Study of repetitive DNA elements in model organisms highlights the role of repetitive elements (REs) in many processes that drive genome evolution and phenotypic change. Because REs are much more dynamic than single‐copy DNA, repetitive sequences can reveal signals of evolutionary history over short time scales that may not be evident in sequences from slower‐evolving genomic regions. Many tools for studying REs are directed toward organisms with existing genomic resources, including genome assemblies and repeat libraries. However, signals in repeat variation may prove especially valuable in disentangling evolutionary histories in diverse non‐model groups, for which genomic resources are limited. Here, we introduce RepeatProfiler, a tool for generating, visualizing, and comparing repetitive element DNA profiles from low‐coverage, short‐read sequence data. RepeatProfiler automates the generation and visualization of RE coverage depth profiles (RE profiles) and allows for statistical comparison of profile shape across samples. In addition, RepeatProfiler facilitates comparison of profiles by extracting signal from sequence variants across profiles which can then be analysed as molecular morphological characters using phylogenetic analysis. We validate RepeatProfiler with data sets from ground beetles (Bembidion), flies (Drosophila), and tomatoes (Solanum). We highlight the potential of RE profiles as a high‐resolution data source for studies in species delimitation, comparative genomics, and repeat biology.

中文翻译：

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RepeatProfiler：重复 DNA 图谱可视化和比较分析的管道

对模式生物中重复 DNA 元件的研究强调了重复元件 (RE) 在驱动基因组进化和表型变化的许多过程中的作用。由于 RE 比单拷贝 DNA 更具动态性，因此重复序列可以揭示短时间范围内的进化历史信号，而这些信号在进化较慢的基因组区域的序列中可能不明显。许多研究 RE 的工具都是针对具有现有基因组资源的生物体，包括基因组组装和重复文库。然而，重复变异中的信号可能在解开基因组资源有限的不同非模型群体的进化历史方面特别有价值。在这里，我们介绍 RepeatProfiler，这是一种用于从低覆盖率、短读长序列数据中生成、可视化和比较重复元件 DNA 图谱的工具。RepeatProfiler 可自动生成和可视化 RE 覆盖深度剖面（RE 剖面），并允许对样本之间的剖面形状进行统计比较。此外，RepeatProfiler 通过从跨谱的序列变体中提取信号来促进谱的比较，然后可以使用系统发育分析将其作为分子形态特征进行分析。我们使用来自地面甲虫 ( Bembidion )、苍蝇 ( Drosophila ) 和西红柿 ( Solanum )的数据集验证 RepeatProfiler 。我们强调 RE 图谱作为物种界定、比较基因组学和重复生物学研究的高分辨率数据源的潜力。