Introduction of plant transposon annotation for beginners

Authors: Gao, Dongying

Submitted to: Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2023
Publication Date: 11/26/2023
Citation: Gao, D. 2023. Introduction of plant transposon annotation for beginners. Biology. 12(12). Article 1468. https://doi.org/10.3390/biology12121468.
DOI: https://doi.org/10.3390/biology12121468

Interpretive Summary: The entire collection of DNA within a plant, known as a genome, contain numerous jumping genes also known as transposons. These jumping genes are pieces of DNA that move from one location to another and were originally discovered by Barbara McClintock in corn over 55 years ago. Initially, this idea of genes that move or jump around was not widely accepted; however, over time scientists began to realize and accept that jumping genes make up a large portion of the DNA in plants and other organisms. Despite their abundance, it is exceedingly difficult to identify transposons or jumping genes accurately for most scientists, as one needs necessary knowledge in both biology and computer science. This review introduces the basics of plant transposons and provides a beginner's guide on their discovery. It also offers helpful information for the public about the history and importance of transposons.

Technical 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 the 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 detections 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 the transposon classification and explains why the terms of “autonomous” and “non-autonomous” cannot be used to classify the superfamilies of transposons. Last, this review also discusses how to identify misannotated transposons and improve the quality of transposon database. This review provides helpful information about plant transposons and a beginner’s guide on annotating these repetitive sequences.