School of Biological Sciences, University of Auckland, Auckland, New Zealand.
School of Biological Sciences, University of Auckland, Auckland, New Zealand; Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France.
Genomics. 2022 Jul;114(4):110430. doi: 10.1016/j.ygeno.2022.110430. Epub 2022 Jul 10.
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties in quantifying copy number mean we lack a comprehensive understanding of how copy number evolves and the consequences. Here we present a genomic sequence read approach to estimate rDNA copy number based on modal coverage to help overcome limitations with existing mean coverage-based approaches. We validated our method using Saccharomyces cerevisiae strains with known rDNA copy numbers. Application of our pipeline to a global sample of S. cerevisiae isolates showed that different populations have different rDNA copy numbers. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations.
核糖体 DNA 基因（rDNA）编码主要的核糖体 RNA，在真核生物中通常形成串联重复阵列。物种具有特征性的 rDNA 拷贝数，但由于 rDNA 重组频繁，种内拷贝数存在大量变异。拷贝数差异可能会产生表型后果，但是由于定量拷贝数存在困难，我们缺乏对拷贝数如何进化以及其后果的全面理解。在这里，我们提出了一种基于模式覆盖的基因组序列读取方法来估计 rDNA 拷贝数，以帮助克服基于现有平均覆盖度方法的局限性。我们使用具有已知 rDNA 拷贝数的酿酒酵母菌株验证了我们的方法。我们的管道应用于全球酿酒酵母分离株样本表明，不同种群具有不同的 rDNA 拷贝数。我们的结果证明了模式覆盖方法的实用性，并强调了种群内和种群间 rDNA 拷贝数变异的高水平。
