Transposable elements (TEs), also known as transposons, a type of mobile genetic elements, are widespread across all investigated eukaryotic organisms and typically constitute the major portion of most genomes, especially in grasses, where they can account for up to 90% of the genome (Vitte et al., 2014). They not only are actively involved in altering gene structure and regulating gene expression, but also have played a profound role in reshaping genomic architecture and maintaining genomic stability (Lisch, 2013). Apart from important biological functions, TEs have been widely exploited as gene tagging and molecular markers for gene function and genetic research (Kumar and Hirochika, 2001). Their active transposition can introduce abundant genetic polymorphisms among individuals considering the presence and absence of insertions, which have been shown to contribute to genome evolution and differentiation between populations (Gonzalez et al., 2008; Studer et al., 2011). A comprehensive profile of transposon insertion polymorphisms (TIPs) is critical to TE family characterization, genetic evolution research as well as molecular marker-assisted breeding. Therefore, a variety of sequencing strategies and bioinformatics algorithms have been developed to efficiently identify TE loci based on next-generation sequencing (NGS) technology, and only few profiles have been constructed in well-studied model organisms, such as Drosophila melanogaster, Caenorhabditis elegans and Homo sapiens (Kofler et al., 2012; Laricchia et al., 2017; Rishishwar et al., 2015). However, it has not been reported in rice and most plants until now.
展开▼
