TERAD: Extraction of transposable element composition from RADseq data

Transposable elements (TEs)—selfish DNA sequences that can move within the genome—comprise a large proportion of the genomes of many organisms. Although low-coverage whole genome sequencing can be used to survey TE composition, it is non-economical for species with large quantities of DNA. Here, we utilize restriction site associated DNA sequencing (RADSeq) as an alternative method to survey TE composition. First, we demonstrate in silico that double digest restriction-site associated DNA sequencing (ddRADseq) markers contain the same TE compositions as whole genome assemblies across arthropods. Next, we show empirically using eight Synalpheus snapping shrimp species with large genomes that TE compositions from ddRADseq and low-coverage whole genome sequencing are comparable within and across species. Finally, we develop a new bioinformatic pipeline, TERAD, to extract TE compositions from RADseq data. Our study expands the utility of RADseq to study the repeatome, making comparative studies of genome structure for species with large genomes more tractable and affordable.