Detection of transposition events of a transposon from short reads of next-generation sequencing (NGS) is challenging because transposons are repetitive and difficult to be distinguished from already existing transposons in the genome. Many transposons generate target site duplication (TSD) as the result of chromosomal integration. Since TSDs flanking the 5'-end (head) and 3'-end (tail) of a transposon has the identical sequences which are absent from the reference copy, the short reads containing the head or tail sequences of the transposon following the same TSD sequence may reveal the evidence of transposition. Transposon Insertion Finder (TIF) focuses on the TSD with flanking sequence of transposon and detects transposition events from NGS data. TIF software is available at https//github.com/akiomiyao/tif .Mapping the genomic location to which transposons jumped is of greatest interest to transposon biologists. Transposon display (TD) is the technique of choice that is easy and fast in determining the neo-insertion positions of a target transposon. Essentially, tagging of transposon is performed by digesting genomic DNA, ligating adaptors to digested DNA ends and PCR amplifying genomic regions flanking the transposon of interest. In this chapter, the experimental procedure of TD is described using Onsen retrotransposon of Arabidopsis as an example.ALE-seq is a method devised to identify pre-integration intermediates of LTR retrotransposons called extrachromosomal linear DNA, which can be used to predict retrotransposition activity. We describe here a bioinformatic methodology to process reads obtained from the ALE-seq protocol for the effective annotation of novel and active retroelements.Extrachromosomal linear DNA (eclDNA) is the reverse-transcribed cDNA intermediate derived from long terminal repeat (LTR) transposable elements (TEs) (Cho et al., Nat Plants 526-33, 2018). Given that the eclDNAs are the final intermediate of LTR-TE life cycle prior to integration to the host chromosomes, their presence is considered a strong indication of active LTR retrotransposons (Cho et al., Nat Plants 526-33, 2018; Lanciano et al., PLoS Genet 13e1006630, 2017). Here, we describe a method of amplification of LTR extrachromosomal DNA followed by sequencing (ALE-seq) which determines the 5' LTR sequences of eclDNAs. Briefly, ALE-seq consists of two steps of amplification, in vitro transcription of adaptor-ligated eclDNAs and subsequent reverse transcription to cDNAs primed at the conserved primer binding site (PBS) (Cho et al., Nat Plants 526-33, 2018). ALE-seq allows the high-throughput identification of novel LTR-TEs which are active in plants that could be potentially useful for crop biotechnology.Transposable elements (TEs) are the main component of eukaryotic genomes. Besides their impact on genome size, TEs are also functionally important as they can alter gene expression and influence phenotypic variation. In plants, most top-down studies focus on extremely clear phenotypes such as the shape or the color of individuals and do not explore fully the role of TEs in evolution. Assessing the impact of TEs in a more systematic manner, however, requires identifying active TEs to further study their impact on phenotypes. In this chapter, we describe an in planta approach that consists in activating TEs by interfering with pathways involved in their silencing. It enables to directly investigate the functional impact of single TE families at low cost.Active transposable elements (TEs) generate insertion polymorphisms that can be detected through genome resequencing strategies. However, these techniques may have limitations for organisms with large genomes or for somatic insertions. Here, we present a method that takes advantage of the extrachromosomal circular DNA (eccDNA) forms of actively transposing TEs in order to detect and characterize active TEs in any plant or animal tissue. Mobilome-seq consists in selectively amplifying and sequencing eccDNAs. It relies on linear digestion of genomic DNA followed by rolling circle amplification of circular DNA. Both active DNA transposons and retrotransposons can be identified using this technique.Miniature inverted-repeat transposable elements (MITEs) are a subset of short, non-autonomous class II transposable elements and also a major source of eukaryotic genomic variation. Therefore, genome-wide identification of MITE insertions can help to shed light on their copy number variation and genome insertion features.  https://www.selleckchem.com/peptide/avexitide.html  Here, we present a protocol for targeted MITE identification and genotyping by high-throughput sequencing. By introducing genome-wide detection of the rice mJing MITE as an example, we describe DNA extraction, DNA fragmentation, targeted DNA fragment enrichment, library construction for high-throughput sequencing, and sequence analysis.Miniature form transposable elements (mTEs) are ubiquitous in plant genomes and directly linked to gene regulation and evolution. With the advantage of completely sequenced genomes of Brassica rapa and Brassica oleracea, an open-source web portal called, BrassicaTED was developed. This database provides a user-friendly interface to explore invaluable information of mTEs in Brassica species and unique visualization and comparison tools. In this chapter, we describe an overview of this database construction and explain the utilities of data search, visualization, and analysis tools. In addition, we show the possible obstacles users may encounter when using this database.Transposable elements (TEs) are important contributors to genome structure and evolution. With the growth of sequencing technologies, various computational pipelines and software programs have been developed to facilitate TE identification and annotation. These computational tools can be categorized into three types based on their underlying approach homology-based, structural-based, and de novo methods. Each of these tools has advantages and disadvantages. In this chapter, we introduce EDTA (Extensive de novo TE Annotator), a new comprehensive pipeline composed of high-quality tools to identify and annotate all types of TEs. The development of EDTA is based on the benchmarking results of a collection of TE annotation methods. The selected programs are evaluated by their ability to identify true TEs as well as to exclude false candidates. Here, we present an overview of the EDTA pipeline and a detailed manual for its use. The source code of EDTA is available at https//github.com/oushujun/EDTA .