Transposable elements in rice detected by TEF

Next generation sequence data of 'World Rice Core Collection' and 'Rice Core Collection of Japanese Landraces' distributing NARO genebank have been analyzed by the software 'Transposable Elements Finder'. This data is an additional supplementary data of the TEF paper. Transposition evidences were detected by direct comparison of NGS short reads between Japonica rice Nipponbare (wrc01) and other cultivars. Nearby 17,500 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. This version is TE list of Oryza sativa detected by TEFv1.6. Compared with TEF v1.4, TEF v1.6 incorporates a revised junction-alignment–based criterion to determine whether detected junctions represent authentic transposon insertions. Positions of TE transpositions were mapped on Os-Nipponbare-Reference-IRGSP-1.0 distributed from The Rice Annotation Project Database. Accession Numbers of NGS data are listed in Japanese page 'World Rice Core Collection' and in NCBI SRA page 'Rice Core Collection of Japanese Landraces'. The TEF software is available at: https://github.com/akiomiyao/tef Miyao, A., Yamanouchi, U. Transposable element finder (TEF): finding active transposable elements from next generation sequencing data. BMC Bioinformatics 23, 500 (2022). https://doi.org/10.1186/s12859-022-05011-3由日本国立农业食品研究开发机构（National Agriculture and Food Research Organization, NARO）基因库保藏的"世界水稻核心种质"与"日本地方稻种核心种质"的下一代测序数据，已通过转座因子查找器（Transposable Elements Finder，TEF）软件完成分析。本数据集为TEF相关研究论文的补充数据集。 通过直接比对粳稻日本晴（wrc01）与其他栽培品种的下一代测序短读段，可检测到转座事件的证据。TEF共鉴定得到约17500对转座因子首尾序列对，数据集涵盖了转座因子的首尾序列、染色体编号、插入位点以及被检测水稻品种的名称。 本次发布的版本为使用TEF v1.6版本鉴定得到的水稻（Oryza sativa）转座因子列表。 相较于TEF v1.4版本，TEF v1.6新增了基于接头比对的修正判定标准，用于甄别检测到的接头序列是否为真实的转座子插入位点。 所有转座事件的插入位点均已比对至由水稻注释项目数据库（The Rice Annotation Project Database, RAP-DB）发布的日本晴参考基因组Os-Nipponbare-Reference-IRGSP-1.0。 下一代测序数据的登录号可在"世界水稻核心种质"日文页面以及美国国家生物技术信息中心序列读取存档（NCBI SRA）的"日本地方稻种核心种质"页面查询获取。 转座因子查找器（TEF）软件的开源获取地址为：https://github.com/akiomiyao/tef 参考文献：Miyao, A., Yamanouchi, U. 转座因子查找器（TEF）：从下一代测序数据中鉴定活性转座因子. 《BMC生物信息学》, 23, 500 (2022). https://doi.org/10.1186/s12859-022-05011-3