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Kōbe-shi, Japan

Nagano A.J.,Japan National Institute of Agrobiological Science | Nagano A.J.,Kyoto University | Sato Y.,Japan National Institute of Agrobiological Science | Mihara M.,Japan National Institute of Agrobiological Science | And 6 more authors.
Cell | Year: 2012

Determining the drivers of gene expression patterns is more straightforward in laboratory conditions than in the complex fluctuating environments where organisms typically live. We gathered transcriptome data from the leaves of rice plants in a paddy field along with the corresponding meteorological data and used them to develop statistical models for the endogenous and external influences on gene expression. Our results indicate that the transcriptome dynamics are predominantly governed by endogenous diurnal rhythms, ambient temperature, plant age, and solar radiation. The data revealed diurnal gates for environmental stimuli to influence transcription and pointed to relative influences exerted by circadian and environmental factors on different metabolic genes. The model also generated predictions for the influence of changing temperatures on transcriptome dynamics. We anticipate that our models will help translate the knowledge amassed in laboratories to problems in agriculture and that our approach to deciphering the transcriptome fluctuations in complex environments will be applicable to other organisms. © 2012 Elsevier Inc. Source


Uchiyama I.,Japan National Institute for Basic Biology | Mihara M.,Dynacom Co. | Nishide H.,Japan National Institute for Basic Biology | Chiba H.,Japan National Institute for Basic Biology
Nucleic Acids Research | Year: 2015

The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome. ad.jp/) is a comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. Because of the rapid increase in microbial genome data owing to the next-generation sequencing technology, it becomes increasingly challenging to maintain high-quality orthology relationships while allowing the users to incorporate the latest genomic data available into an analysis. Because many of the recently accumulating genomic data are draft genome sequences for which some complete genome sequences of the same or closely related species are available, MBGD now stores draft genome data and allows the users to incorporate them into a userspecific ortholog database using the MyMBGD functionality. In this function, draft genome data are incorporated into an existing ortholog table created only from the complete genome data in an incremental manner to prevent low-quality draft data from affecting clustering results. In addition, to provide high-quality orthology relationships, the standard ortholog table containing all the representative genomes, which is first created by the rapid classification program DomClust, is now refined using DomRefine, a recently developed program for improving domain-level clustering using multiple sequence alignment information. © The Author(s) 2014. Source


Kumagai M.,Japan National Institute of Agrobiological Science | Kim J.,Japan National Institute of Agrobiological Science | Itoh R.,Japan National Institute of Agrobiological Science | Itoh R.,Dynacom Co. | Itoh T.,Japan National Institute of Agrobiological Science
Bioinformatics | Year: 2013

Because an enormous amount of sequence data is being collected, a method to effectively display sequence variation information is urgently needed. tasuke is a web application that visualizes large-scale resequencing data generated by next-generation sequencing technologies and is suitable for rapid data release to the public on the web. The variation and read depths of multiple genomes, as well as annotations, can be shown simultaneously at various scales. We demonstrate the use of TASUKE by applying it to 50 rice and 100 human genome resequencing datasets.Availability and implementation: The tasuke program package and user manual are available from http://tasuke.dna.affrc.go.jp/. Contact: © 2013 The Author 2013. Published by Oxford University Press. Source


Okuda T.,Tokyo Medical University | Wakaguri H.,Tokyo Medical University | Wakaguri H.,Dynacom Co. | Suzuki Y.,Tokyo Medical University | Sugano S.,Tokyo Medical University
Gene | Year: 2012

Gene expression profile upon endoplasmic reticulum (ER) stress was analyzed by deep shotgun sequencing of mRNAs (DSSR) using RNAs from polysomes or cytoplasm of the HT29 cell. Two time points, 4. h after tunicamycin treatment when IRE1α signaling pathway is active and 16. h after the treatment when it is inactive, were used. There was a transient decrease in the proportion of shorter mRNA species (< 1000. bp) in polysome, while it increased transiently in the cytoplasm. Despite such an overall change and decrease in total amount of polysomes, the majority of the 6966 genes analyzed had less than 2 fold change in their expressions. We searched for the genes whose expression was elevated by 2 folds or more in both polysome and cytoplasm and confirmed the results with RT-PCR. There were 7 genes elevated only at 4. h (Group I), 20 genes only at 16. h (Group II) and 7 genes both at 4 and 16. h (Group III). There were 3 genes involved in ribosomal RNA biogenesis in Group I and 2 genes involved mTOR control in Group III. This was consistent with the concept that the ribosome is the essential site for managing ER stress. DSSR is a useful tool for the search of candidates of ER stress responsive genes. © 2012 Elsevier B.V. Source


Uchiyama I.,National Institutes of Natural science | Uchiyama I.,Japan National Institute for Basic Biology | Mihara M.,Dynacom Co. | Nishide H.,Japan National Institute for Basic Biology | Chiba H.,National Institutes of Natural science
Nucleic Acids Research | Year: 2013

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire mi-crobial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity. © The Author(s) 2012. Source

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