Biology subjects

Toyoda, A.

Publications and source records attributed to Toyoda, A..

At least 19 recordsLinked to original sources

bioRxiv2026

An iPSC-based experimental framework for investigating phenotypic variation associated with Jomon ancestry in the present-day Japanese population

Ancestry-related genomic variation may contribute to phenotypic diversity. However, its cellular consequences remain difficult to evaluate. To address this, we developed a human induced pluripotent stem cell (hiPSC)-based framework for investigating such phenotypes. We used the Japanese population as a model of Jomon-related and continental East Asian ancestry admixture. Jomon ancestry, estimated using the Jomon allele score (JAS), was associated with clinical measures, including renal-related traits and serum triglycerides in 34,152 Tohoku Medical Megabank participants. Peripheral blood mononuclear cell transcriptomics of donors from the upper and lower extremes of the JAS distribution (n = 10) suggested group-level differences in immune-related gene expression. To test whether the serum triglyceride association coincided with hepatic cellular phenotypes, we differentiated hiPSCs from these donors into hepatocyte-like cells. Neither intracellular triglycerides nor lipid-related gene expression differed between groups. These findings highlight the value of a genetically characterized hiPSC-based framework for investigating ancestry-associated phenotypes across cellular contexts.

genomics↗

bioRxiv2026

Whole genome sequences and annotations of Japanese and French strains of Heterosigma akashiwo

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.

genomics↗

bioRxiv2026

Genome-resolved biogeography reveals multidimensional structuring of freshwater giant viruses across global deep lakes

Giant viruses (GV) are increasingly recognized as important ecosystem regulators. While metagenomics has uncovered extensive GV diversity, the global distributions of individual species and the biogeographic processes driving the pattern remain poorly understood. Here, we reconstructed GV metagenome-assembled genomes (MAGs) from 35 globally distributed deep freshwater lakes spanning five continents, aiming to identify their biogeographic patterns. The resulting 1663 non-redundant MAGs significantly expanded the known freshwater GV diversity, with [~]84% lacking a previously reported species representative. These MAGs were grouped into cosmopolitan and geographically restricted lineages. We identified 27 cosmopolitan GV species spanning multiple viral lineages, including families of Imitervirales, Pimascovirales, and mirusviruses order Styxvirales. The cosmopolitan species were characterized by their larger genomes and expanded gene repertoires of host-interaction functions, which may facilitate interactions with diverse hosts and contribute to their global distributions. The presence of geographically restricted species and the stronger distance-decay in community similarity observed in freshwater than marine ecosystems suggest that physical connectivity between ecosystems is an important factor influencing GV dispersal. We identified 312 and 177 GV MAGs almost exclusively associated with the epilimnion and hypolimnion, respectively. This water-layer preference of individual MAGs was highly consistent across lakes, suggesting conserved vertical partitioning in association with the thermal stratification of the water column. Overall, our findings reveal that GV biogeography in deep freshwater lakes is structured by the combined influence of horizontal dispersal limitation, vertical partitioning, and lineage-specific evolutionary histories.

microbiology↗

bioRxiv2026

Long-read sequencing based genomic data of a dipluran species, Occasjapyx japonicus

We present the genome dataset of a dipluran species, Occasjapyx japonicus, representing the first dipluran genome assembled using HiFi long-read sequencing technology. The assembled genome is approximately 439.3 Mbp in size, comparable to those of other dipluran species available in public databases. The N50 value of 15.5 Mbp exceeds that reported for other dipluran species. The assembled gene set contains 19,635 genes, a number not significantly different from those estimated in previous analyses of two other dipluran species. Functional gene annotation was conducted using predicted amino acid sequences derived from the gene set. BUSCO analysis indicated that the assembled genome contains the majority of conserved core genes. These findings suggest that the O. japonicus genome and associated data are of sufficient quality to serve as a reference genome. The dataset will be valuable for studies in comparative or evolutionary biology, particularly in understanding hexapod evolution and the emergence of insects.

