Mika Sakamoto

Neuropeptides and their G protein-coupled receptors (GPCRs) control much of insect physiology and behaviour, but in Gryllus bimaculatus , an emerging model and edible insect, receptor sequence similarity hinders the mapping of which peptide each GPCR activates. We re-annotated a chromosome-scale genome (BUSCO 95.3%, from 86.7% on insecta_odb12) with comprehensive curation of 48 neuropeptide precursor families (51 loci, including seven not previously identified) and 134 candidate GPCRs (66 rhodopsin-class, 68 secretin-class), providing a near complete neuropeptide-receptor interactome catalogue. We modelled all 15,946 peptide-receptor pairs with AlphaFold3 and Boltz-2 and scored each interface with pLDDT and ipSAE. Ranking these scores, and cross-checking the top candidate for each family against a receptor phylogeny of known ligand specificity, gave a confident, phylogenetically related receptor for 27 of 35 curated receptor groups. These matches confirm the structural scorings with existing deorphanization data and propose receptors for peptides with no prior functional evidence. The annotation, curated peptide and receptor sets, and ranked complexes are available through CricketBase ( https://cricket.annotation.jp ), a genome browser with a structure viewer of peptide-receptor complexes, providing a resource for G. bimaculatus endocrinology and a workflow to deorphanize GPCRs in other non-model insects. Graphical Figure 2.

High-quality reference genomes provide an essential foundation for elucidating the molecular basis of organismal ecophysiology. Here, we sequenced and assembled chromosome-scale genomes of two Heterosigma akashiwo strains isolated from coastal waters of Japan and France. The assembly sizes were 1.18 Gb and 1.43 Gb for the Japanese and French strains, respectively. The scaffold N50 of the Japanese strain assembly was 66 Mb, whereas the one of the unscaffolded French strain assembly was 33 Mb. To our knowledge, these assemblies represent among the largest and most contiguous genome resources currently available for members of the Stramenopiles (Ochrophyta). Evidence-based gene prediction in the Japanese strain recovered approximately 90% of conserved stramenopile core genes, indicating a highly complete gene repertoire, and was complemented by extensive functional annotation. In the French strain, homology-based gene prediction recovered approximately 80% of conserved core genes. Comparative genome analysis revealed extensive synteny conservation between the two strains, although several putative duplication and translocation events were detected. These genomic resources provide a robust framework for investigating the molecular, cellular, and ecological mechanisms underlying the physiology, adaptation, and bloom-forming capacity of H. akashiwo .

Dynamic changes in chromatin accessibility at cis-regulatory elements underlie cell fate transitions during development. Primordial germ cells (PGCs) represent a rare population whose chromatin dynamics remain poorly understood compared to known epigenetic landscapes. Here, we utilized the chicken PGC model to bridge this gap, leveraging its capacity for in vitro expansion and in vivo colonization. We adapted the ATAC-seq workflow to obtain reproducible accessible chromatin region (ACR) profiles from as few as 200 cells, even after cryopreservation. Integrative analysis identified over 10,000 PGC-specific ACRs, many absent from somatic tissues, and revealed inherent Tn5 transposase sequence biases in the chicken genome. To validate these ACRs, we established an in vitro PGC differentiation system and utilized in vivo embryonic transplantation. Reporter assays confirmed enhancer activities in cultured PGCs, while transcriptome integration associated these ACRs with genes expressed at embryonic day 2.5. In vivo transplantation demonstrated that these enhancers exhibited early stage-specific activity, becoming silenced upon gonadal settlement. Our results provide a practical strategy for identifying functional regulatory elements from minimal starting material, facilitating the study of chromatin dynamics in rare cell populations.

