School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, Western Australia, Australia.
Nat Plants. 2018 Oct;4(10):762-765. doi: 10.1038/s41477-018-0264-0. Epub 2018 Oct 1.
Several recently published Brassicaceae genome annotations show strong differences in resistance (R)-gene content. We believe that this is caused by different approaches to repeat masking. Here we show that some of the repeats stored in public databases used for repeat masking carry pieces of predicted R-gene-related domains, and demonstrate that at least some of the variance in R-gene content in recent genome annotations is caused by using these repeats for repeat masking. We also show that other classes of genes are less affected by this phenomenon, and estimate a false positive rate of R genes (0 to 4.6%) that are in reality transposons carrying the R-gene domains. These results may partially explain why there has been a decrease in published novel R genes in recent years, which has implications for plant breeding, especially in the face of pathogens changing as a response to climate change.
最近发表的几篇 Brassicaceae 基因组注释显示，抗性（R）基因含量存在很大差异。我们认为这是由于重复屏蔽的方法不同造成的。在这里，我们展示了一些用于重复屏蔽的公共数据库中存储的重复序列携带预测的 R 基因相关结构域的片段，并证明了最近基因组注释中 R 基因含量的差异至少部分是由于使用这些重复序列进行重复屏蔽造成的。我们还表明，其他类别的基因受此现象的影响较小，并估计了实际上是携带 R 基因结构域的转座子的 R 基因的假阳性率（0 到 4.6%）。这些结果可能部分解释了为什么近年来发表的新 R 基因数量减少，这对植物育种具有重要意义，尤其是在面对由于气候变化而发生变化的病原体时。