genomics↗

bioRxiv2026

Chromosome-scale genome assembly of Cycas revoluta provides insights into cycad diversification and species diversity

Cycads are an ancient group of seed plants. Despite their ancient origin, many extant cycad genera exhibit high species diversity. The specialized reproductive traits in cycads, dioecy governed by the XY sex-determination system and the elaborate co-evolutionary synergy with insect pollinators, may facilitate lineage diversification. Here, we present a chromosome-scale genome sequence of Cycas revoluta, the species in which plant spermatozoids were discovered in 1896. The genome sequence spanned 11.6 Gb, 98.4% of which were anchored onto the 11 cycad chromosomes. Repetitive sequences occupied 9.8 Gb, and 31,481 genes were predicted. Based on this genome assembly, the X- and Y-associated genomic regions were characterized, and candidate genes for sex determination were identified. In addition, the genomic positions of genes for sex-related traits were determined. Subsequently, we analyzed transcriptomes for thermogenesis responsible for attracting insect pollinators. Through these comprehensive analyses, we provide new insights into the genomic basis of cycad diversification and species diversity.

genomics↗

bioRxiv2026

Akkermansia muciniphila-derived LPS links gut dysbiosis to pathogenic miR-21 signaling in experimental autoimmune encephalomyelitis.

Multiple sclerosis (MS) is a chronic T cell-mediated autoimmune disease characterized by blood-brain barrier (BBB) disruption, neuroinflammation, and demyelination of the central nervous system (CNS). Emerging evidence links gut microbiota to disease pathogenesis, but the microbial factors that regulate pathogenic microRNA (miRNA) programs are largely unknown. Here, using experimental autoimmune encephalomyelitis (EAE, a MS mouse model), we investigated whether gut microbiota exacerbate EAE pathogenesis by modulating host miRNA expression. Antibiotic-induced depletion of the gut microbiota markedly attenuated EAE scores and reduced circulating inflammatory miRNAs, with miR-21 emerging as the dominant pathogenic candidate. Functional inhibition of miR-21 significantly ameliorated disease severity and reduced CNS T-cell infiltration. Mechanistically, miR-21 enhanced IL-17 and GM-CSF production by CD4 T cells and promoted immune-cell entry into the CNS through endothelial activation and blood-brain barrier dysfunction. We identified a transient expansion of Akkermansia muciniphila during the prodromal phase of EAE that positively correlated with circulating miR-21 levels. Colonization of antibiotic-treated mice with A. muciniphila exacerbated EAE and increased serum miR-21, whereas monocolonization of germ-free mice was insufficient to induce systemic miR-21, indicating a requirement for an inflammatory host environment. Further analyses revealed that atypical lipopolysaccharides (LPS) derived from A. muciniphila induce epithelial miR-21 production through coordinated TLR2/TLR4 signaling. Circulating miR-21 subsequently promoted endothelial dysfunction through the TIMP3-ADAM17 pathway, facilitating pathogenic T-cell migration into the CNS. Importantly, circulating miR-21 was also elevated in patients with MS. Collectively, these findings identify a previously unrecognized A. muciniphila-LPS-miR-21 axis linking gut dysbiosis to neuroinflammation and suggest that host-derived miRNAs function as systemic mediators through which microbial signals influence CNS autoimmunity.

immunology↗

bioRxiv2026

MCM10 and RECQL4 have cooperative and redundant roles in activating the CMG helicase during the replication initiation

DNA replication initiation requires activation of the CMG helicase to establish the replisome. This process involves the extrusion of single-stranded DNA (ssDNA) from the central channel of MCM double hexamers, allowing the two CMG helicases to pass each other; however, the factors that mediate this process in human cells remain unclear. We show that degron-mediated depletion of either MCM10 or RECQL4 alone causes only mild replication defects, whereas simultaneous depletion of both proteins completely blocks CMG activation. ChIP-seq analyses demonstrate that RECQL4 localises to replication initiation zones (IZs) independently of MCM10, whereas MCM10 recruitment to IZs is enhanced upon RECQL4 depletion, suggesting RECQL4 primarily functions in CMG activation, and MCM10 acts as a backup or supporting factor. Rescue experiments further indicate that RECQL4 cooperates with MCM10 through direct interaction, and that their ssDNA-binding activity underlies their functional overlap. We propose MCM10 and RECQL4 act cooperatively and redundantly to promote CMG activation.

molecular biology↗

bioRxiv2026

An evolutionary landscape of sesame: chromosomal variation, allopolyploid speciation and metabolic specialization.

