The Dark Side of the Genome: Revealing Hidden Sequences to Determine the Absolute Repeat Content of a Genome

At the heart of the genome sequencing era, the role of repeated sequences in genome analysis has gained importance both for technical and biological aspects. However, in genome-scale projects, repeats can pose problems unless correctly identified and quantified.

We present a method that provides a more precise quantification and a direct comparison of repeated sequences within and between genomes exploiting the strengths of second-generation sequencing technologies. Our method is based on the alignment of a set of sequences that represent an entire genome or genome assembly to a curated repeat library. Hit abundance reflects the absolute repeat content of a genome, including fractions that could not be assembled into a genome assembly. The identification of repeats currently approaches the superfamily level describing the evolution of repeat content through time. Multi-species comparisons reveal repeat dynamics in time, such as the proliferation and suppression of different types of repetitive sequences between closely-related lineages.

This simple method allows one to consider the whole repeat complement of a species, regardless of the genome assembly outcome. It can be applied to any organism, providing an immediate characterization of a genome.