Department of Integrative Biology, University of Guelph, Guelph, ON, N1G2W1, Canada.
G3 (Bethesda). 2024 Jul 8;14(7). doi: 10.1093/g3journal/jkae105.
Ribosomal DNA (rDNA) has a vital role in ribosome biogenesis as it contains the genes that encode ribosomal RNA (rRNA) separated by intergenic spacers (IGSs). The rRNA genes occur in hundreds to tens of thousands of copies per haploid genome in eukaryotes and are generally highly conserved with low variation within species. Due to the repetitive nature and large size of rDNA arrays, detecting intraindividual variation can be difficult. In this study, we use whole-genome sequences of 169 Daphnia pulex individuals from 10 natural populations to measure the copy number and sequence variation in rDNA. This revealed that variation in rDNA copy number between individuals spans an order of magnitude. We further observed a substantial level of sequence variation within individual genomes. As expected, single-nucleotide polymorphisms occurred in regions of lower functional constraint such as the IGS and expansion segments of the rRNA genes. The presence of strong linkage disequilibrium among variants facilitated identification of haplotypes within each population. Although there was evidence of recombination among haplotypes from different populations, it is insufficient to eliminate linkage disequilibrium within populations. Estimating copy number and haplotype diversity within individuals revealed that the level of intraindividual sequence variation is not strongly correlated with copy number. The observed patterns of variation highlight a complex evolutionary history of rDNA in D. pulex. Future research should explore the functional implications of rDNA copy number and sequence variation on organismal phenotypes.
核糖体 DNA（rDNA）在核糖体生物发生中起着至关重要的作用，因为它包含编码核糖体 RNA（rRNA）的基因，这些基因被基因间间隔区（IGS）隔开。真核生物的 rRNA 基因每个单倍体基因组中存在数百到数万份拷贝，通常在物种内具有高度保守性和低变异性。由于 rDNA 序列的重复性质和庞大尺寸，检测个体内的变异可能很困难。在这项研究中，我们使用了来自 10 个自然种群的 169 个 Daphnia pulex 个体的全基因组序列来测量 rDNA 的拷贝数和序列变异。结果表明，个体之间 rDNA 拷贝数的变异跨度达到了一个数量级。我们进一步观察到个体基因组内存在大量的序列变异。正如预期的那样，单核苷酸多态性发生在功能约束较低的区域，如 IGS 和 rRNA 基因的扩展片段。变体之间存在强烈的连锁不平衡，这有助于在每个种群中识别单倍型。尽管不同种群的单倍型之间存在重组的证据，但这不足以消除种群内的连锁不平衡。估计个体内的拷贝数和单倍型多样性表明，个体内序列变异的水平与拷贝数没有很强的相关性。观察到的变异模式突出了 D. pulex 中 rDNA 的复杂进化历史。未来的研究应该探索 rDNA 拷贝数和序列变异对生物体表型的功能影响。
