Biology subjects

Ono, E.

Publications and source records attributed to Ono, E..

10 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

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↗

bioRxiv2025

A trehalase-derived MAMP triggers LecRK-V-mediated immune responses in Arabidopsis

Plant-parasitic nematodes (PPNs) cause major agricultural losses worldwide, yet the molecular basis of plant immunity against these pathogens remains poorly understood. To investigate how plants recognize PPNs, we aimed to identify microbe-associated molecular patterns (MAMPs) from nematodes and the corresponding plant immune components. Due to the limited availability of material from obligate PPNs, we used Caenorhabditis elegans, a free-living nematode, as a MAMP source. C. elegans extracts activated MAMP-triggered immune responses in Arabidopsis Col-0. Through chromatography-based purification, we identified a secreted trehalase and pinpointed a conserved peptide region essential for its MAMP activity. A corresponding peptide from root-knot nematode trehalase enabled the identification of lectin receptor kinases LecRK-V.5 and LecRK-V.6 as key components in immune induction. Notably, this peptide region is conserved across insect and fungal pathogens, with LecRK-Vs required for immune responses to these peptides, highlighting the role of LecRK-V-mediated mechanism for broad-spectrum pathogen detection via trehalase-derived peptides. TeaserTrehalase-derived peptides trigger LecRK-V-mediated immune responses in plants, enabling broad detection of nematodes, insects, and fungi.

plant biology↗

bioRxiv2024

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

Chromosomal sex determining systems with male heterogamety include actively male-determining-Y and X-A balance systems, both of which are found in animals and plants. The sex-determining genes have been identified in several active-Y plant systems, but the evolution and functioning of X-A balance systems remains mysterious. To study this, we sequenced and compared the genomes of two hop species. The evolution of the hop X-A balance system involved an ancient recombination suppression event across a large X chromosome region shared by both species. In one species, an autosome fused to this ancestral sex chromosome, and recombination was subsequently suppressed again. The two evolutionary strata created in this neo-X have degenerated to different degrees, and evolved correspondingly different dosage compensation levels that correlate with histone modification patterns. Finally, we identified an X-specific ETR1-like ethylene receptor in the ancestral X region. Its dosage may affect sex determination, as part of the counting mechanism of this X-A balance system. One sentence summaryBased on whole genome sequences of the cultivated hop, Humulus lupulus, and its wild relative H. japonicus, we describe the evolution of sex chromosomal regions, three of which that evolved region-specific dosage compensation, and identify a candidate gene involved in their X-A balance sex determining system.

evolutionary biology↗

bioRxiv2024

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

Aberrant meiosis in plants often leads to aneuploidy, genetic instability, and sterility. This can occur due to several factors, including chromosome misalignment, defective synapsis or environmental factors that may result in unusual genetic combinations in the offsprings. Unusual chromosome behavior during male meiosis in Humulus lupulus is linked to irregular chromosome segregation and genome instability. However, the origin of meiotic instability remains unclear. We analyzed the centromeric landscape of H. lupulus to determine its role in aberrant chromosomal segregation during cell division. Using a combination of bioinformatic, molecular and cytogenetic approaches, we identified new centromeric repeats and revealed two types of centromeric organizations. Cytogenetic localization on metaphase chromosomes confirmed the genomic distribution of major repeat arrays and revealed unique features that contribute to aberrant segregation. Two centromeric types are composed of the major repeats SaazCEN and SaazCRM1 which are further accompanied by chromosome-specific centromeric satellites, Saaz40, Saaz293, Saaz85, and HuluTR120. Chromosome 2 displays unbalanced segregation during the cell division, implicating an important role for its centromere structure in segregation patterns. Moreover, Saaz293 is a new marker for studying aneuploidy in hop. Our findings provide new insights on chromosome segregation in hop and highlight the diversity and complexity of the centromere organization in H. lupulus.

plant biology↗

bioRxiv2023

Discovery of the apiosyltransferase, celery UGT94AX1 that catalyzes the biosynthesis of a flavone glycoside, apiin

Apiose is a unique branched-chain pentose found in plant glycosides and a key component of the cell wall-polysaccharide pectin and other specialized metabolites. More than 1,200 plant-specialized metabolites contain apiose residues, represented by apiin, a distinctive flavone glycoside found in celery and parsley in the family Apiaceae. The physiological functions of apiin remain obscure, partly due to our lack of knowledge on apiosyltransferase during apiin biosynthesis. Here, we identified celery UGT94AX1 (AgApiT) as a novel apiosyltransferase, responsible for catalyzing the last sugar-modification step in apiin biosynthesis. AgApiT showed strict substrate specificity for the sugar donor, UDP-apiose, and moderate specificity for acceptor substrates, thereby producing various apiose-containing flavone glycosides in celery. Homology modeling of AgApiT with UDP-apiose, followed by site-directed mutagenesis experiments, identified unique Ile139, Phe140, and Leu356 residues in AgApiT, which are seemingly crucial for the recognition of UDP-apiose in the sugar donor pocket. Sequence comparison and molecular phylogenetic analysis of celery glycosyltransferases paralogous to AgApiT suggested that AgApiT is the sole apiosyltransferase-encoding gene in the celery genome. This is the first report on the identification of a plant apiosyltransferase gene that will enhance our understanding of the physio-ecological functions of apiose and apiose-containing compounds.

