Introduction of Plant Transposon Annotation for Beginners

Abstract

Transposons are mobile DNA sequences that contribute large fractions of many plant genomes. They provide exclusive resources for tracking gene and genome evolution and for developing molecular tools for basic and applied research. Despite extensive efforts, it is still challenging to accurately annotate transposons, especially for beginners, as transposon prediction requires necessary expertise in both transposon biology and bioinformatics. Moreover, the complexity of plant genomes and the dynamic evolution of transposons also bring difficulties for genome-wide transposon discovery. This review summarizes the three major strategies for transposon detection including repeat-based, structure-based, and homology-based annotation, and introduces the transposon superfamilies identified in plants thus far, and some related bioinformatics resources for detecting plant transposons. Furthermore, it describes transposon classification and explains why the terms ‘autonomous’ and ‘non-autonomous’ cannot be used to classify the superfamilies of transposons. Lastly, this review also discusses how to identify misannotated transposons and improve the quality of the transposon database. This review provides helpful information about plant transposons and a beginner’s guide on annotating these repetitive sequences.

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

“…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). This strategy heavily relies on the availability and quality of a suitable TE library for the species of interest.…”