(i) TEs online annotation(find more details).
(ii) Genes and TEs(find more details).

The first module aims to identify TEs from genomic data. The second module is used to study the interaction between TEs and genes.

TEs online annotation is used to comprehensively identify and annotate TEs in the genome assemblies uploaded by users. HiTE, a TE annotation tool developed by our group, used in WebTE is superior to the popular methods (such as RepeatScout, EDTA and RepeatModeler2) in the accuracy of identifying full-length transposons.

First of all, a species name needs to be selected or customized. Secondly, the user needs to upload the genome assembly, which is going to be analyzed. Finally, the user can set the online annotation parameters, and an email will be sent when the job is done. In Results > Online Annotation page, the status of jobs can be monitored at any time, and the annotated TE library can be downloaded by user.

Long Terminal Repeat (LTR) replicating via an RNA intermediate (copy-and-paste mechanism) has been proven to be the main driver of genome size evolution, which is the most concerning transposable element in plant genomics research. There is ample evidence demonstrating that most phylogenetic studies of LTR-retrotransposons performed to date have relied on the analysis of RT, RH, and INT protein domains because they are well characterized and relatively well conserved, and some studies have performed comprehensive LTR-retrotransposon phylogeny analysis. However, due to a lack of reference databases and clear classification guidelines, elements that belonging to the same family have occasionally been described under different names. Fortunately, there is a database of retrotransposon protein domains named REXdb, which is a comprehensive database reflecting phylogenetic relationships and serving as a guide for efficient and unified annotation of LTR-retrotransposons in plant genomes.

Ty1/copia and Ty3/gypsy account for the majority of LTR-retrotransposons in plants. Although they should be further divided into plenty of families, LTR-retrotransposons are often classified only to superfamily level, which is far from satisfactory. Besides, many phylogenetic relationships between families are lost, and the comparison of retrotransposons from more distant taxa is not available.

To solve these problems, this module provides phylogenetic analysis on the basis of the conserved protein domains (RT, RH, and INT) in Ty1/copia and Ty3/gypsy. By aligning the identified TEs with REXdb, the predicted protein domains are extracted. Then, MUSCLE performs a multiple sequence alignment for these domains, and the phylogenetic tree of multiple species is jointly constructed based on neighbor-joining algorithms. In this way, the Copia and Gypsy super families can be divided into more detailed families.

The user can select multiple annotated TE libraries generated in the TEs Online Annotation module. For the construction of the phylogenetic tree, a super family and a type of protein domain must be selected. In the Results > Phylogenetic Relationship Analysis page, the status of jobs can be monitored at any time. A phylogenetic trees and lineage information for TE families are shown in the page.

With the discovery of transposable elements about 70 years ago in maize, the view that non-coding DNA regions are regarded as junk DNA has changed, which has put plants at the forefront of studying the effects of TEs on genome structure and expression. Numerous studies show that TEs play an important role in genetic diversity, genome size, and the evolutionary potential of crop genomes. TEs can cause genetic changes in the pattern of gene expression and regulation of gene function, including (i) TE insertions in coding regions or introns lead to gene inactivation, (ii) differential gene expression due to TE insertions in or near regulatory regions.

To investigate the relationships between TEs and genes, the annotated TE library is combined with the gene annotation files to generate association information. Interactive visual tools that support conditional filtering are used to display the related information. The user can search for specific topics of interest in combination with different filter conditions and navigate to the exact position by clicking the jump button after each row of the table. To reduce the storage pressure of data, the maximum distance threshold between TEs and genes is set to 1000 bp.