The liverwort Marchantia polymorpha is a key model organism for understanding land plant evolution, development, and gene regulation. To support the growing demand for high-quality genomic resources, we present MarpolBase, a comprehensive and integrated genome database that hosts newly assembled, high-accuracy reference genomes for both the male Tak-1 and female Tak-2 accessions, designated as ver. 7.1 reference genomes. These new assemblies, generated using PacBio HiFi long-read sequencing, represent nearly telomere-to-telomere chromosome-level genomes, with improvements in assembly continuity, annotation accuracy, and structural resolution—especially for repeat-rich regions and sex chromosomes. MarpolBase offers not only access to genome sequences and gene annotations but also provides a unified platform for data exploration, comparative analysis, and community-driven gene nomenclature for M. polymorpha. It includes keyword-searchable gene pages with structural and functional annotations, expression data integration, genome browser visualization, and online analytical and utility tools. By unifying genome assembly, annotation, nomenclature, and analysis tools in a single platform, MarpolBase serves as a central resource for functional genomics and evolutionary studies in M. polymorpha, and a model for future plant genome databases. The genomic resources of MarpolBase are freely available at https://marchantia.info.

Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes, a useful model organism studied in diverse biological fields. Chromosome-scale genome sequences of the Hd-rR strain of this species were obtained in 2007, and its improved version has facilitated various genome-wide studies. However, despite its widespread utility, omics data for O. latipes are dispersed across various public databases and lack a unified platform. To address this, the medaka section of the National Bioresource Project (NBRP) of Japan established a genome informatics team in 2022 tasked with providing various in silico solutions for bench biologists. This initiative led to the launch of MedakaBase (https://medakabase.nbrp.jp), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides on-demand browsing of diverse genome-wide datasets, including tissue-specific transcriptomes and intraspecific genomic variations, integrated with gene models from different sources. Additionally, the platform offers gene models optimized for single-cell transcriptome analysis, which often requires coverage of the 3′ untranslated region (UTR) of transcripts. Currently, MedakaBase provides genome-wide data for seven Oryzias species, including original data for O. mekongensis and O. luzonensis produced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase.

Cell fate specification during development is orchestrated by dynamic changes in gene expression, driven by the accessibility of cis-regulatory elements. To profile such functional regulatory elements at the genome-wide level, bulk ATAC-seq is a powerful method. Yet, its application has still been technically limited in rare cell types. Here, we optimized and titrated the ATAC-seq protocol for cultured chicken primordial germ cells (PGCs) and obtained high-quality chromatin accessibility profiles from as few as 200 cells, even after cryopreservation. Integrative analysis of our ATAC-seq with published RNA-seq and tissue ATAC-seq datasets identified over 10,000 PGC-specific accessible chromatin regions (ACRs), many absent from somatic tissues. Reporter assays demonstrated activity of selected enhancers in cultured PGCs, while transcriptome integration revealed preferential association of PGC-specific ACRs with genes highly expressed at embryonic day 2.5. In vivo transplantation confirmed that these enhancers are active in an early-stage-specific manner, but become silenced upon gonadal settlement. In conclusion, this streamlined method provides a practical and cost-effective approach to the epigenomic analysis of scarce cell populations, facilitating future investigations in developmental biology, germline research, and beyond.

Medaka, a group of small, mostly freshwater fishes in the teleost order Beloniformes, includes the rice fish Oryzias latipes , which is a prominent model organism for diverse biological fields. Chromosome-scale genome sequences of the Hd-rR strain of this species were obtained in 2007, and its improved version has facilitated various genome-wide studies. However, despite its widespread utility, omics data for O. latipes are dispersed across various public databases and lack a centralized platform. To address this, the medaka section of the National Bioresource Project (NBRP) of Japan established a genome informatics team in 2022 tasked with providing versatile in silico solutions for bench biologists. This initiative led to the launch of MedakaBase ( https://medakabase.nbrp.jp ), a web server that enables gene-oriented analysis including exhaustive sequence similarity searches. MedakaBase also provides genome-wide browsing of diverse datasets, including tissue-specific transcriptomes and intraspecific genomic variations, integrated with gene models from different sources. Additionally, the platform offers gene models optimized for single-cell transcriptome analysis, which often requires coverage of the 3′ untranslated region (UTR) of transcripts. Currently, MedakaBase provides genome-wide data for seven Oryzias species, including original data for O. mekongensis and O. luzonensis produced by the NBRP team. This article outlines technical details behind the data provided by MedakaBase.

