A5009003438- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Helicobacter pylori-related gastroenterology studies
- Biomedical Text Mining and Ontologies
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Probiotics and Fermented Foods
- Bacterial Genetics and Biotechnology
- Semantic Web and Ontologies
- CRISPR and Genetic Engineering
- Wastewater Treatment and Nitrogen Removal
- Bioinformatics and Genomic Networks
- Chromosomal and Genetic Variations
- Bacteriophages and microbial interactions
- Antimicrobial Resistance in Staphylococcus
- Molecular Biology Techniques and Applications
- Legume Nitrogen Fixing Symbiosis
- Natural Language Processing Techniques
- Photosynthetic Processes and Mechanisms
- Glycosylation and Glycoproteins Research
- Algal biology and biofuel production
- Protein Structure and Dynamics
- Plant Pathogenic Bacteria Studies
- Gene expression and cancer classification
National Institute for Basic Biology
2014-2025
National Institutes of Natural Sciences
2014-2025
Virginia Tech
2021
National Research Institute
2020
NTL Institute for Applied Behavioral Science
2019
Universidad de Murcia
2017
The Graduate University for Advanced Studies, SOKENDAI
2014-2016
National Institute of Genetics
2003
Okazaki National Research Institutes
2000-2003
Naval Research Laboratory Information Technology Division
2000-2003
The mosses and flowering plants diverged >400 million years ago. have haploid-dominant life cycles, whereas the are diploid-dominant. common ancestors of land been inferred to be haploid-dominant, suggesting that genes used in diploid body were recruited from haploid during evolution plants. To assess this evolutionary hypothesis, we constructed an EST library moss Physcomitrella patens , compared transcriptome genome Arabidopsis thaliana . We full-length enriched cDNA libraries...
We present herein the first complete genome sequence of a thermophilic Bacillus-related species, Geobacillus kaustophilus HTA426, which is composed 3.54 Mb chromosome and 47.9 kb plasmid, along with comparative analysis five other mesophilic bacillar genomes. Upon orthologous grouping six sequenced genomes, it was found that 1257 common groups 1308 genes (37%) are shared by all bacilli, whereas 839 (24%) in G.kaustophilus were to be unique species. able find prokaryotic sperm protamine P1...
Scrub typhus ('Tsutsugamushi' disease in Japanese) is a mite-borne infectious disease. The causative agent Orientia tsutsugamushi, an obligate intracellular bacterium belonging to the family Rickettsiaceae of subdivision alpha-Proteobacteria. In this study, we determined complete genome sequence O. tsutsugamushi strain Ikeda, which comprises single chromosome 2 008 987 bp and contains 1967 protein coding sequences (CDSs). much larger than those other members Rickettsiaceae, 46.7% was...
Abstract Ipomoea is the largest genus in family Convolvulaceae. nil (Japanese morning glory) has been utilized as a model plant to study genetic basis of floricultural traits, with over 1,500 mutant lines. In present study, we have second- and third-generation-sequencing platforms, reported draft genome I. scaffold N50 2.88 Mb (contig 1.87 Mb), covering 98% 750 genome. Scaffolds 91.42% assembly are anchored 15 pseudo-chromosomes. The enabled identification cataloguing Tpn1 transposons, known...
Abstract Background The genome of Helicobacter pylori , an oncogenic bacterium in the human stomach, rapidly evolves and shows wide geographical divergence. high incidence stomach cancer East Asia might be related to bacterial genotype. We used newly developed comparative methods follow evolution Asian H. genomes using 20 complete sequences from Japanese, Korean, Amerind, European, West African strains. Results A phylogenetic tree concatenated well-defined core genes supported divergence...
A nearly complete genome sequence of Candidatus 'Acetothermum autotrophicum', a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis subsurface thermophilic microbial mat community. Phylogenetic based on the concatenated sequences proteins common among 367 prokaryotes suggests that Ca. 'A. autotrophicum' is one earliest diverging bacterial lineages. It possesses folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway CO(2) fixation, predicted to have...
Abstract Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions photosynthesis. One of the major LHCs are fucoxanthin chlorophyll / c -binding proteins (FCPs) present diatoms, group organisms having important contribution to global carbon cycle. Here, we report 2.40-Å resolution structure diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The is composed 16 different FCPI subunits surrounding...
MBGD is a workbench system for comparative analysis of completely sequenced microbial genomes. The central function to create an orthologous gene classification table using precomputed all-against-all similarity relationships among genes in multiple In MBGD, automated algorithm has been implemented so that users can their own by specifying set organisms and parameters. This feature especially useful when the user's interest focused on some taxonomically related organisms. created stored into...
