RTRIP: a comprehensive profile of transposon insertion polymorphisms in rice

A comprehensive profile of transposon insertion polymorphisms (TIPs) is critical to TE family characterization, genetic evolution research as well as molecular marker‐assisted breeding. [...]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). The average number of TE loci is 6304 for each accession, and shows large difference among accessions, varying from 4898 to 10 155. [...]19 160 TE loci are inserted within or nearby genes (200 bp flanking regions), which may have a potential effect on gene function. [...]Search by varieties’ has been designed to facilitate their application as molecular markers for gene mapping and molecular‐assisted breeding. [...]Search by Genes’ submodule is customized for TE loci associated with genes and will be applied to the study of gene function.