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Repetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes, yet remain understudied in most taxonomic groups. We investigated REs across 601 insect species and report wide variation in RE dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across insects, including notably elevated RE–gene associations in lineages with abundant long interspersed nuclear elements (LINEs). We leveraged this large, empirical data set to quantify impacts of long-read technology on RE detection and investigate fundamental challenges to RE annotation in diverse groups. In long-read assemblies, we detected ∼36% more REs than short-read assemblies, with long terminal repeats (LTRs) showing 162% increased detection, whereas DNA transposons and LINEs showed less respective technology-related bias. In most insect lineages, 25%–85% of repetitive sequences were “unclassified” following automated annotation, compared with only ∼13% inDrosophilaspecies. Although the diversity of available insect genomes has rapidly expanded, we show the rate of community contributions to RE databases has not kept pace, preventing efficient annotation and high-resolution study of REs in most groups. We highlight the tremendous opportunity and need for the biodiversity genomics field to embrace REs and suggest collective steps for making progress toward this goal.
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RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles
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.
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- Award ID(s):
- 1844693
- PAR ID:
- 10454418
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology Resources
- Volume:
- 21
- Issue:
- 3
- ISSN:
- 1755-098X
- Page Range / eLocation ID:
- p. 969-981
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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