biochemistry↗

bioRxiv2020

Lumi-Map, a real-time luciferase bioluminescence screen of mutants combined with MutMap, reveals Arabidopsis genes involved in PAMP-triggered immunity

Plants recognize pathogen-associated molecular patterns (PAMPs) to activate PAMP-triggered immunity (PTI). However, our knowledge of PTI signaling remains limited. In this report, we introduce Lumi-Map, a high-throughput platform for identifying causative single nucleotide polymorphisms (SNPs) to studying PTI signaling components. In Lumi-Map, a transgenic reporter plant line is produced that contains a firefly luciferase (LUC) gene driven by a defense gene promoter, which generates luminescence upon PAMP treatment. The line is mutagenized and the mutants with altered luminescence patterns are screened by a high-throughput real-time bioluminescence monitoring system. Selected mutants are subjected to MutMap analysis, a whole genome sequencing (WGS)-based method of rapid mutation identification, to identify the causative SNP responsible for the luminescence pattern change. We generated nine transgenic Arabidopsis reporter lines expressing LUC gene fused to multiple promoter sequences of defense-related genes. These lines generate luminescence upon activation of FLAGELLIN-SENSING 2 (FLS2) by flg22, a PAMP derived from bacterial flagellin. We selected the WRKY29-promoter reporter line to identify mutants in the signaling pathway downstream of FLS2. After screening 24,000 ethylmethanesulfonate (EMS)-induced mutants of the reporter line, we isolated 22 mutants with altered WRKY29 expression upon flg22 treatment (abbreviated as awf mutants). While five flg22-insensitive awf mutants harbored mutations in FLS2 itself, Lumi-Map revealed three genes not previously associated with PTI. Lumi-Map has the potential to identify novel PAMPs and their receptors as well as signaling components downstream of the receptors.

plant biology↗

bioRxiv2020

RLP23 is required for Arabidopsis immunity against the grey mould pathogen Botrytis cinerea

Necrosis- and ethylene-inducing-like proteins (NLPs) are secreted by fungi, oomycetes and bacteria. Conserved nlp peptides derived from NLPs are recognized as pathogen-associated molecular patterns (PAMPs), leading to PAMP-triggered immune responses. RLP23 is the receptor of the nlp peptides in Arabidopsis thaliana; however, its actual contribution to plant immunity is unclear. Here, we report that RLP23 is required for Arabidopsis immunity against the necrotrophic fungal pathogen Botrytis cinerea. Arabidopsis rlp23 mutants exhibited enhanced susceptibility to B. cinerea compared with the wild-type plants. Notably, microscopic observation of the B. cinerea infection behaviour indicated the involvement of RLP23 in pre-invasive resistance to the pathogen. B. cinerea carried two NLP genes, BcNEP1 and BcNEP2; BcNEP1 was expressed preferentially before/during invasion into Arabidopsis, whereas BcNEP2 was expressed at the late phase of infection. Importantly, the nlp peptides derived from both BcNEP1 and BcNEP2 induced the production of reactive oxygen species in an RLP23-dependent manner. In contrast, other necrotrophic fungus Alternaria brassicicola did not express the NLP gene in the early infection phase and exhibited no enhanced virulence in the rlp23 mutants. Collectively, these results strongly suggest that RLP23 contributes to Arabidopsis pre-invasive resistance to B. cinerea via NLP recognition at the early infection phase.

plant biology↗

bioRxiv2019

Establishment of a novel method for the production of chimeric mouse embryos using oil droplets.

The production of chimeric animals is frequently necessary for the constructing genetically modified animals, and has gained popularity in regenerative medicine in the recent years for the reconstruction of xenogeneic organs. The aggregation method and the injection method are generally used for producing chimeric mice. In the aggregation method, the chimeras are produced by co-culturing embryos and stem cells, and keeping them physically adhered. In the injection method, the chimeras are produced by injecting stem cells into the zona pellucida using microcapillaries. These methods only focus on the generation of chimeric animals, and are not expected to produce reproducible results or allow quantitative evaluation. This study aimed to establish a novel method for producing chimeric embryos via droplets for improving on the conventional methods that are used for producing chimeric embryos. In this study, the embryonic stem cells and embryos were successfully isolated in the droplets, and the emergence of chimeric embryos was confirmed by co-culture for 6 hours. By this method, the control and operability of stem cell numbers can be regulated, and the method allows better reproducibility and quantification during the production of chimeric embryos. In addition to the conventional methods for producing chimeric embryo, the novel method described herein could be employed for the efficient production of chimeric animals.

bioengineering↗