The liverwort Marchantia polymorpha is a key model organism for understanding land plant evolution, development, and gene regulation. To support the growing demand for high-quality genomic resources, we present MarpolBase, a comprehensive and integrated genome database that hosts newly assembled, high-accuracy reference genomes for both the male Tak-1 and female Tak-2 accessions, designated as ver. 7.1 reference genomes. These new assemblies, generated using PacBio HiFi long-read sequencing, represent nearly telomere-to-telomere chromosome-level genomes, with improvements in assembly continuity, annotation accuracy, and structural resolution, especially for repeat-rich regions and sex chromosomes. MarpolBase offers not only access to genome sequences and gene annotations but also provides a unified platform for data exploration, comparative analysis, and community-driven gene nomenclature. It includes keyword-searchable gene pages with structural and functional annotations, expression data integration, genome browser visualization, and online analytical and utility tools. By unifying genome assembly, annotation, nomenclature, and analysis tools in a single platform, MarpolBase serves as a central resource for functional genomics and evolutionary studies in M. polymorpha, and a model for future plant genome databases.

Objectives: Autosomal dominant polycystic kidney disease (ADPKD) is a common inherited disease in cats. In most cases, the responsible abnormality is a nonsense single nucleotide polymorphism in exon 29 of the PKD1 gene (chrE3:g.42858112C>A, the conventional PKD1 variant). The aim of this study was to conduct a large-scale epidemiological study of ADPKD caused by the conventional PKD1 variant in Japan and to search for novel polymorphisms by targeted resequencing of the PKD1 using a next-generation sequencer. Methods: A total of 1281 cats visiting the Veterinary Medical Center of the University of Tokyo were included in this study. DNA was extracted from the blood of each cat. We established a novel TaqMan real-time PCR genotyping assay for the conventional PKD1 variant, and all cases were examined for the presence of this variant. Targeted resequencing of all exons of the PKD1 was performed on the DNA of 23 cats with the conventional PKD1 variant, six cats diagnosed with cystic kidneys but without this variant, and 61 wild-type normal cats. Results: Among the 1281 cats examined in this study, 23 (1.8%) harboured the conventional PKD1 variant. The odds of having the conventional PKD1 variant were significantly higher in Persian cats, Scottish Folds and Exotic Shorthairs than in the other breeds, although the number of cases in each breed was small. Furthermore, we identified four variants unique to cats with cystic kidneys that were not found in wild-type normal cats, all of which were in exon 15. In particular, two (chrE:g.42848725delC, pGly1641fs and chrE:g.42850283C>T, pArg2162Trp) were candidate variants. Conclusions and relevance: This study revealed that the conventional PKD1 variant was prevalent in Scottish Fold, Persian and Exotic Shorthair breeds in Japan, and variants in exon 15 of PKD1, in addition to the conventional variant in exon 29, would be key factors in the pathogenesis of ADPKD in cats.

GlycoMaple is a new tool to predict glycan structures based on the expression levels of 950 genes encoding glycan biosynthesis-related enzymes and proteins using RNA-seq data. The antioxidant response, protecting cells from oxidative stress, has been focused on because its activation may relieve pathological conditions, such as neurodegenerative diseases. Genes involved in the antioxidant response are defined within the GO:0006979 category, including 441 human genes. Fifteen genes overlap between the glycan biosynthesis-related genes defined by GlycoMaple and the antioxidant response genes defined by GO:0006979, one of which is FUT8. 5-Hydroxy-4-phenyl-butenolide (5H4PB) extracted from Chinese aromatic vinegar induces the expression of a series of antioxidant response genes that protect cells from oxidative stress via activation of the nuclear factor erythroid 2-related factor 2–antioxidant response element pathway. Here, we show that FUT8 is upregulated in both our RNA-seq data set of 5H4PB-treated cells and publicly available RNA-seq data set of cells treated with another antioxidant, sulforaphane. Applying our RNA-seq data set to GlycoMaple led to a prediction of an increase in the core fucose of N-glycan that was confirmed by flow cytometry using a fucose-binding lectin. These results suggest that FUT8 and core fucose expression may increase upon the antioxidant response.