The RNA-binding pentatricopeptide repeat (PPR) family comprises hundreds to thousands of genes in most plants, but only a few dozen in algae, indicating massive gene expansions during land plant evolution. The nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant lineages. In this study, we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family, focusing on the proteins typically associated with RNA editing, which show the most spectacular variation in numbers and domain composition across the plant kingdom. We characterize over 2 250 000 PPR motifs in over 400 000 proteins. In lycophytes, polypod ferns, and hornworts, nearly 10% of expressed protein-coding genes encode putative PPR editing factors, whereas they are absent from algae and complex-thalloid liverworts. We show that rather than a single expansion, most land plant lineages with high numbers of editing factors have continued to generate novel sequence diversity. We identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing co-factors. Finally, using the sequence variations across the datasets, we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors, given their phylogenetic distribution and sequence characteristics.

RNA结合的五肽重复序列（PPR）家族在大多数植物中包含成百上千个基因，但在藻类中仅包含几十个基因，这表明陆地植物进化过程中发生了大规模的基因扩增。由于可从早期分化的陆生植物世系获得的稀疏序列数据，这些扩展的性质和时机尚未得到很好的定义。在这项研究中，我们利用来自不同植物和藻类的1000多个转录组的综合OneKP数据集，为建立这一庞大基因家族的进化图景提供了清晰的图像，重点研究了通常与RNA编辑相关的蛋白质，这些蛋白质显示出最显着的变异。植物界的数量和域组成。我们表征了超过40万种蛋白质中的225万个PPR基序。在苔藓植物，蕨类植物蕨类植物和金缕梅中，几乎有10％的表达蛋白编码基因编码推定的PPR编辑因子，而藻类和复杂类藻类的艾蒿却不存在这些基因。我们表明，具有大量编辑因子的大多数陆地植物谱系而不是单一的扩展，仍在继续产生新颖的序列多样性。我们确定暗示种子植物与非种子植物中PPR蛋白之间功能差异的序列变异，并且我们建议将变异与种子植物特异性编辑辅因子联系起来。最后，使用整个数据集中的序列变异，我们开发了与C-to-U编辑相关的催化性DYW结构域的结构模型，并确定了一系列独特的DYW变体，它们是U-to-C RNA编辑因子的强力候选者，考虑到它们的系统发育分布和序列特征。