RepeatModeler2: automated genomic discovery of transposable element families

By Jullien M. Flynn, Robert M. Hubley, Clément Goubert, Jeb Rosen, Andrew G. Clark, Cédric Feschotte, Arian F. A. Smit. bioRxiv, 2019

1,040 citations recorded by the source corpus.

The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a new pipeline that greatly facilitates this process. This new program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete LTR retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately three times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. The program had an extremely low false positive rate when applied to simulated genomes devoid of TEs. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, https://github.com/Dfam-consortium/TETools). Significance Genome sequences are being produced for more and more eukaryotic species. The bulk of these genomes is composed of parasitic, self-mobilizing transposable elements (TEs) that play important roles in organismal evolution. Thus there is a pressing need for developing software that can accurately identify the diverse set of TEs dispersed in genome sequences. Here we introduce RepeatModeler2, an easy-to-use package for the curation of reference TE libraries which can be applied to any eukaryotic species. Through several major improvements over the previous version, RepeatModeler2 is able to produce libraries that recapitulate the known composition of three model species with some of the most complex TE landscapes. Thus RepeatModeler2 will greatly enhance the discovery and annotation of TEs in genome sequences.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/b566141867b621be4cfb1ad52f7c73d33dabb119

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Citations in the corpus

The Dfam community resource of transposable element families, sequence models, and genome annotations (2020, methodology): “It also infers ancestral CpG sites by accounting for the frequency of TG and CA dimers in neighboring columns [17].”
Ensembl 2023 (2022, methodology): “To improve the quality of the libraries we updated to using the recently released version 2 of RepeatModeler (34).”
Ensembl 2022 (2021, methodology): “We built an extensive collection of repeat libraries via RepeatModeler (11) to identify and classify repeat regions in greater detail.”
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA (2023, positive): “Before running the experiments, we soft-masked repeats in the genomic sequences using RepeatModeler2 (Flynn et al., 2020).”