Atsushi Toyoda

A multi-tissue RNA-seq atlas of adult medaka (Oryzias latipes) under salinity and winter-summer sampling contrasts

The paper generates a multi-tissue RNA-seq atlas of adult medaka under salinity and seasonal contrasts to study gene-expression plasticity and comparative biology.

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

The paper develops a hiPSC-based framework to study ancestry-related phenotypic variation in the Japanese population, finding no hepatic triglyceride differences despite genetic associations.

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

This study shows MCM10 and RECQL4 work together and can replace each other in activating the CMG helicase during DNA replication initiation.

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

This study shows cohesin maintains condensed euchromatic domains in human cells by preventing local mixing, which is crucial for transcriptional insulation.

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

The paper presents high-quality chromosome-scale genome assemblies for two Heterosigma akashiwo strains from Japan and France, revealing extensive synteny and gene content.

Cold adaptation in Upper Paleolithic hunter-gatherers of eastern Eurasia

This study analyzes 42 genomes from Jomon hunter-gatherers to show they adapted to cold environments through positive selection during the Last Glacial Maximum.

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

This study identifies biogeographic patterns of freshwater giant viruses using MAGs from deep lakes, revealing cosmopolitan and restricted species, and factors influencing their distribution.

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

The paper presents the first HiFi long-read assembled genome of the dipluran species Occasjapyx japonicus, providing a high-quality reference for comparative and evolutionary studies.

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

The paper presents a chromosome-scale genome assembly of Cycas revoluta and identifies genes related to sex determination and thermogenesis, offering insights into cycad diversification.

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

This study identifies an A. muciniphila-LPS-miR-21 axis linking gut dysbiosis to neuroinflammation in MS by showing how gut microbiota modulate miRNA expression and CNS autoimmunity.

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

The paper uses CaMPARI-seq to identify neuronal subtypes in the zebrafish pretectum involved in distinguishing optic flow patterns for different behaviors.

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

This study reconstructs the genome and karyotype evolution of Sesamum and related species, revealing hybridization events and genetic changes linked to metabolic specialization.

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

The paper identifies a miR-3260 mutation in the loop structure of Bombyx mori and shows it does not affect dicing activity or phenotypic outcomes.

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

This study generates a new genome assembly for Japanese-reared naked mole rats, identifies novel gene models and genomic variations, and provides functional annotations.

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

The paper presents a chromosome-level genome assembly of Gerbera hybrida using HiFi and Hi-C technologies, providing annotated nuclear, mitochondrial, and chloroplast genomes.

Giant genome of the vampire squid reveals the derived state of modern octopod karyotypes

The paper presents a draft genome of the vampire squid, revealing ancestral chromosomal features and evolutionary changes in octopod karyotypes.

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

The paper presents chromosome-level genome assemblies for two wild cherry species, revealing structural variations and insights into their evolutionary relationships.

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

This study identifies the oldest vertebrate sex chromosomes in sharks and rays, revealing a unique dosage-dependent sex determination mechanism distinct from other vertebrates.

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

This study identifies multiple fertility restorer loci in wild tomato relatives that restore fertility in cytoplasmic male sterile lines.

Evolution and functioning of an X-A balance sex determination system in hops

The paper studies the evolution of an X-A balance sex determination system in hops by analyzing genome sequences of two hop species and identifies a candidate gene involved in the system.

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

This paper presents a chromosome-level genome assembly and transcriptome for Bradybaena similaris, a terrestrial snail in the superfamily Helicoidea, enhancing genomic resources for evolutionary studies.

Replication-dependent histone (Repli-Histo) labeling dissects the physical properties of euchromatin/heterochromatin in living human cells.

The paper develops Repli-Histo labeling to study nucleosome motion in euchromatin and heterochromatin, finding that euchromatic regions exhibit greater motion and influence replication timing.

Rapid and dynamic evolution of a giant Y chromosome in Silene latifolia

The paper describes the discovery of genes underlying male-female flower differences in Silene latifolia and relates findings to the evolution of the Y chromosome's non-recombining regions.

Sequencing and chromosome-scale assembly of the giant Pleurodeles waltl genome

The paper presents the chromosome-scale assembly of the giant Pleurodeles waltl genome, revealing insights into its expansion and regeneration-related genes.

A chromosome-level genome assembly of amodel conifer plant, the Japanese cedar,Cryptomeria japonica D. Don

The paper presents a chromosome-level genome assembly for the Japanese cedar, using long-read and Hi-C sequencing to achieve high contiguity and accuracy.

Centromeric repeat diversity underlies non-Mendelian segregation pattern in hop (Humulus lupulus)

The paper identifies centromeric repeat diversity in hop that contributes to non-Mendelian segregation patterns and genome instability during meiosis.

Tameness selection pressure affects gut virome diversity in mice

This study examines how selective breeding for tameness in mice affects gut virome diversity and identifies phage-host interactions linked to host behavior.

Comprehensive analysis of end-modified long dsDNA donors in CRISPR-mediated endogenous tagging

This study analyzes end-modified long dsDNA donors in CRISPR-mediated endogenous tagging, showing that 5 biotinylation reduces imprecise insertions and enhances HDR efficiency.

Decoding the Centromeric Region with a Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa

The paper presents a near complete genome assembly of the Oshima cherry, identifies centromeric regions, and compares them with related species to study genetic diversity and evolution.

Transposon fusion gave birth to Fem, Bombyx mori female determining gene

The paper identifies Fem, a W-linked piRNA precursor in Bombyx mori, as a chimeric sequence derived from transposons, challenging previous hypotheses about its origin.