Masahiko Kumagai

Prehistoric population movements played a central role in shaping the genetic diversity across Eurasia. As the eastern terminus of the Eurasian continent, the Japanese archipelago provides a pivotal context for reconstructing the genetic interplay between prehistoric indigenous lineages and continental migrations. However, high-resolution genomic evidence from mainland Japan is limited due to poor DNA preservation. In the present study, we report two low-contamination, high-coverage ancient genomes from mainland Japan, namely an Initial Jomon individual (>67-fold) and a Middle Yayoi individual (>46-fold). The genomes enabled diploid genotyping and individual-level demographic inferences at unparalleled resolutions. Demographic reconstructions revealed that while both lineages underwent population contractions during the Last Glacial Maximum (LGM), their subsequent trajectories diverged; the Jomon lineage was characterized by long-term postglacial stability with no discernible expansion, whereas the Yayoi-related ancestral population exhibited gradual and sustained growth. Our analysis further identified a distinct genetic continuity between the Middle Yayoi and present-day mainland Japanese, refining the evolutionary trajectory of modern genetic profiles. Furthermore, the genomic profile of the Yayoi individual reflected a complex ancestral background shaped by continental interactions before their arrival on the archipelago. Notably, the higher salivary amylase ( AMY1 ) copy number observed in the Initial Jomon individual suggests that AMY1 copy number variation, potentially relevant to starch-rich diets, was already present before the large-scale expansion of rice farming in the Japanese Archipelago. Collectively, the findings demonstrate that high-coverage ancient genomic approaches can provide a powerful framework for deciphering the contrasting population histories and evolutionary trajectories of human lifestyles.

High-throughput sequencing technologies have enabled the generation of high-quality reference genomes for numerous rice cultivars. However, inferring gene functions, associated phenotypes, and causal variants from these sequences remains challenging. The Rice Annotation Project Database (RAP-DB; https://rapdb.dna.affrc.go.jp ) is a curated genomic resource that provides comprehensive gene annotations for the reference genome of Oryza sativa ssp. japonica cv. ‘Nipponbare.’ Since its major update in 2013, gene models and functional annotations have been continuously revised through expert manual curation of newly published literature related to rice genes. As of March 2025, a total of 6,631 transcripts corresponding to 6,371 loci have been curated based on 4,699 peer-reviewed publications. These curated genes are functionally characterized and are frequently associated with agronomic traits, including yield components, stress tolerance, and disease resistance. To support molecular breeding, RAP-DB now provides a curated catalogue of 904 agronomically important loci, including gene symbols, functional descriptions, and associated traits, together with more than 1,000 functionally characterized alleles compiled from the literature. In addition to in-house expert curation, RAP-DB integrates community-curated datasets for major gene families, such as WRKY transcription factors, S-domain receptor-like kinases, and leucine-rich repeat-containing receptors, thereby expanding coverage of key regulatory and defense-related genes. RAP-DB also incorporates reanalyzed RNA sequencing expression profiles alongside microarray-based expression data and co-expression networks, offering gene-centric views of expression patterns across tissues, conditions, and developmental stages. Furthermore, RAP-DB is linked to genome-wide variation datasets from diverse rice varieties through the TASUKE+ genome browser, enabling exploration of allelic diversity across varieties. To enhance annotation quality and long-term sustainability, AI-assisted literature screening and a web-based feedback system have been introduced, allowing users to submit corrections to gene models and report newly characterized genes or relevant publications. Together, these developments strengthen RAP-DB as a primary, literature-based gene annotation resource and provide a practical foundation for molecular breeding in rice.

The purpose of this study is to understand the actual situation of the organization, the required roles and issues in the villages that may be isolated in Tottori prefecture. From survey results of Tottori Prefecture, reduction of aging and activities personnel of actors is remarkable. As an issue, since there are many elderly households in the area, many areas are worried about the initial response and evacuation support system. In the future, if conditions such as being geographically close to each other, several villages will be considered as a comprehensive range and the connections between villages will be strengthened.

The genus Prevotella plays an important role in polysaccharide degradation and fermentation in the rumen. To further understand the function of the phylogenetically diverse genus Prevotella , it is necessary to explore the individual characteristics at the species level. In this study, Gram-negative anaerobic bacterial strains isolated from the rumen of Holstein cows were identified. Strain R5019^T was classified within the genus Prevotella based on 16S rRNA gene sequence-based phylogenetic analysis. The values of 16S rRNA gene sequence similarity, average nucleotide identity and digital DNA–DNA hybridization between strain R5019^T and its phylogenetically nearest species Prevotella multisaccharivorax PPPA20^T were 89.8, 82.6, and 29.3 %, respectively. The genome size of R5019^T was estimated to be ca. 4.19 Mb with a genomic G+C content of 49.5 mol%. The major cellular fatty acids and menaquinones were C_15 : 0 anteiso and C_17 : 0 anteiso and MK-11 and MK-12, respectively. Succinate, lactate, malate, acetate and formate were produced as the fermentation end products using glucose. Based on phylogenetic, physiological, biochemical and genomic differences between 11 strains and other phylogenetically related Prevotella species, a novel species, Prevotella lacticifex sp. nov., is proposed within the genus Prevotella . The type strain is R5019^T (=JCM 34664^T=DSM 112675^T).

Recent revolutionary advancements in sequencing technologies have made it possible to obtain mass quantities of genome-scale sequence data in a cost-effective manner and have drastically altered molecular biological studies. To utilize these sequence data, genome-wide association studies (GWASs) have become increasingly important. Hence, there is an urgent need to develop a visualization tool that enables efficient data retrieval, integration of GWAS results with diverse information and rapid public release of such large-scale genotypic and phenotypic data. We developed a web-based genome browser TASUKE+ (https://tasuke.dna.affrc.go.jp/), which is equipped with the following functions: (i) interactive GWAS results visualization with genome resequencing data and annotation information, (ii) PCR primer design, (iii) phylogenetic tree reconstruction and (iv) data sharing via the web. GWAS results can be displayed in parallel with polymorphism data, read depths and annotation information in an interactive and scalable manner. Users can design PCR primers for polymorphic sites of interest. In addition, a molecular phylogenetic tree of any region can be reconstructed so that the overall relationship among the examined genomes can be understood intuitively at a glance. All functions are implemented through user-friendly web-based interfaces so that researchers can easily share data with collaborators in remote places without extensive bioinformatics knowledge.

Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20–345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320–350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.

In this study, the usefulness of three-dimensional angiographic imagings from helical scanning computed tomography (CT) enhanced by contrast media were evaluated based on results from three patients with a cervical mass, e.g. thyroid cancer and carotid body tumor. Three-dimensional CT (3D-CT) angiographic imagings in these cases clearly demonstrated secondary dislocation or distortion of the major cervical vessels caused by the tumor or metastatic lymph nodes. It was remarkable that in the highly vascularized tumor in case 3, all features of the tumor were delineated by 3D-CT angiography. Our results indicate that 3D-CT angiographic imagings are especially useful for preoperative evaluation of the relationship of the cervical mass to major cervical vessels as well as in the observation of tumors rich in vasculature.