Sesame (Sesamum indicum) is one of the earliest domesticated oilseed crops and is valued for antioxidant lignans that stabilize oil quality. However, the genomic and evolutionary history of the genus Sesamum, including the origin of its allotetraploid relative S. radiatum and the diversification of lignan metabolism, remains poorly understood owing to limited chromosome-scale genomic resources. Here we present chromosome-level genome assemblies for three wild Sesamum species, two Ceratotheca species and a Japanese sesame cultivar to reconstruct genome and karyotype evolution across the Sesamum-Ceratotheca complex. Comparative analyses show that the derived x=16 lineage originated from an ancestral x=13 karyotype through chromosome fission, fusion and translocation, whereas another x=13 lineage underwent extensive restructuring associated with retrotransposon expansion. Phylogenomics places Ceratotheca within the x=16 Sesamum clade and reveals that S. radiatum originated through hybridization involving a C. sesamoides-like ancestor. The antioxidative lignan gene CYP92B14 was reintroduced via the BB progenitor, linking hybridization with restoration of oil-stabilizing metabolism during sesame evolution.

genomics↗

bioRxiv2026

Identification of a microRNA with a mutation in the loop structure in the silkworm Bombyx mori

MicroRNAs (miRNAs) play essential roles in the posttranscriptional regulation of gene expression in organisms. In the process of synthesizing mature miRNAs from miRNA precursors, the miRNA precursors are cleaved via Dicer at their loop structure, after which the miRNA precursors become mature and regulate transcription. However, the consequences of altering the loop sequence are not fully understood. The silkworm Bombyx mori is a lepidopteran insect with many genetic strains. We identified a mutant of the miRNA miR-3260 whose the part of the loop structure was lacking in a silkworm strain with translucent larval skin. Here, we aimed to analyze the role of wild-type miR-3260 and the influence of the mutation of the loop structure in B. mori. First, we identified the genomic region responsible for the translucent larval skin phenotype and determined that the mutated miR-3260 nucleotide sequences. Then, we predicted the binding partners of wild-type miR-3260 using the RNA hybrid tool and found two juvenile hormone (JH)-related genes as targets of wild-type miR-3260. Next, we assessed the relationships between miR-3260 and JH and found that miR-3260 was highly expressed in the Corpora allata and its expression responded to JH treatment. Meanwhile, miR-3260 mimic and inhibitor did not induce the typical phenotypes associated with JH in B. mori. Then, we compared the dicing products from wild-type and mutant miR-3260 precursors and observed that neither form underwent Dicer-mediated cleavage when the loop structure was altered. These results suggest that loop mutations in the miR-3260 precursor may not influence dicing activity, consistent with the lack of observable phenotypic effects.

molecular biology↗

bioRxiv2025

Chromosome-scale genomes of two wild flowering cherrys (Cerasus itosakura and C. jamasakura) provide insights into structural evolution in Prunus

