A5033437931- Plant Molecular Biology Research
- Genetic Mapping and Diversity in Plants and Animals
- Photosynthetic Processes and Mechanisms
- Wheat and Barley Genetics and Pathology
- Plant Stress Responses and Tolerance
- Plant Disease Resistance and Genetics
- Chromosomal and Genetic Variations
- Plant nutrient uptake and metabolism
- Plant-Microbe Interactions and Immunity
- Legume Nitrogen Fixing Symbiosis
- Plant Gene Expression Analysis
- Plant Genetic and Mutation Studies
- Plant Parasitism and Resistance
- Genomics and Phylogenetic Studies
- Plant tissue culture and regeneration
- Algal biology and biofuel production
- Genetics and Plant Breeding
- Soybean genetics and cultivation
- Plant Micronutrient Interactions and Effects
- Plant and animal studies
- Reproductive Biology and Fertility
- Biofuel production and bioconversion
- Animal Genetics and Reproduction
- CRISPR and Genetic Engineering
- Plant Reproductive Biology
Yokohama City University
2016-2025
RIKEN Center for Sustainable Resource Science
2016-2025
Nagasaki University
2021-2025
Kihara Institute for Biological Research
2016-2025
Hiroshima University
2024
RIKEN
2022-2024
Okayama University
2016-2022
Suzuki (Japan)
2019
United States Department of Agriculture
2011
Oregon State University
2011
Abstract Genetic diversity is key to crop improvement. Owing pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence species (known as ‘pan-genome’ 1 ). Multiple high-quality assemblies are an indispensable component pan-genome infrastructure. Barley ( Hordeum vulgare L.) important cereal with long history cultivation that adapted wide range agro-climatic conditions 2 . Here we report construction chromosome-scale for...
Plant-specific NAC transcription factors (TFs) play important roles in regulating diverse biological processes, including development, senescence, growth, cell division and responses to environmental stress stimuli. Within the soybean genome, we identified 152 full-length GmNAC TFs, 11 membrane-bound members. In silico analysis of GmNACs, together with their Arabidopsis rice counterparts, revealed similar architecture. Next, explored Affymetrix array Illumina transcriptome sequence data...
Abstract Knowledge of phosphorylation events and their regulation is crucial to understand the functional biology plants. Here, we report a large-scale phosphoproteome analysis in model monocot rice (Oryza sativa japonica ‘Nipponbare’), an economically important crop. Using unfractionated whole-cell lysates cells, identified 6,919 phosphopeptides from 3,393 proteins. To investigate conservation phosphoproteomes between plant species, developed novel phosphorylation-site evaluation method...
Report6 May 2008Open Access Large-scale phosphorylation mapping reveals the extent of tyrosine in Arabidopsis Naoyuki Sugiyama Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan Human Metabolome Technologies, Search more papers by this author Hirofumi Nakagami RIKEN Plant Science Center, Yokohama, Keiichi Mochida Arsalan Daudi Masaru Tomita Ken Shirasu Corresponding Author Yasushi Ishihama PRESTO, and Technology Agency, Tokyo, Information Sugiyama1,2,‡, Nakagami3,‡,...
Over the past several years, Brachypodium distachyon (Brachypodium) has emerged as a tractable model system to study biological questions relevant grasses. To place its relevance in larger context of plant biology, we outline here expanding adoption grass and compare this early history another model, Arabidopsis thaliana. In context, followed an accelerated path which development genomic resources, most notably whole genome sequence, occurred concurrently with generation other experimental...
Abstract Plants synthesize a sulfur-containing lipid, sulfoquinovosyldiacylglycerol, which is one of three nonphosphorus glycerolipids that provide the bulk structural lipids in photosynthetic membranes. Here, identification novel gene, UDP-glucose pyrophosphorylase3 (UGP3), required for sulfolipid biosynthesis described. Transcriptome coexpression analysis demonstrated highly correlated expression UGP3 with known genes Arabidopsis thaliana. Liquid chromatography–mass spectrometry leaf two...
In plants, the auxin response factor (ARF) transcription factors play important roles in regulating diverse biological processes, including development, growth, cell division and responses to environmental stimuli. An exhaustive search of soybean genome revealed 51 GmARFs, many which were formed by duplications. The typical GmARFs (43 members) contain a DNA-binding domain, an ARF domain auxin/indole acetic acid (AUX/IAA) dimerization whereas remaining eight members lack domain. Phylogenetic...
