A5045411840- Genomics and Phylogenetic Studies
- Plant tissue culture and regeneration
- RNA Research and Splicing
- Genetic Mapping and Diversity in Plants and Animals
- Plant Virus Research Studies
- Genomics and Chromatin Dynamics
- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Nuclear Structure and Function
- Transgenic Plants and Applications
- Genomics and Rare Diseases
- Plant Disease Resistance and Genetics
- Genetic diversity and population structure
- Plant-Microbe Interactions and Immunity
- Rice Cultivation and Yield Improvement
- Cancer-related Molecular Pathways
- GABA and Rice Research
- Cytomegalovirus and herpesvirus research
- Herpesvirus Infections and Treatments
- Viral-associated cancers and disorders
- RNA and protein synthesis mechanisms
- Plant Gene Expression Analysis
- Genomic variations and chromosomal abnormalities
- Toxin Mechanisms and Immunotoxins
- Plant Genetic and Mutation Studies
RIKEN Center for Integrative Medical Sciences
2018-2024
Research Organization of Information and Systems
2024
Shizuoka General Hospital
2023
Kazusa DNA Research Institute
2012-2021
University of Florida
2020
Iwate Biotechnology Research Center
2012-2016
Nara Institute of Science and Technology
2008-2010
Keio University
2004-2009
Institute of Agrobiological Sciences
1995-2005
University of Tsukuba
1990-1991
The majority of agronomically important crop traits are quantitative, meaning that they controlled by multiple genes each with a small effect (quantitative trait loci, QTLs). Mapping and isolation QTLs is for efficient breeding marker-assisted selection (MAS) better understanding the molecular mechanisms underlying traits. However, since it requires development DNA markers linkage analysis, QTL analysis has been time-consuming labor-intensive. Here we report rapid identification plant...
The cell cycle-dependent nucleocytoplasmic transport of proteins is predominantly regulated by CDK kinase activities; however, it currently difficult to predict the thus regulated, largely because low prediction efficiency motifs involved. Here, we report successful CDK1-regulated shuttling using a system for nuclear localization signals (NLSs). By systematic amino acid replacement analyses in budding yeast, created activity-based profiles different classes importin-alpha-dependent NLSs that...
The importin alpha/beta pathway mediates nuclear import of proteins containing the classical localization signals (NLSs). Although consensus sequences NLSs have been defined, there are still many that do not match rule and nonfunctional consensus. We report here six different NLS classes specifically bind to distinct binding pockets alpha. By screening random peptide libraries using an mRNA display, we selected peptides bound by alpha identified NLSs, including three novel classes. Two...
Structural variations (SVs) or copy number (CNVs) greatly impact the functions of genes encoded in genome and are responsible for diverse human diseases. Although a existing SV detection algorithms can detect many types SVs using whole sequencing (WGS) data, no single algorithm call every type with high precision recall.We comprehensively evaluate performance 69 multiple simulated real WGS datasets. The results highlight subset that accurately depending on specific size ranges determine...
The TCP domain is a plant-specific DNA binding found in proteins from diverse array of species, including the cycloidea (cyc) and teosinte branched1 (tb1) gene products PCF1 PCF2 proteins. To understand role transcriptional regulation with this domain, we have analysed dimerization specificity protein family using rice PCF proteins, further evaluated potential targets for protein. seven members five newly isolated were able to be grouped into two classes, I II, based on sequence similarity...
Advances in genome sequencing technologies have enabled researchers and breeders to rapidly associate phenotypic variation sequence differences. We recently took advantage of next-generation technology develop MutMap, a method that allows rapid identification causal nucleotide changes rice mutants by whole resequencing pooled DNA mutant F2 progeny derived from crosses made between candidate the parental line. Here we describe MutMap+, versatile extension identifies mutations comparing SNP...
In Batesian mimicry, animals avoid predation by resembling distasteful models. the swallowtail butterfly Papilio polytes, only mimetic-form females resemble unpalatable Pachliopta aristolochiae. A recent report showed that a single gene, doublesex (dsx), controls this mimicry; however, detailed molecular mechanisms remain unclear. Here we determined two whole-genome sequences of P. polytes and related species, xuthus, identifying ∼130-kb autosomal inversion, including dsx, between mimetic...
Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this genome through comparison with its wild relatives, F. iinumae, nipponica, nubicola, orientalis by de novo whole-genome sequencing on an Illumina Roche 454 platforms. total length of the assembled sequences obtained was 698 Mb for ananassa, ∼200 each four species. Subsequently, a virtual reference termed FANhybrid_r1.2 constructed integrating homoeologous...
