plastid genomes (plastomes) of non-photosynthetic plants generally undergo gene loss and pseudogenization. Despite massive plastomes reported in different parasitism types of the broomrape family (Orobanchaceae), more plastomes representing different degradation patterns in a single genus are expected to be explored. Here, we sequence and assemble the complete plastomes of three holoparasitic Cistanche species (C. salsa, C. mongolica, and C. sinensis) and compare them with the available plastomes of Orobanchaceae. We identified that the diverse degradation trajectories under purifying selection existed among three Cistanche clades, showing obvious size differences in the entire plastome, long single copy region, and non-coding region, and different patterns of the retention/loss of functional genes. With few exceptions of putatively functional genes, massive plastid fragments, which have been lost and transferred into the mitochondrial or nuclear genomes, are non-functional. In contrast to the equivalents of the Orobanche species, some plastid-derived genes with diverse genomic locations are found in Cistanche. The early and initially diverged clades in different genera such as Cistanche and Aphyllon possess obvious patterns of plastome degradation, suggesting that such key lineages should be considered prior to comparative analysis of plastome evolution, especially in the same genus.

中文翻译：

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整寄生寄生肉蓉中质体降解的不同轨迹和丢失质体基因的基因组位置。

非光合植物的质体基因组（质体组）通常经历基因损失和假原化。尽管在帚柄科的不同寄生类型（Orobanchaceae）中报道了大量的塑性组，但仍有望探索更多的代表单个属的不同降解模式的塑性组。在这里，我们对三种全寄生的肉stan蓉物种（C. salsa，C。mongolica和C. sinensis）的完整质体进行测序和组装，并将它们与Orobanchaceae的可用质体进行比较。我们发现，在三个肉Ci蓉分支中存在纯化选择下的多种降解轨迹，显示出整个质体组，长单拷贝区和非编码区的大小差异明显，以及功能基因的保留/丢失模式不同。除假定的功能基因外，极少的质体片段已失去功能并转移到线粒体或核基因组中，它们是无功能的。与Orobanche物种的等价物相反，在肉stan蓉中发现了一些具有不同基因组位置的质体衍生基因。肉as蓉和Aphyllon等不同属的早期和最初分化的进化枝具有明显的质体降解模式，这表明在比较分析质体进化之前应考虑这些关键谱系，特别是在同一属中。在肉Ci蓉中发现了一些具有不同基因组位置的质体衍生基因。肉as蓉和Aphyllon等不同属的早期和最初分化的进化枝具有明显的质体降解模式，这表明在比较分析质体进化之前应考虑这些关键谱系，特别是在同一属中。在肉Ci蓉中发现了一些具有不同基因组位置的质体衍生基因。肉as蓉和Aphyllon等不同属的早期和最初分化的进化枝具有明显的质体降解模式，这表明在比较分析质体进化之前应考虑这些关键谱系，特别是在同一属中。