Flowering cherries (genus Cerasus) are iconic trees in Japan, celebrated for their cultural and ecological significance. Despite their prominence, high-quality genomic resources for wild Cerasus species have been limited. Here, we report chromosome-level genome assemblies of two representative Japanese cherries: Cerasus itosakura, a progenitor of the widely cultivated C. xyedoensis Somei-yoshino, and Cerasus jamasakura, a traditional popular wild species endemic to Japan. Using deep PacBio long-read and Illumina short-read sequencing, combined with reference-guided scaffolding based on near-complete C. speciosa genome, we generated assemblies of 259.1 Mbp (C. itosakura) and 312.6 Mbp (C. jamasakura), with both >98% BUSCO completeness. Consistent with their natural histories, C. itosakura showed low heterozygosity, while C. jamasakura displayed high genomic diversity. Comparative genomic analyses revealed structural variations, including large chromosomal inversions. Notably, the availability of both the previously published C. speciosa genome and our new C. itosakura genome enabled the reconstruction of proxy haplotypes for both parental lineages of Somei-yoshino. Comparison with the phased genome of Somei-yoshino revealed genomic discrepancies, suggesting that the cultivar may have arisen from genetically distinct or admixed individuals, and may also reflect intraspecific diversity. Our results offer genomic foundations for evolutionary and breeding studies in Cerasus and Prunus.

genomics↗

bioRxiv2025

Cohesin prevents local mixing of condensed euchromatic domains in living human cells

The human genome is folded into chromatin loops by the cohesin complex, forming functional chromatin domains that underlie transcription and DNA replication/repair. However, how cohesin organizes these domains in living cells, especially in active euchromatin, remains elusive. To address this question, we combined single-nucleosome imaging/tracking and super-resolution 3D-structured illumination microscopy (3D-SIM) with euchromatin-specific labeling of histone H3.3. Using this nanoscopic approach, we revealed that euchromatin forms condensed domains that are constrained by cohesin-mediated loops. This organization refines the classical textbook view of euchromatin as largely open, in line with emerging evidence. Transcription machinery appears to be located near the condensed domain surfaces/borders. Cohesin loss increased nucleosome fluidity within these domains without altering their overall compaction, leading to local mixing of domains and compromising transcriptional insulation. These findings uncover an unexpected physical role of cohesin in maintaining the integrity of condensed euchromatic domains and ensuring proper higher-order regulation of gene expression.

cell biology↗

bioRxiv2025

Chromosome-level genome assembly of the gerbera (Gerbera hybrida) using HiFi long-read and Hi-C technologies

Gerbera hybrida is one of the most popular ornamental plants and also serves as a valuable model plant within the Asteraceae family. Here, we report both the nuclear and organellar genome assemblies and annotations of G. hybrida, which was developed through hybridization of two wild species. Sequencing was performed using a combination of PacBio high fidelity (HiFi) reads and chromatin capture reads (Omni-C). The total span of the nuclear genome assembly is 2.32 gigabases, and 99.3% of the sequence assembled into 25 scaffolds, consistent with the known chromosome number. Genome annotation of the nuclear genome identified 36,160 protein-coding genes and 11,572 non-coding transcripts. The mitochondrial genome had 363,511 bp and contains 36 protein-coding genes, 3 rRNAs, and 21 tRNAs, while the chloroplast genome is 151,898 bp in length and includes 85 protein-coding genes, 8 rRNAs, and 37 tRNAs. This reference genome provides a foundational resource for future molecular breeding and genetic research in Gerbera and the broader Asteraceae family.

plant biology↗

bioRxiv2025

Molecular and functional dissection using CaMPARI-seq reveals the neuronal organization for dissociating optic flow-dependent behaviors

Optic flow processing is critical for the visual control of body and eye movements in many animals. Rotational and translational binocular optic flow patterns need to be clearly distinguished to induce different behavior outputs. However, the specific neuron types and their connectivity involved in this computation remain unclear. Here, we developed a method to link the functional labeling using a photoconvertible calcium indicator called CaMPARI2 and single-cell RNA-sequencing (CaMPARI-seq) to investigate the transcriptional profile of the pretectum, a center for processing optic flow in larval zebrafish. Using this technique, we identified a pretectal cluster expressing tcf7l2, which can be further classified into molecularly distinct subclusters. In vivo calcium imaging and cell ablation revealed that nkx1.2lb-positive pretectal neurons are commissural inhibitory neurons required for the optomotor response but not for the optokinetic response. Our genetic and functional dissection using CaMPARI-seq uncovered the neuronal organization essential for dissociating different optic flow-dependent behaviors.