Summary Chinese liquorice/licorice ( Glycyrrhiza uralensis ) is a leguminous plant species whose roots and rhizomes have been widely used as herbal medicine natural sweetener. Whole‐genome sequencing essential for gene discovery studies molecular breeding in liquorice. Here, we report draft assembly of the approximately 379‐Mb whole‐genome sequence strain 308‐19 G. ; this contains 34 445 predicted protein‐coding genes. Comparative analyses suggested well‐conserved genomic components...
Abstract Bread wheat (Triticum aestivum) is a hexaploid species with A, B, and D ancestral genomes. Most bread genes are present in the genome as triplicated homoeologous (homoeologs) derived from species. Here, we report that both genetic epigenetic alterations have occurred homoeologs of class E MADS box gene. Two identified wheat, SEPALLATA (WSEP) LEAFY HULL STERILE1 (WLHS1), which homologs Os MADS45 MADS1 rice (Oryza sativa), respectively. The three WSEP showed similar genomic structures...
Two-component systems (TCSs) play vital functions in the adaptation of plants to environmental stresses. To identify soybean TCS genes involved regulation drought stress response, we performed tissue-specific expression profiling all 83 putative subjected dehydration. Under well-watered conditions, majority were expressed higher root tissues. Additionally, a high variability transcript abundance was observed for both roots and shoots. dehydration, more responsive shoots than roots. Further...
Summary Rhizoctonia solani is a soil‐borne fungus causing sheath blight. In consistent with its necrotrophic life style, no rice cultivars fully resistant to R. are known, and agrochemical plant defense activators used for blast, which upregulate phytohormonal salicylic acid (SA)‐dependent pathway, ineffective towards this pathogen. As result of the unavailability genetics, infection process remains unclear. We model monocotyledonous plants Brachypodium distachyon rice, evaluated effects...
Abstract The role of resource availability in determining the incidence masting has been widely studied, but how floral transition and initiation are regulated by level is unclear. We tested hypothesis that stimulated high availabiltiy Fagus crenata based on a new technique, expression analyses flowering genes. isolated F. orthologues FLOWERING LOCUS T , LEAFY APETALA1 confirmed their functions using transgenic Arabidopsis thaliana . monitored gene levels for 5 years detected cycle off...
Mongolian grasslands, including the Gobi Desert, have been exposed to drought conditions with few rains. In such harsh environments, plants highly resistant abilities against stress survive over long periods. We hypothesized that these could harbor novel and valuable genes for enhancing resistance. this study, we identified Chloris virgata, a grassland plant strong RNA-seq-based transcriptome analysis was performed uncover associated resistance in C. virgata. De novo assembly revealed 25,469...
Abstract Plant cell culture has multiple applications in biotechnology and horticulture, from plant propagation to the production of high-value biomolecules. However, interplay between cellular diversity ambient conditions influences metabolism cultured tissues; understanding these factors detail will inform efforts optimize conditions. This study presents multiomics datasets callus cultures tobacco ( Nicotiana tabacum ), rice Oryza sativa two bamboo species Phyllostachys nigra P....
Abstract Ser acetyltransferase (SERAT), which catalyzes O-acetyl-Ser (OAS) formation, plays a key role in sulfur assimilation and Cys synthesis. Despite several studies on SERATs from various plant species, the vivo function of multiple SERAT genes cells remains unaddressed. Comparative genomics with five gene family Arabidopsis thaliana indicated that all three subfamilies are conserved across species available genome sequences. Single knockout mutants members were analyzed. All quadruple...
Abstract The Triticeae Full-Length CDS Database (TriFLDB) contains available information regarding full-length coding sequences (CDSs) of the crops wheat (Triticum aestivum) and barley (Hordeum vulgare) includes functional annotations comparative genomics features. TriFLDB provides a search interface using keywords for gene function related Gene Ontology terms similarity DNA deduced translated amino acid to access (TriFLCDS) entries. Annotations consist results against several sequence...
A large collection of full-length cDNAs is essential for the correct annotation genomic sequences and functional analysis genes their products. We obtained a total 39,936 soybean cDNA clones (GMFL01 GMFL02 clone sets) in full-length-enriched library which was constructed from plants that were grown under various developmental environmental conditions. Sequencing 5' 3' ends generated 68 661 expressed sequence tags (ESTs). The EST clustered into 22,674 scaffolds involving 2580 sequences. In...
Cassava is an important crop that provides food security and income generation in many tropical countries known for its adaptability to various environmental conditions. Despite global importance, the development of cassava microarray tools has not been well established. Here, we describe a 60-mer oligonucleotide Agilent representing ∼20 000 genes how it can be applied expression profiling under drought stress using three genotypes (MTAI16, MECU72 MPER417-003). Our results identified about...