Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR 97331, USA.
Department of Biology, University of Rochester, 402 Hutchison Hall, PO Box 270211, Rochester, NY 14627, USA.
Syst Biol. 2020 Nov 1;69(6):1137-1148. doi: 10.1093/sysbio/syaa030.
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 multigene 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. [Bembidion; Carabidae; copy number variation profiles; rapid genome evolution; ribosomal DNA; species delimitation.].
基因组结构是生物体的一种复杂的、多维特性，由基因组组成部分的内容和空间组织定义。对模式生物的整个基因组结构进行比较研究，揭示了基因组调控、进化和多样化的机制，但此类研究需要昂贵的分析方法，这使得大多数群体都无法进行广泛的比较研究。然而，衡量单一结构成分（例如，一类重复序列的分布）的低成本方法具有作为进化研究的新数据源的潜力，因为该方法与更复杂的生物现象相关，并且可以作为解释框架的一部分。我们研究了核糖体 DNA(rDNA)中的拷贝数变异(CNV)谱作为反映基因组中 rDNA 亚成分分布的简单指标。我们发现，rDNA CNV 谱中的特征与短柄属(Bembidion)的 breve 物种群的物种边界强烈相关，并且在 Plataphus 亚属的更广泛分类学采样中发生变化。一些物种的图谱显示 rDNA 样序列在整个基因组中的重排迹象，揭示了快速基因组进化的证据（包括在姐妹对之间），这从传统数据源（如多基因数据集）的分析中并不明显。rDNA 样序列的主要重排经常发生在 Plataphus 的进化历史中。我们通过荧光原位杂交证实，CNV 图谱代表了基因组结构的一个方面（即 rDNA 成分在基因组中的线性分布）。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谱作为一种低成本工具的潜力，用于在物种划分和基因组进化研究中纳入基因组结构变异的信号。[短柄属；步甲科；拷贝数变异谱；快速基因组进化；核糖体 DNA；物种划分。]。
