Extended t-cores for the de novo identification of transposable elements and other inexact repeats from short read RNAseq data

Transcribed repeats represent a major challenge in the de novo assembly of transcriptomes from short RNA-seq reads. Young transposable elements (TEs) and other inexact repeats create dense and ambiguous regions in the assembly graph, preventing the correct assembly of transcripts. In this paper, we introduce a fully de novo method based on the discovery of dense regions in the compacted De Bruijn graph (DBG) to identify such repeats directly from short reads RNA-seq data, without requiring a reference genome or repeat database. Our approach defines the extended t-cores, subgraphs of the DBG that capture the complex topology induced by highly expressed inexact repeats appearing in RNA-seq reads. Independently of its interest for transcriptome assembly, the proposed method appears to be effective for the de novo identification of repeats in transcriptomes. After classifying cores using sequence-based motifs to distinguish simple repeats from potential TEs, we demonstrate its potential for the de novo discovery of transposable elements. We validate the approach on a Mus musculus dataset using expressed TE consensus sequences, showing that extended t-cores correspond to known expressed TE families. We also illustrate its de novo discovery potential on a non-model species, Canis lupus familiaris, where the method was also able to recover known transposable elements.