Magnaporthe oryzae (anamorph Pyricularia oryzae) is the causal agent of blast disease Poaceae crops and their wild relatives. To understand genetic mechanisms that drive host specialization M. oryzae, we carried out whole genome resequencing four isolates from rice (Oryza sativa), one foxtail millet (Setaria italica), three S. viridis, isolate each finger (Eleusine coracana), wheat (Triticum aestivum) oat (Avena in addition to an a sister species grisea, infects grass Digitaria sanguinalis....
We have previously defined the promoter elements, sites IIa and IIb, in rice proliferating cell nuclear antigen (PCNA) gene that are essential for meristematic tissue-specific expression. In this study, we isolated characterized cDNAs encoding proteins specifically bind to IIb. The two DNA binding proteins, designated PCF1 PCF2, share > 70% homology common conserved sequences at N-terminal regions. regions responsible homodimer heterodimer formation, they contain a putative basic...
The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination different new-generation multiplex sequencing platforms. total length the non-redundant sequences 568,887,315 bp, consisting 45,088 scaffolds, which covered 91% 622 Mb genome estimated by k-mer analysis. N50 values contigs and scaffolds were 16,644 bp 60,737 respectively, longest scaffold 1,287,144 bp. average GC content contig 36%. A 1050, 13, 92 143 genes for tRNAs, rRNAs,...
Proteins bearing nuclear export signals (NESs) are translocated to the cytoplasm from nucleus mainly through CRM1‐dependent pathway. However, NES consensus sequence remains poorly defined, and there currently no high‐throughput methods for identifying NESs. In this study, we report development of an efficient yeast selection system detecting activity as well several reliable sequences identified using method. Our is based on export‐dependent rescue Tys1p, essential cytoplasmic protein that...
Abstract Motivation: Genome assemblies generated with next-generation sequencing (NGS) reads usually contain a number of gaps. Several tools have recently been developed to close the gaps in these NGS reads. Although gap-closing efficiently gaps, they entail high rate misassembly at sites. Results: We found that assembly error rates caused by are 20–500-fold higher than errors introduced into contigs de novo assemblers. here describe GMcloser, tool accurately closes preassembled contig set...
Zoysiais a warm-season turfgrass, which comprises 11 allotetraploid species (2n= 4x= 40), each possessing different morphological and physiological traits. To characterize the genetic systems of Zoysia plants to analyse their structural functional differences in individual accessions, we sequenced genomes using HiSeq MiSeq platforms. As reference sequence species, generated high-quality draft genome Z. japonica accession 'Nagirizaki' (334 Mb) 59,271 protein-coding genes were predicted. In...
Recent advances in long-read sequencing solve inaccuracies alternative transcript identification of full-length transcripts short-read RNA-Seq data, which encourages the development methods for isoform-centered functional analysis. Here, we present tappAS, first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, is effective at revealing impact context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation coding and non-coding...
We generated Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL), a high-depth whole-genome sequencing dataset comprising 3256 individuals from across Japan. Analysis JEWEL revealed genetic characteristics the population that were not discernible using microarray data. First, rare variant–based analysis an unprecedented fine-scale structure. Together with genetics analysis, present-day can be decomposed into three ancestral components. Second, we identified unreported...
Accurate identification of DNA polymorphisms using next-generation sequencing technology is challenging because a high rate error and incorrect mapping reads to reference genomes. Currently available short read aligners variant callers suffer from these problems. We developed the Coval software improve quality alignments. designed minimize incidence spurious alignment reads, by filtering mismatched that remained in alignments after local realignment correction reads. The executed based on...
Abstract Short- and long-read sequencing technologies are routinely used to detect DNA variants, including SNVs, indels, structural variations (SVs). However, the differences in quality quantity of variants detected between short- data not fully understood. In this study, we comprehensively evaluated variant calling performance long-read-based SNV, indel, SV detection algorithms (6 for 12 13 SVs) using a novel evaluation framework incorporating manual visual inspection. The results showed...
Summary Plants have recently been found to E2F‐like and Rb‐like proteins, regulators responsible for the G 1 (G 0 )‐S phase transition of cell cycle in animals. Here we show that E2F is involved transcription plant genes proliferating nuclear antigen (PCNA), which required DNA replication. Potential binding sites rice PCNA promoters mediated transcriptional activation actively dividing cells tissues tobacco, but not repression terminally differentiated tissues, as also observed PCF...
E2F transcription factors are major regulators of cell proliferation, and each factor contributes differently to cycle control. Arabidopsis contains six homologs, which three proteins that exhibit an overall similarity animal E2Fs interact with DPa DPb stimulate DNA binding. Here we describe the other E2F-like fromArabidopsis, E2L1–3, have two copies a domain limited only binding E2F. Unlike known E2Fs, E2L failed could efficiently bind sites in monomeric form through dual-type domain....