Rapid plant genome evolution is crucial to adapt to environmental changes. Chromosomal rearrangements and gene copy number variation (CNV) are two important tools for genome evolution and sources for the creation of new genes. However, their emergence takes many generations. In this study, we show that in Arabidopsis thaliana, a significant loss of ribosomal RNA (rRNA) genes with a past history of a mutation for the chromatin assembly factor 1 (CAF1) complex causes rapid changes in the genome structure. Using long-read sequencing and microscopic approaches, we have identified up to 15 independent large tandem duplications in direct orientation (TDDOs) ranging from 60 kb to 1.44 Mb. Our data suggest that these TDDOs appeared within a few generations, leading to the duplication of hundreds of genes. By subsequently focusing on a line only containing 20% of rRNA gene copies (20rDNA line), we investigated the impact of TDDOs on 3D genome organization, gene expression, and cytosine methylation. We found that duplicated genes often accumulate more transcripts. Among them, several are involved in plant–pathogen response, which could explain why the 20rDNA line is hyper-resistant to both bacterial and nematode infections. Finally, we show that the TDDOs create gene fusions and/or truncations and discuss their potential implications for the evolution of plant genomes.

中文翻译：

---

大串联重复影响基因表达、3D 组织和植物病原体反应

植物基因组的快速进化对于适应环境变化至关重要。染色体重排和基因拷贝数变异 (CNV) 是基因组进化的两个重要工具，也是创造新基因的来源。然而，它们的出现需要很多代。在这项研究中，我们表明在拟南芥中, 核糖体 RNA (rRNA) 基因的显着丢失以及染色质组装因子 1 (CAF1) 复合体的突变历史会导致基因组结构的快速变化。使用长读长测序和显微镜方法，我们已经确定了多达 15 个独立的大串联重复序列 (TDDO)，大小从 60 kb 到 1.44 Mb。我们的数据表明，这些 TDDO 出现在几代之内，导致数百个基因的重复。通过随后关注仅包含 20% rRNA 基因拷贝的线（20rDNA 线），我们研究了 TDDO 对 3D 基因组组织、基因表达和胞嘧啶甲基化的影响。我们发现重复的基因通常会积累更多的转录本。其中，有几个参与植物病原体反应，这可以解释为什么 20rDNA 系对细菌和线虫感染都具有超强抗性。最后，我们展示了 TDDO 产生基因融合和/或截断，并讨论了它们对植物基因组进化的潜在影响。