TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidenee for Abundant New Transposable Elements in the Maize Genome

作     者：Weijia Su Xun Gu Thomas Peterson 

作者机构：Department of GeneticsDevelopment and Cell BiologyIowa State UniversityAmesIA50011-3260USA Department of AgronomyIowa State UniversityAmesIA50011-3260USA 

出 版 物：《Molecular Plant》 (分子植物（英文版）)

年 卷 期：2019年第12卷第3期

页      面：447-460页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 

基　　金：supported by the USDA National Institute of Food and Agriculture Hatch Project by State of Iowa funds 

主　　题：maize genomes TIR transposable element annotation pipeline machine learning 

摘      要：Transposable elements (TEs) make up a large and rapidly evolving proportion of plant genomes. Among Class II DNA TEs, TIR elements are flanked by characteristic terminal inverted repeat sequences (TIRs). TIR TEs may play important roles in genome evolution, including generating allelic diversity, inducing structural variation, and regulating gene expression. However, TIR TE identification and annotation has been hampered by the lack of effective tools, resulting in erroneous TE annotations and a significant underestimation of the proportion of TIR elements in the maize genome. This problem has largely limited our understanding of the impact of TIR elements on plant genome structure and evolution. In this paper, we propose a new method of TIR element detection and annotation. This new pipeline combines the advantages of current homology-based annotation methods with powerful de novo machine-learning approaches, resulting in greatly increased efficiency and accuracy of TIR element annotation. The results show that the copy number and genome proportion of TIR elements in maize is much larger than that of current annotations. In addition, the distribution of some TIR superfamily elements is reduced in centromeric and pericentromeric positions, while others do not show a similar bias. Finally, the incorporation of machine-learning techniques has enabled the identification of large numbers of new DTA (hAT) family elements, which have all the hallmarks of bona fide TEs yet which lack high homology with currently known DTA elements. Together, these results provide new tools forTE research and new insight into the impact ofTIR elements on maize genome diversity .