Efficient homology‐based annotation of transposable elements using minimizers

Abstract

PremiseTransposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long‐read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies.Methods and ResultsWe present a new functionality of the Next‐Generation Sequencing Experience Platform (NGSEP) to perform efficient homology‐based TE annotation. Sequences in a reference library are treated as long reads and mapped to an input genome assembly. A hierarchical annotation is then assigned by homology using the annotation of the reference library. We tested the performance of our algorithm on genome assemblies of different plant species, including Arabidopsis thaliana, Oryza sativa, Coffea humblotiana, and Triticum aestivum (bread wheat). Our algorithm outperforms traditional homology‐based annotation tools in speed by a factor of three to >20, reducing the annotation time of the T. aestivum genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95.ConclusionsNGSEP allows rapid analysis of TEs, especially in very large and TE‐rich plant genomes.

A phased genome assembly of a Colombian Trypanosoma cruzi TcI strain and the evolution of gene families

“…We mapped this initial database to the genome using Repeat Masker ( http://www.repeatmasker.org/ ). We also executed the TransposonsFinder command of NGSEP 87 to map the database generated with Repeat Modeler and annotate the regions including transposable elements in the genome assembly of T. cruzi (Dm25). We executed a separate process for each haplotype and executed two rounds of identification.…”