The intergenic spacer (IGS) of rDNA is frequently built of long blocks of tandem repeats. To estimate the intragenomic variability of such knotty regions, we employed PacBio sequencing of the Cucurbita moschata genome, in which thousands of rDNA copies are distributed across a number of loci. The rRNA coding regions are highly conserved, indicating intensive interlocus homogenization and/or high selection pressure. However, the IGS exhibits high intragenomic structural diversity. Two repeated blocks, R1 (300-1250 bp) and R2 (290-643 bp), account for most of the IGS variation. They exhibit minisatellite-like features built of multiple periodically spaced short GC-rich sequence motifs with the potential to adopt non-canonical DNA conformations, G-quadruplex-folded and left-handed Z-DNA. The mutual arrangement of these motifs can be used to classify IGS variants into five structural families. Subtle polymorphisms exist within each family due to a variable number of repeats, suggesting the coexistence of an enormous number of IGS variants. The substantial length and structural heterogeneity of IGS minisatellites suggests that the tempo of their divergence exceeds the tempo of the homogenization of rDNA arrays. As frequently occurring among plants, we hypothesize that their instability may influence transcription regulation and/or destabilize rDNA units, possibly spreading them across the genome.

中文翻译：

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南瓜中基因间核糖体DNA间隔区的Intragenomic异质性是由具有可变潜力形成非规范DNA构象的DNA小卫星确定的。

rDNA的基因间隔区（IGS）通常由较长的串联重复序列构建。为了估计这种棘手区域的基因组内变异性，我们采用南瓜葫芦基因组的PacBio测序，其中数千个rDNA拷贝分布在多个基因座上。rRNA编码区高度保守，表明强烈的位点间均质化和/或高选择压力。但是，IGS表现出很高的基因组内部结构多样性。I1变异的大部分是两个重复的片段，R1（300-1250 bp）和R2（290-643 bp）。它们显示出由多个周期性间隔的短的富含GC的短序列基序构成的类似微型卫星的特征，具有采用非规范DNA构象，G-四链折叠和左手Z-DNA的潜力。这些基序的相互排列可用于将IGS变体分类为五个结构家族。由于重复序列的数目可变，每个家族中都存在微妙的多态性，这表明大量IGS变体并存。IGS小卫星的长度和结构异质性表明，它们发散的速度超过了rDNA阵列均质化的速度。由于在植物中经常发生，我们假设它们的不稳定性可能会影响转录调控和/或使rDNA单元不稳定，从而可能将其分散到整个基因组中。IGS小卫星的长度和结构异质性表明，它们发散的速度超过了rDNA阵列均质化的速度。由于在植物中经常发生，我们假设它们的不稳定性可能会影响转录调控和/或使rDNA单元不稳定，从而可能将其分散到整个基因组中。IGS小卫星的长度和结构异质性表明，它们发散的速度超过了rDNA阵列均质化的速度。由于在植物中经常发生，我们假设它们的不稳定性可能会影响转录调控和/或使rDNA单元不稳定，从而可能将其分散到整个基因组中。