title: TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice.
abstract: Here we present TENOR (Transcriptome ENcyclopedia Of Rice, http://tenor.dna.affrc.go.jp), a database that encompasses large-scale mRNA sequencing (mRNA-Seq) data obtained from rice under a wide variety of conditions. Since the elucidation of the ability of plants to adapt to various growing conditions is a key issue in plant sciences, it is of great interest to understand the regulatory networks of genes responsible for environmental changes. We used mRNA-Seq and performed a time-course transcriptome analysis of rice, Oryza sativa L. (cv. Nipponbare), under 10 abiotic stress conditions (high salinity; high and low phosphate; high, low and extremely low cadmium; drought; osmotic; cold; and flood) and two plant hormone treatment conditions (ABA and jasmonic acid). A large number of genes that were responsive to abiotic stresses and plant hormones were detected by differential expression analysis. Furthermore, several responsive genes were found to encode transcription factors that could control the transcriptional network of stress responses, but the timing of the induction of these genes was not uniform across conditions. A significant number of cis-regulatory elements were enriched in the promoter regions of the responsive genes and were shared among conditions. These data suggest that some key components of gene regulation networks are shared between different stress signaling pathways. All the resources (novel genes identified from mRNA-Seq data, expression profiles, co-expressed genes and cis-regulatory elements) can be searched for and are available in TENOR.
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Kawahara
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Youko
authors.initials: Y
authors.lastname: Oono
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan Life Science Research Center, BITS. Co., Ltd., 5-201 Kandamatsunaga-cho, Chiyoda-ku, Tokyo, 101-0023 Japan.
authors.forename: Hironobu
authors.initials: H
authors.lastname: Wakimoto
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Ogata
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kanamori
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Harumi
authors.initials: H
authors.lastname: Sasaki
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Satomi
authors.initials: S
authors.lastname: Mori
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Matsumoto
authors.affiliation: Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan taitoh@affrc.go.jp.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Itoh
mesh_terms: D002104:Cadmium / Q000378:metabolism; D016000:Cluster Analysis; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D012275:Oryza / Q000187:drug effects / Q000235:genetics* / Q000502:physiology; D010937:Plant Growth Regulators / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D013312:Stress, Physiological; D059467:Transcriptome
chemical_list: D010937:Plant Growth Regulators; D012333:RNA, Messenger; D018749:RNA, Plant; D002104:Cadmium
keywords: Abiotic stress; Database; Next-generation sequencing; Plant hormone; Rice; mRNA-Seq