Biology subjects

Toyonaga, H.

Publications and source records attributed to Toyonaga, H..

4 recordsLinked to original sources

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↗

bioRxiv2025

Parasitism-mediated horizontal transfer of a functional cytochrome P450 gene entails transposon colonization in newly gained introns

Plants produce a wide variety of specialized metabolites that are typically present only in specific lineages. However, some specialized metabolites are found sporadically across distantly related plant species. While the latter cases have been explained as outcomes of convergent evolution, the molecular mechanism behind such metabolic evolution has remained largely elusive. Here, we report that parasitic dodders belonging to the genus Cuscuta accumulate sesamin, and that this accumulation may be attributed to the acquisition of enzymatically active homologs of Sesamum indicum CYP81Q1, which encodes piperitol/sesamin synthase (PSS). Phylogenetic analysis of CYP81Q homologs in Cuscuta and Grammica subgenera supports a trajectory in which ancestral Cuscuta species acquired CYP81Q from an ancestral host plant of Lamiales through horizontal gene transfer (HGT), and that the gene has been maintained during the speciation of Cuscuta. The evolution of the CYP81Q genes was accompanied by sequential intron gains, which likely involved the colonization of transposons. Experiments involving C. campestris and S. indicum suggested that expression of the host CYP81Q gene could be induced by parasitism, and physical connection to the host plant allowed the transfer of genetic elements to Cuscuta. These data suggest that parasitism-mediated HGT contributed to the transfer of a gene encoding a key enzyme in specialized lignan metabolism to Cuscuta, and that the acquired metabolic gene underwent structural modification while retaining its enzymatic function in dodders.

plant biology↗

bioRxiv2025

TCP3-mediated regulation of cell expansion in Arabidopsis thaliana

(1) Cell expansion is crucial for organ morphogenesis in multicellular organisms. Apoplast acidification triggers plant cell expansion. Plant hormones and transcription factors such as TEOSINTE BRANCHED, CYCLOIDEA, and PROLIFERATING CELL NUCLEAR ANTIGEN BINDING FACTORs (TCPs) control cell expansion. However, details regarding the regulatory mechanism of cell expansion for organ morphogenesis remain unclear. (2) In this study, we used molecular, biochemical, cellular, genetic, atomic force microscopy, and tensile testing analyses and showed that miR319-targeted TCPs integrated cell expansion with organ morphogenesis in Arabidopsis thaliana. (3) We found that TCPs directly induce the expression of genes encoding cell wall loosening proteins and SMALL AUXIN UP RNAs (SAURs), activators of plasma membrane-localized H+-ATPases. TCP-mediated activation of plasma membrane- localized H+-ATPases stimulates apoplast acidification, reduce cell stiffness, promote cell expansion, and thus exaggerate elongation of the hypocotyl. Ectopic expression of a SAUR gene in sextuple tcp mutant plants substantially recovered the hypocotyl morphology of the tcp mutant, providing genetic evidence of TCP-mediated SAUR regulation. (4) Collectively, our data show that TCPs regulate apoplast acidification for cell expansion.

plant biology↗

bioRxiv2025

Chromosome-scale Genome Assemblies of Two Allopolyploid Cuscuta Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid Evolution

Dodders (Cuscuta spp.) is an obligated parasitic plant, which lost a large part of photosynthetic genes but gained host genes through parasitism-mediated horizontal gene transfer (HGT). Their migratory ecology across the world would contribute to complexity of the speciation via geographic isolation. Here we report the de novo genome assemblies of the two phylogenetically distinct dodders; C. chinensis (2n=4x=60) and C. campestris (2n=4x=60) that are classified into Clade B and Clade H of subgenus Grammica, respectively. Relatively low completeness of BUSCO genes ca.87% indicated progressive gene loss after evolution of parasitic lifestyle due to release from functional constraints as photosynthesis and organ development. Comparative genomics uncovered that both species are the genome size is completely different regardless of the same cytotypes and allopolyploid through the independent ancient hybridization between different parents. Various genomic rearrangements including 1) gene gain and loss events, 2) homoeologous recombination between two subgenomes and 3) the lineage-specific proliferation of transposable elements likely contribute to their genomic diversity and sexual isolation of the two lineages partly sharing their habitats. Our findings not only provide genomic basis to survey parental species for allopolyploidization but also help to understand unique speciation of parasitic dodders through these chromosomal natures.

genomics↗