Transposable elements in rice detected by TEF

<p>Next generation sequence data of '<a href="https://www.gene.affrc.go.jp/databases-core_collections_wr_en.php">World Rice Core Collection</a>' and '<a href="https://www.gene.affrc.go.jp/databases-core_collections_jr_en.php">Rice Core Collection of Japanese Landraces</a>'&nbsp;distributing NARO genebank have been analyzed by the software '<a href="https://pubmed.ncbi.nlm.nih.gov/36418944/">Transposable Elements Finder</a>'. This data is an additional supplementary data of the TEF paper.</p> <p>Transposition evidences were detected by direct comparison of NGS short reads between Japonica rice Nipponbare (wrc01) and other cultivars. Nearby 21,000 kinds of head and tail sequence pairs of TE have been identified by TEF. Head and tail sequences of TE, chromosome number, position, and name of detected rice cultivar were listed.&nbsp;&nbsp;&nbsp;</p> <ul> <li>This version is TE list of <em>Oryza sativa</em> detected by TEFv1.4.</li> <li>Positions of TE transpositions were mapped on&nbsp;<a href="https://rapdb.dna.affrc.go.jp/download/archive/irgsp1/IRGSP-1.0_genome.fasta">Os-Nipponbare-Reference-IRGSP-1.0</a>&nbsp;distributed from&nbsp;<a href="https://rapdb.dna.affrc.go.jp/">The Rice Annotation Project Database</a>.</li> <li>Accession Numbers of NGS data are listed in Japanese page '<a href="https://www.gene.affrc.go.jp/databases-core_collections_wr.php">World Rice Core Collection</a>' and in NCBI SRA page '<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=DRP006572&amp;o=acc_s%3Aa">Rice Core Collection of Japanese Landraces</a>'.</li> <li>The TEF software is available at:&nbsp;<a href="https://github.com/akiomiyao/tef">https://github.com/akiomiyao/tef</a></li> <li>Miyao, A., Yamanouchi, U. Transposable element finder (TEF): finding active transposable elements from next generation sequencing data.&nbsp;<em>BMC Bioinformatics</em>&nbsp;<strong>23</strong>, 500 (2022). <a href="https://doi.org/10.1186/s12859-022-05011-3">https://doi.org/10.1186/s12859-022-05011-3</a></li> </ul>