Organelle biogenesis and function is dependent on the concerted action of both organellar-encoded (if present) and nuclear-encoded proteins. Differences between homologous organelles across the Plant Kingdom arise, in part, as a result of differences in the cohort of nuclear-encoded proteins that are targeted to them. However, neither the rate at which differences in protein targeting accumulate nor the evolutionary consequences of these changes are known. Using phylogenomic approaches coupled to ancestral state estimation, we show that the plant organellar proteome has diversified in proportion with molecular sequence evolution such that the proteomes of plant chloroplasts and mitochondria lose or gain on average 3.6 proteins per million years. We further demonstrate that changes in organellar protein targeting are associated with an increase in the rate of molecular sequence evolution and that such changes predominantly occur in genes with regulatory rather than metabolic functions. Finally, we show that gain and loss of protein target signals occurs at a higher rate following gene duplication, revealing that gene and genome duplication are a key facilitator of plant organelle evolution.

中文翻译：

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基因复制加速了植物细胞器蛋白质获得和损失的步伐。

细胞器的生物发生和功能取决于细胞器编码蛋白（如果存在）和核编码蛋白的协同作用。整个植物界中同源细胞器之间的差异部分是由于针对它们的核编码蛋白队列的差异而引起的。但是，既不知道蛋白质靶向差异累积的速率，也不知道这些变化的进化结果。使用系统遗传学方法结合祖先状态估计，我们表明植物细胞器蛋白质组与分子序列进化成比例地多样化，使得植物叶绿体和线粒体的蛋白质组每百万年平均损失或增加3.6个蛋白质。我们进一步证明，靶向细胞器蛋白的变化与分子序列进化速率的增加有关，并且这种变化主要发生在具有调节功能而不是代谢功能的基因中。最后，我们表明基因复制后蛋白质靶信号的获得和丢失发生率更高，这表明基因和基因组复制是植物细胞器进化的关键促进因素。