neuroscience↗

bioRxiv2025

Genome assembly and annotation of the naked mole rat Heterocephalus glaber reared in Japan

The naked mole rat (NMR, Heterocephalus glaber) is a eusocial rodent that is native to northeastern Africa. NMRs exhibit extraordinary traits such as longevity, resistance to age-related decline, and remarkable hypoxia tolerance. Although the reference genome of this species has been determined because of its unique characteristics, the significance or role of intraspecific genomic variations remains unknown. In this study, we used PacBio long-read sequencing to generate a genome assembly of NMR reared in Japan. The assembled genome is 2.56 Gb. Benchmarking Universal Single-Copy Orthologs (BUSCO) revealed high completeness (95.2%). BRAKER3 estimated 26,714 protein-coding genes, and we successfully added functional annotations for 26,232 protein-coding genes using the functional annotation workflow. We identified 417 gene models that were previously undetectable in the reference genome of this species. We also identified structural and amino acid sequence variations between our assembly and the reference genome, suggesting the presence of intraspecific genomic variations. This new genomic resource could help uncover the molecular mechanisms underlying the behavioral and physiological traits of NMR.

genomics↗

bioRxiv2025

Chromosomal fusions and subsequent rearrangements shaped octopus genomes

Why some animal groups retain ancestral chromosomal complements while others change significantly is a fundamental question in evolutionary genomics. Few systems exist where accumulations of chromosomal changes can be studied in the context of morphological innovation. In coleoid cephalopods (octopus, squid, cuttlefish), an ancient coleoid chromosomal rearrangement event (ACCRE) has led to a substantial increase in the chromosome number and a new set of chromosomal homologies. Compared to typical molluscan or bilaterian genomes, ACCRE has enabled the origin of many novel regulatory regions in coleoid cephalopods. However, the discrepancies between extant octopodiform (octopus, [~]30 chromosomes) and decapodiform (squid and cuttlefish, [~]46 chromosomes) karyotypes and the direction of these evolutionary changes remain unexplained. Here we provide a draft genome assembly of the vampire squid Vampyroteuthis sp., the largest cephalopod genome sequenced to-date (over 10 gigabasepairs). Through syntenic comparisons, we infer that this basally branching octopodiform species shows partial retention of the chromosomal complement of Decapodiformes, indicating its more ancestral state and the derived nature of the octopod karyotype. Together with the analysis of a new chromosome-level assembly of the pelagic octopod Argonauta hians, we identified irreversible chromosomal fusion-with-mixing events followed by inter-chromosomal translocations in octopods. We show that this secondary reduction and mixing within octopod chromosomes has enabled the origin of a more entangled genomic configuration, shedding light onto the early evolutionary transitions within the clade. Our results offer broader insights into general patterns of chromosomal evolution following large-scale rearrangement events in animal genomes. Significance statementHow changes to the ancient animal synteny result in novel chromosomal homologies is difficult to dissect due to the lack of intermediate states. Here we report that the genome of Vampyroteuthis, one of the largest animal genomes sequenced to-date (over 11 gigabasepairs), despite its phylogenetic position within the octopodiform cephalopods, partially retains squid and cuttlefish chromosomal complement, reflecting an ancestral karyotypic state that existed at the time of divergence between these cephalopod lineages. Our findings reveal karyotype reductions through chromosomal fusions were followed by inter-chromosomal translocations in octopods, leading to a more specialized genomic and gene regulatory architecture. These data show how chromosomal fusions can act as drivers of further inter-chromosomal rearrangements in animal genomes.

