The good, the bad and the ugly of transposable elements annotation tools

Abstract

Transposable elements are repetitive and mobile DNA segments that can be found in virtually all organisms investigated to date. Their complex structure and variable nature are particularly challenging from the genomic annotation point of view. Many softwares have been developed to automate and facilitate TEs annotation at the genomic level, but they are highly heterogeneous regarding documentation, usability and methods. In this review, we revisited the existing software for TE genomic annotation, concentrating on the most often used ones, the methodologies they apply, and usability. Building on the state of the art of TE annotation software we propose best practices and highlight the strengths and weaknesses from the available solutions.

Expression of Transposable Elements throughout the Fasciola hepatica Trematode Life Cycle

“…Unknown elements constitute a significant portion, which causes challenges for annotation by making the program unable to assign them to known groups. Annotation of Unknown elements is a labor-intensive task and merits a separate study, given the numerous nuances involved [ 56 , 57 , 58 ]. Considering the differences in sequencing methodologies and assembly techniques, slight variations in TE composition may be attributed to assembly artifacts or intraspecific polymorphism.…”

TEtrimmer: a novel tool to automate the manual curation of transposable elements

“…TE annotation is typically based on three main strategies, i.e., repository-based, repeat-based, and structure-based methods. The most-used strategy is the repository-based approach (Loreto et al, 2023), which takes advantage of public pre-constructed TE libraries for whole-genome TE annotation. Since closely related species share a common origin and exhibit genome sequence similarity, the established TE library can be used to identify homologous TEs in related genomes as well (Gao, 2023).…”