Introduction of Plant Transposon Annotation for Beginners

Simple Summary Transposons are the most abundant repeats in plant genomes, and many of them can produce transcripts and encode proteins that may result in overestimating and incorrectly annotating functional genes. Thus, accurate transposon annotation is essential for all plant genome sequencing projects and other research. Although numerous tools have been developed, it is still challenging to annotate plant transposons for most scientists. The aims of this review are to introduce the basic knowledge about plant transposons and to provide a beginner's guide on plant transposon annotation. I accentuate the importance of transposons and summarize the general strategies for transposon annotation. I briefly introduce the unique features of different transposon superfamilies in plants and the related resources for annotating plant transposons. I further present the information on improving the quality of transposon annotation. The challenges and future prospects for plant transposon annotation are also discussed.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.