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 … Show more
“…A search in the Transcriptome Encyclopedia of Rice (TENOR) database (Kawahara et al 2016) was performed and changes in the expression levels were observed for the EUL genes after different abiotic stresses and plant hormone treatments. Figure 5 shows the expression profiles for the different OsEUL genes based on the expression data after application of drought or osmotic stress as well as after exogenous application of absiscic acid (ABA, 100 μM) or jasmonic acid (JA, 100 μM).Fig.…”
Section: Resultsmentioning
confidence: 99%
“…Motif mapping information was combined with a set of up to 200 co-expressed genes (according their Pearson correlation coefficient)from the TENOR database (Kawahara et al 2016). With the help of the RAP-DB ID convertor tool (http://rapdb.dna.affrc.go.jp/tools/converter) the RAP DB identifiers were converted to MSU locus numbers and used for the subsequent motif enrichment analysis.…”
Background: Lectins, defined as 'Proteins that can recognize and bind specific carbohydrate structures', are widespread among all kingdoms of life and play an important role in various biological processes in the cell. Most plant lectins are involved in stress signaling and/or defense. The family of Euonymus-related lectins (EULs) represents a group of stress-related lectins composed of one or two EUL domains. The latter protein domain is unique in that it is ubiquitous in land plants, suggesting an important role for these proteins. Results: Despite the availability of multiple completely sequenced rice genomes, little is known on the occurrence of lectins in rice. We identified 329 putative lectin genes in the genome of Oryza sativa subsp. japonica belonging to nine out of 12 plant lectin families. In this paper, an in-depth molecular characterization of the EUL family of rice was performed. In addition, analyses of the promoter sequences and investigation of the transcript levels for these EUL genes enabled retrieval of important information related to the function and stress responsiveness of these lectins. Finally, a comparative analysis between rice cultivars and several monocot and dicot species revealed a high degree of sequence conservation within the EUL domain as well as in the domain organization of these lectins.
“…A search in the Transcriptome Encyclopedia of Rice (TENOR) database (Kawahara et al 2016) was performed and changes in the expression levels were observed for the EUL genes after different abiotic stresses and plant hormone treatments. Figure 5 shows the expression profiles for the different OsEUL genes based on the expression data after application of drought or osmotic stress as well as after exogenous application of absiscic acid (ABA, 100 μM) or jasmonic acid (JA, 100 μM).Fig.…”
Section: Resultsmentioning
confidence: 99%
“…Motif mapping information was combined with a set of up to 200 co-expressed genes (according their Pearson correlation coefficient)from the TENOR database (Kawahara et al 2016). With the help of the RAP-DB ID convertor tool (http://rapdb.dna.affrc.go.jp/tools/converter) the RAP DB identifiers were converted to MSU locus numbers and used for the subsequent motif enrichment analysis.…”
Background: Lectins, defined as 'Proteins that can recognize and bind specific carbohydrate structures', are widespread among all kingdoms of life and play an important role in various biological processes in the cell. Most plant lectins are involved in stress signaling and/or defense. The family of Euonymus-related lectins (EULs) represents a group of stress-related lectins composed of one or two EUL domains. The latter protein domain is unique in that it is ubiquitous in land plants, suggesting an important role for these proteins. Results: Despite the availability of multiple completely sequenced rice genomes, little is known on the occurrence of lectins in rice. We identified 329 putative lectin genes in the genome of Oryza sativa subsp. japonica belonging to nine out of 12 plant lectin families. In this paper, an in-depth molecular characterization of the EUL family of rice was performed. In addition, analyses of the promoter sequences and investigation of the transcript levels for these EUL genes enabled retrieval of important information related to the function and stress responsiveness of these lectins. Finally, a comparative analysis between rice cultivars and several monocot and dicot species revealed a high degree of sequence conservation within the EUL domain as well as in the domain organization of these lectins.
“…The shoot and root RNA‐seq data were downloaded from the Sequence Read Archive (Leinonen et al ), accession numbers DRX005898, DRX005899, DRX005930, DRX005931, DRX005886, DRX005887, DRX005910 and DRX005911, for two ABA‐treated root samples and controls, two ABA‐treated shoot samples and controls. The roots and shoots were obtained from 10‐day‐old seedlings and treated with 100 μ M ABA for 3 h (Kawahara et al ). Several time points of ABA treatment were available, but the 3 h time point was chosen because it was the closest to the 4 h time point used for the aleurone cells.…”
Seeds serve as a great model to study plant responses to drought stress, which is largely mediated by abscisic acid (ABA). The ABA responsive element (ABRE) is a key cis-regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA-induced genes in rice aleurone cells, suggesting other ABREs may exist. To identify novel ABREs, RNA sequencing was performed on aleurone cells of rice seeds treated with 20 μM ABA. Gibbs sampling was used to identify enriched elements, and particle bombardment-mediated transient expression studies were performed to verify the function. Gene ontology analysis was performed to predict the roles of genes containing the novel ABREs. This study revealed 2443 ABA-inducible genes and a novel ABRE, designated as ABREN, which was experimentally verified to mediate ABA signalling in rice aleurone cells. Many of the ABREN-containing genes are predicted to be involved in stress responses and transcription. Analysis of other species suggests that the ABREN may be monocot specific. This study also revealed interesting expression patterns of genes involved in ABA metabolism and signalling. Collectively, this study advanced our understanding of diverse cis-regulatory sequences and the transcriptomes underlying ABA responses in rice aleurone cells.
“…Here are just some of the topics covered in PAG conference during the computer demo sessions. 1) how to use public resources in The Arabidopsis Information Resource (TAIR) including registration, data searches, stock ordering, data submission and downloading large datasets (Reiser 2016), 2) presentation of Transcriptome ENcyclopedia Of Rice (TENOR) (http://tenor.dna.affrc.go.jp), a database that encompasses large-scale mRNASeq data obtained from rice under a wide variety of conditions (Kawahara et al 2016), 3) TreeGenes, a web-based database that provides interfaces and tools to collect, curate, visualize, and analyze data from over 1,700 forest tree species. The map-based CartograTree interface connects geo referenced trees with curated phenotypic and genetic data as well as environmental metrics from sources such as Ameriflux and WorldClim (Demurjian 2016), 4) Apollo, composed of a web-based client, an annotation-editing engine, and a server-side data service.…”
This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.Plant Breed. Biotech. 2016 (February)
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