We isolated the methicillin-resistant Macrococcus caseolyticus strain JCSC5402 from animal meat in a supermarket and determined its whole-genome nucleotide sequence. This is first report on genome analysis of macrococcal species that evolutionarily closely related to human pathogens Staphylococcus aureus Bacillus anthracis. The essential biological pathways M. are similar those staphylococci. However, has small chromosome (2.1 MB) lacks many sugar amino acid metabolism plethora virulence...
Identifying population structure forms an important basis for genetic and evolutionary studies. Most current methods to identify have limitations in analyzing haplotypes recombination across the genome. Recently, a method of chromosome painting silico has been developed overcome these shortcomings applied multiple human genome sequences. This detects genome-wide transfer DNA sequence chunks through homologous recombination. Here, we apply it frequently recombining bacterial species...
Background The production of staphylocoagulase (SC) causing the plasma coagulation is one important characteristics Staphylococcus aureus. Although SCs have been classified into 10 serotypes based on differences in antigenicity, genetic bases for their diversities and relatedness to chromosome types are poorly understood. Methodology/Principal Findings We compared nucleotide sequences 105 SC genes (coa), 59 which were determined this study. D1 regions, contain prothrombin-activating -binding...
The microbial genome database (MBGD) for comparative analysis is a platform genomics based on automated ortholog group identification. A prominent feature of MBGD that it allows users to create groups using specified subgroup organisms. constantly updated and now contains almost 1000 genomes. To utilize the as comprehensive resource investigating diversity, we have developed following advanced functionalities: (i) enhanced assignment functional annotation, including external links each...
The birth and death of genes is central to adaptive evolution, yet the underlying genome dynamics remain elusive. availability closely related complete sequences helps follow changes in gene contents clarify their relationship overall organization. Helicobacter pylori , bacteria our stomach, are known for extreme plasticity through mutation recombination will make a good target such an analysis. In comparing sequences, we found that gain loss (loci) outer membrane proteins, which mediate...
The microbial genome database for comparative analysis (MBGD) (available at http://mbgd.genome.ad.jp/) is a comprehensive ortholog flexible of genomes, where the users are allowed to create an table among any specified set organisms. Because rapid increase in data owing next-generation sequencing technology, it becomes increasingly challenging maintain high-quality orthology relationships while allowing incorporate latest genomic available into analysis. many recently accumulating draft...
Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below seafloor (mbsf) or more. Previous PCR-based molecular analysis showed presence reductive dehalogenase gene (rdhA) homologs in marine sediment, suggesting that anaerobic respiration organohalides is one possible energy-yielding pathways organic-rich sedimentary habitat. However, primer-independent characterization rdhA has remained to be demonstrated. Here, we...
The application of semantic technologies to the integration biological data and interoperability bioinformatics analysis visualization tools has been common theme a series annual BioHackathons hosted in Japan for past five years. Here we provide review activities outcomes from held 2011 Kyoto 2012 Toyama. In order efficiently implement life sciences, participants formed various sub-groups worked on following topics: Resource Description Framework (RDF) models specific domains, text mining...
Urodele newts have unique biological properties, notably including prominent regeneration ability. The Iberian ribbed newt, Pleurodeles waltl, is a promising model amphibian distinguished by ease of breeding and efficient transgenic genome editing methods. However, limited genetic information available for P. waltl. We conducted an intensive transcriptome analysis waltl using RNA-sequencing to build annotate gene models. generated 1.2 billion Illumina reads from wide variety samples across...
Accurate determination of the evolutionary relationships between genes is a foundational challenge in biology. Homology-evolutionary relatedness-is many cases readily determined based on sequence similarity analysis. By contrast, whether or not two directly descended from common ancestor by speciation event (orthologs) duplication (paralogs) more challenging, yet provides critical information history gene. Since 2009, this task has been focus Quest for Orthologs (QFO) Consortium. The sixth...
The microbial genome database for comparative analysis (MBGD) is a comprehensive platform genomics. central function of MBGD to create orthologous groups among multiple genomes from precomputed all-against-all similarity relationships using the DomClust algorithm. now contains >300 published and number continues grow. For researchers who are interested in ongoing projects, we have started new service called 'My MBGD,' which allows users add their own sequences purpose identifying orthologs...
Ortholog identification is a crucial first step in comparative genomics. Here, we present rapid method of ortholog grouping which effective enough to allow the comparison many genomes simultaneously. The takes as input all-against-all similarity data and classifies genes based on traditional hierarchical clustering algorithm UPGMA. In course clustering, detects domain fusion or fission events, splits clusters into domains if required. subsequent procedure resulting trees such that...