genomics↗

bioRxiv2025

Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms

Sex determination has been investigated across vertebrate lineages to reveal stepwise evolution of sex chromosomes and diversity of responsible molecular mechanisms. However, these studies hardly encompass cartilaginous fishes deeply isolated from the rest of vertebrates, which hinders the comprehensive view of vertebrate sex determination. Here, we produced chromosome-scale genome assemblies of egg-laying shark species and comparatively investigated genome sequences and transcriptome profiles across diverse cartilaginous fishes. Sex chromosome identification, supported by cytogenetic experiments, elucidated the homology of X chromosomes between sharks and rays as well as an extensively degenerating Y chromosome harboring no male-specific genes. These sex chromosomes scarcely included orthologs of previously documented sex determining genes. Transcriptomic analyses combined with histology of embryonic gonads revealed female-biased expressions of X-linked genes including those implicated in TGF-{beta} and IGF signaling pathways, which are attributed to their incomplete dosage compensation. Our findings indicate that sharks and rays share the oldest vertebrate sex chromosomes that originated around 300 million years ago and the dosage-dependent sex determination mechanism comprised of distinct molecules from other vertebrates. This study highlights the antiquity of sex chromosomes and uniqueness of sex determination mechanisms in sharks and rays, which advance our understanding on evolutionary plasticity of vertebrate sex determination.

evolutionary biology↗

bioRxiv2025

Multiple fertility restorer loci for cytoplasmic male sterility caused by orf137 in tomato

Cytoplasmic male sterility (CMS) in plants is caused by incompatibility between nuclear and cytoplasmic genetic information. Fertility can be restored through the action of fertility restoration (RF) genes, which are usually present in the nucleus. CMS lines of tomato (Solanum lycopersicum) have been developed from asymmetric cell fusions, in these lines, cultivated tomato served as a nuclear donor and its wild relative, S. acaule, as a cytoplasm donor. Although RF genes are present in wild relatives of tomato, no genetic or genomic information on the RF genes is yet available. This study reports an RF genetic locus, RF1, on chromosome 1 of S. pimpinellifolium LA1670 and S. lycopersicum var. cerasiforme LA1673 that was revealed by bulked segregant analysis and sequencing. An additional RF locus, RF2, was identified on chromosome 2 of LA1670. A transgenic approach identified two other candidate genes that also restored fertility. The genomic sequence of S. cheesmaniae LA0166 was assembled using high-fidelity, long-read sequencing technology. Sequence comparisons identified further candidate RF genes on chromosome 1 of S. cheesmaniae LA0166. These results suggested that multiple gene loci control the fertility restoration trait in wild relatives of tomato.

plant biology↗

bioRxiv2024

Chromosome-level genome assembly of the Asian tramp snail Bradybaena similaris (Stylommatophora: Camaenidae)

While terrestrial land snails have long been subjected to evolutionary research, a lack of high-quality genomic resources has impeded recent progress. Bradybaena snails in particular have numerous intriguing traits that make them a good model for studying evolution, including shell pattern polymorphism and convergent evolution. They are also introduced and invasive across the world. In this study, we present a chromosome-level genome assembly of the Asian tramp snail Bradybaena similaris utilizing 88-fold Illumina short-read sequences, 125-fold Nanopore long-read sequences, 63-fold PacBio HiFi sequences, and 47-fold Hi-C sequences. The assembled genome of 2.18 Gb is anchored to 28 chromosomes, and exhibits high completeness (98.8% metazoan BUSCO completeness) and contiguity (N50 of 75.6 Mb). Additionally, we also obtained a high-quality transcriptome for annotation. This resource represents the first chromosome-level assembly for snails in the superfamily Helicoidea, which includes more than 5,000 species of terrestrial snails, and will facilitate genomic study in Bradybaena and, more broadly, in the superfamily Helicoidea. SIGNIFICANCE STATEMENTWhile the Helicoidea is the largest land snail superfamily, consisting of more than 5,000 species, many of interest to evolutionary studies, no chromosome-level assembly has been available for any species. Previously, the genus Bradybaena in the Helicoidea has been studied in the context of speciation, adaptation and invasive biology, and thereby has high potential for further research. In this study, we present a chromosome-level assembly and transcriptome of the Asian tramp snail Bradybaena similaris. These high-quality genomic resources will facilitate research on related species, and eventually enhance our understanding of many areas of evolutionary biology.

genomics↗