Genome architecture is a complex, multidimensional property of an organism defined by the content and spatial organization of the genome's component parts. Comparative study of entire genome architecture in model organisms is shedding light on mechanisms underlying genome regulation, evolution, and diversification; but such studies require costly analytical approaches which make extensive comparative study impractical for most groups. However, lower-cost methods that measure a single architectural component (e.g., distribution of one class of repeats) have potential as a new data source for evolutionary studies insofar as that measure correlates with more complex biological phenomena, and for which it could serve as part of an explanatory framework. We investigated copy number variation (CNV) profiles in ribosomal DNA (rDNA) as a simple measure reflecting the distribution of rDNA subcomponents across the genome. We find that signatures present in rDNA CNV profiles strongly correlate with species boundaries in the breve species group of Bembidion, and vary across broader taxonomic sampling in Bembidion subgenus Plataphus. Profiles of several species show evidence of re-patterning of rDNA-like sequences throughout the genome, revealing evidence of rapid genome evolution (including among sister pairs) not evident from analysis of traditional data sources such as multi-gene data sets. Major re-patterning of rDNA-like sequences has occurred frequently within the evolutionary history of Plataphus. We confirm that CNV profiles represent an aspect of genomic architecture (i.e., the linear distribution of rDNA components across the genome) via fluorescence in-situ hybridization. In at least one species, novel rDNA-like elements are spread throughout all chromosomes. We discuss the potential of copy number profiles of rDNA, or other repeats, as a low-cost tool for incorporating signal of genomic architecture variation in studies of species delimitation and genome evolution.

中文翻译：

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重复的 DNA 谱揭示了基因组快速进化的证据并反映了地面甲虫的物种边界

基因组结构是生物体的一种复杂的多维属性，由基因组组成部分的内容和空间组织定义。模式生物全基因组结构的比较研究揭示了基因组调控、进化和多样化的潜在机制；但此类研究需要昂贵的分析方法，这使得对大多数群体进行广泛的比较研究不切实际。然而，测量单个体系结构组件（例如，一类重复的分布）的低成本方法具有作为进化研究的新数据源的潜力，因为该测量与更复杂的生物现象相关，并且可以作为解释性框架的一部分。我们研究了核糖体 DNA (rDNA) 中的拷贝数变异 (CNV) 谱，作为反映 rDNA 子成分在整个基因组中分布的简单措施。我们发现 rDNA CNV 配置文件中存在的特征与 Bembidion 的短物种组中的物种边界密切相关，并且在 Bembidion 亚属 Plataphus 中更广泛的分类抽样中有所不同。几个物种的概况显示了整个基因组中 rDNA 样序列重新模式化的证据，揭示了快速基因组进化（包括姐妹对之间）的证据，这在传统数据源（如多基因数据集）的分析中并不明显。在 Plataphus 的进化历史中经常发生 rDNA 样序列的主要重新模式化。我们确认 CNV 谱代表了基因组结构的一个方面（即，rDNA 组分在整个基因组中的线性分布）通过荧光原位杂交。在至少一个物种中，新的 rDNA 样元件遍布所有染色体。我们讨论了 rDNA 或其他重复序列的拷贝数图谱作为将基因组结构变异信号纳入物种定界和基因组进化研究的低成本工具的潜力。