Transcription factors (TFs) regulate plant gene expression in different tissues. To investigate TF genes in rice (Oryza sativa L.), a genome‐wide TF identification was conducted with the japonica rice genome. This study identified 3078 putative TFs in 59 families. The TF number of the top 10 TF families accounted for 58% of the 3078 rice TFs. The three largest TF families were the myeloblastosis (MYB) superfamily, basic helix–loop–helix (bHLH), and far‐red‐impaired response (FAR1), which contained 413, 228, and 210 TF members, respectively. The expression profiles of the 3078 TF genes were surveyed with the RNA sequencing (RNA‐seq) data of 13 rice tissue types. Based on these expression profiles, we validated 1087 TFs expressed in 13 rice tissue types, which accounted for 35.32% of the 3078 putative TFs. We further analyzed the tissue‐specific TFs in rice. In total, 28, 14, 14, 10, 9, 5, 5, 4, 3, 3, 2, 11, and 1 tissue‐specific TF sequences were identified in the dry seed, pistil, spikelet, aleurone, anther, ovules, embryo 25 d after pollination (DAP), seed 5 DAP, root, leaf, seed 10 DAP, shoot, and endosperm 25 DAP, respectively. Moreover, we constructed RicetissueTFDB (http://221.237.158.212:50009/index), a comprehensive and public rice TF database that integrates tissue expression characters, genomic location, and Gene Ontology (GO) terms for each TF. The RicetissueTFDB database will facilitate the identification of target TFs and the functional studies about rice TFs.

中文翻译：

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RicetissueTFDB：水稻中组织特异性转录因子的全基因组鉴定。

转录因子（TFs）调节不同组织中植物基因的表达。为了研究水稻基因TF（水稻L.），利用粳稻基因组进行了全基因组TF鉴定。这项研究在59个家庭中鉴定出3078个假定的TF。前10个TF家族的TF数量占3078个水稻TF的58％。最大的三个TF家族是成纤维细胞增生（MYB）超家族，基本螺旋-环-螺旋（bHLH）和远红性受损反应（FAR1），分别包含413、228和210个TF成员。使用13种水稻组织的RNA测序（RNA-seq）数据调查了3078 TF基因的表达谱。基于这些表达谱，我们验证了在13种水稻组织中表达的1087个TF，占3078个假定TF的35.32％。我们进一步分析了水稻中组织特异性的TF。总共28、14、14、10、9、5、5、4、3、3、2、11 在干燥的种子，雌蕊，小穗，糊粉，花药，胚珠，授粉后25 d（DAP），种子5 DAP，根，叶，种子10 DAP，幼芽和胚乳25中鉴定出1种组织特异性TF序列DAP分别。此外，我们构建了RicetissueTFDB（http://221.237.158.212:50009/index），这是一个全面的公共水稻TF数据库，该数据库集成了每个TF的组织表达特征，基因组位置和基因本体（GO）术语。RicetissueTFDB数据库将有助于目标TF的鉴定和有关水稻TF的功能研究。一个全面的公共水稻TF数据库，该数据库整合了每个TF的组织表达特征，基因组位置和基因本体论（GO）术语。RicetissueTFDB数据库将有助于目标TF的鉴定和有关水稻TF的功能研究。一个全面的公共水稻TF数据库，该数据库整合了每个TF的组织表达特征，基因组位置和基因本体论（GO）术语。RicetissueTFDB数据库将有助于目标TF的鉴定和有关水稻TF的功能研究。