Efficient and precise discovery of LTR-retrotransposon families using HiRepEat
Long Terminal Repeat Retrotransposons (LTR-RTs) are mobile genetic elements that replicate within host genomes using an RNA intermediate. Recent high quality genome assemblies provide new opportunities to study these repetitive elements across evolutionary timescales. We adapt the Myers O(Nd) wavefront alignment algorithm to produce a new fast LTR detection, clustering and phylogenetically-informed consensus approach for identifying LTR-RT families in new genome sequences. We present an iterative approach to identifying and removing repeats, initially tandem repeats, that we call TACO (TAndem COmpressor), and a corresponding coordinate mapping system we call SALSA (Sorted Array for Liftover of Sequence Addresses). Together these allow us to read and write in reduced genome space and search for LTR-RTs and tandem repeats in a series of operations. This greatly reduces confounding between different repeat types and allows us to uncover nested insertions. We show results from our clustering and consensus approach across the >500 genomes in the Vertebrate Genomes Project, with analysis completing in most cases in under 60 minutes with 15Gb memory and 16 cores. We also present cross-genome LTR-RT clustering across 30 Drosophila species, as well as across the VGP, providing fine-grained resolution on species-sharing patterns of LTR-RTs and revealing candidates for horizontal transfer.