Review
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Introduction of Plant Transposon Annotation for Beginners
Version 1
: Received: 9 November 2023 / Approved: 10 November 2023 / Online: 10 November 2023 (07:32:14 CET)
A peer-reviewed article of this Preprint also exists.
Gao, D. Introduction of Plant Transposon Annotation for Beginners. Biology 2023, 12, 1468. Gao, D. Introduction of Plant Transposon Annotation for Beginners. Biology 2023, 12, 1468.
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.
Keywords
Transposon annotation; plant; genome; bioinformatics pipeline; database
Subject
Biology and Life Sciences, Biology and Biotechnology
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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