Abstract
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.
Highlights
Repetitive DNA elements have been understudied for decades due to technical and computational challenges associated with their sequencing and assembly
DNA sequences can cause the concerted evolution of repetitive elements (REs) within species and the rapid fixation of differences between species
These rapid evolutionary dynamics can be useful for understanding species boundaries, but repetitive sequences are rarely used in this context
Summary
Repetitive DNA elements (e.g., transposable elements, tandem repeats, high-copy genes) have been understudied for decades due to technical and computational challenges associated with their sequencing and assembly. Because repetitive regions can evolve much more rapidly than unique DNA sequences (e.g., protein-coding genes), repetitive sequences can reveal signals of evolutionary history over short time scales that may not be evident in slower-evolving genomic regions Despite their critical roles in genome and phenotype evolution and their known rapid turnover between closely related species One caveat to using REs in evolutionary studies is that their abundance may fluctuate widely across samples, even below the species level (Bosco, Campbell, Leiva-Neto, & Markow, 2007; McLain, Rai, & Fraser, 1987; Mestrović, Plohl, Mravinac, & Ugarković, 1998; Raskina, Barber, Nevo, & Belyayev, 2008). Development of approaches that can extract evolutionary signal despite repeat abundance variation can potentially increase the resolution of evolutionary studies among populations and species (Sproul, Barton, & Maddison, 2020)
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