Plant meristems are structured organs consisting of distinct layers of stem cells, which differentiate into new plant tissue. Mutations in meristematic layers can propagate into large sectors of the plant. However, the characteristics of meristematic mutations remain unclear, limiting our understanding of the genetic basis of somaclonal phenotypic variation. Here, we analyse the frequency and distribution of somatic mutations in an apricot tree. We separately sequence the epidermis (developing from meristem layer 1) and the flesh (developing from meristem layer 2) of several fruits sampled across the entire tree. We find that most somatic mutations (> 90%) are specific to individual layers. Interestingly, layer 1 shows a higher mutation load than layer 2, implying different mutational dynamics between the layers. The distribution of somatic mutations follows the branching of the tree. This suggests that somatic mutations are propagated to developing branches through axillary meristems. In turn, this leads us to the unexpected observation that the genomes of layer 1 of distant branches are more similar to each other than to the genomes of layer 2 of the same branches. Finally, using single-cell RNA sequencing, we demonstrate that layer-specific mutations were only transcribed in the cells of the respective layers and can form the genetic basis of somaclonal phenotypic variation. Here, we analyse the frequency and distribution of somatic mutations with meristematic origin. Our observations on the layer specificity of somatic mutations outline how they are distributed, how they propagate, and how they can impact clonally propagated crops.

中文翻译：

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植物中绝大多数体细胞突变是层特异性的


植物分生组织是由不同层干细胞组成的结构化器官，可分化成新的植物组织。分生组织层的突变可以传播到植物的大部分区域。然而，分生组织突变的特征仍不清楚，限制了我们对体细胞克隆表型变异遗传基础的理解。在这里，我们分析了杏树体细胞突变的频率和分布。我们分别对整棵树上采样的几个果实的表皮（从分生组织层 1 发育而来）和果肉（从分生组织层 2 发育而来）进行测序。我们发现大多数体细胞突变（> 90%）是针对各个层的。有趣的是，第 1 层显示出比第 2 层更高的突变负载，这意味着各层之间的突变动态不同。体细胞突变的分布遵循树的分支。这表明体细胞突变通过腋生分生组织传播到发育中的分支。反过来，这导致我们意外地观察到，相距较远的分支的第 1 层的基因组彼此之间比相同分支的第 2 层的基因组更相似。最后，利用单细胞RNA测序，我们证明层特异性突变仅在相应层的细胞中转录，并且可以形成体细胞克隆表型变异的遗传基础。在这里，我们分析了具有分生组织起源的体细胞突变的频率和分布。我们对体细胞突变层特异性的观察概述了它们如何分布、如何繁殖以及它们如何影响克隆繁殖的作物。