Biology subjects

Nagano, A. J.

Publications and source records attributed to Nagano, A. J..

At least 19 recordsLinked to original sources

bioRxiv2026

Elucidation of the second-phase freezing acclimation mechanism: plants accumulate sugars via photosynthesis under frozen conditions

Overwintering plants increase their tolerance to freezing in two phases: the first-phase, known as cold acclimation (CA), occurs at chilling temperatures, followed by second-phase acclimation at sub-zero temperatures. We previously showed that second-phase freezing acclimation (2PFA), in which cold-acclimated Arabidopsis is exposed to -2{degrees}C with extracellular ice formation under light, confers the highest freezing tolerance (LT50 below -20{degrees}C) through a pathway requiring photosynthetic electron transport, possibly independent of the CBF-COR pathway. However, how light enhances freezing tolerance in frozen plants remains unclear. Here, we developed a system to measure chlorophyll fluorescence in intact plants maintained in a frozen state, and found that PSII retained substantial photochemical capacity (Fv/Fm) in frozen leaves. Comparative transcriptomics revealed that 2PFA under light induced genes involved in starch, sucrose and galactose metabolism. Consistently, soluble sugars, mainly sucrose, glucose and fructose, accumulated to levels approximately 8-fold higher than those in CA plants, and total sugar content was strongly correlated with freezing tolerance. This accumulation was suppressed by the photosynthetic electron transport inhibitor DCMU. These results suggest that photosynthetic activity is maintained in frozen plants and supplies sugars that may contribute to the freezing tolerance acquired during second-phase acclimation, beyond the level achieved by first-phase CA, unveiling a previously unrecognized mechanism in the winter survival strategy of plants.

plant biology↗

bioRxiv2025

From model to field: predictive design of microbial communities for resilient crop performance

Synthetic microbial communities (SynComs) represent a promising approach to enhance crop growth and stress resilience through microbiome engineering. However, the systematic design and field validation of SynComs remain limited. Here, we present a predictive framework for SynCom optimization, integrating plant phenotyping, microbial genomics, and machine learning. Using tomato as a model, we tested over 800 SynCom-temperature combinations consisting of root endophytic bacteria and rhizosphere metabolites. An Elastic Net regression model trained on plant biomass data accurately predicted the performance of unseen SynComs, with prediction accuracy plateauing at [~]5% (301/6144) of all possible SynCom-temperature combinations. Incorporating genomic features significantly improved model performance, whereas microbiome compositional data alone were not informative. We applied the model to design novel SynComs, which were tested in both laboratory and field conditions using a commercial tomato cultivar. The model-informed SynCom enhanced plant growth in field trials and improved heat stress tolerance under controlled laboratory conditions. Multi-omics analyses and feature importance metrics identified specific microbial taxa, including Sphingobium sp., whose enrichment was linked to host plant metabolite (e.g., tomatine) and stress-responsive gene expression. Our results demonstrate a scalable strategy for the predictive design of beneficial microbiomes to improve resilient crop performance under real-world conditions.

systems biology↗

bioRxiv2025

Year-long transcriptome survey highlights a resource allocation strategy at the late growth stage in a monocarpic plant

Day length and temperature drastically changes along the annual cycle in temperate zone. Temperate plants are thought to adapt to the annual cycle by various physiological responses in appropriate season. In the previous study, the annual transcriptome dynamics of Arabidopsis halleri, which is a polycarpic sister species of A. thaliana, was obtained in natural habitats and annual environments simulated by growth chambers. Here, we performed year-long transcriptome analysis of A. thaliana (Col-0 and FRISf2) under annual environments simulated by growth chambers. Comparing gene expressions in FRISf2 and A. helleri, most genes had similar annual expression pattens. However, in February-March conditions, 2,787 genes, containing LHCB and TGG1, exhibited significantly lower expressions in FRISf2 than those in A. helleri. LHCB and TGG1 were not downregulated in cold treatments for a month. These results suggest that factors other than temperature, such as age, are involved in the down-regulations of LHCB and TGG1. Resource translocation to seeds occurs at the end of the growing season in annual plants. The down-regulation of photosynthesis-related proteins and defense-related proteins, known to be highly abundant in leaves, is possibly an adaptive strategy of monocarpic A. thaliana.

plant biology↗

bioRxiv2025

Systematic measurements of dose-dependent responses for combinatorial treatments of SA and JA led to the development of transcriptomic biomarkers

Plants coordinate defence against pathogens and herbivores through the crosstalk between salicylic acid (SA) and jasmonic acid (JA) signalling pathways. However, little is known about how plants integrate the phytohormone concentration profiles to shape defence states in complex field environments. Here we show that systematically varying combinatorial SA and JA concentrations in Arabidopsis thaliana reveals 43 distinct combination-specific transcriptional signatures beyond SA-JA antagonism. Leveraging these data, we developed and validated machine-learning-based transcriptomic biomarkers that enabled independent quantification of SA and JA response states. By applying these biomarkers to field-grown A. thaliana, we revealed that SA/JA response states were dynamically shaped by abundant and co-occurrence of herbivores on individual plants. Our study provides a strategy to decode hormonal responses to biotic environments from field transcriptomes, bridging the gap between molecular signalling and ecological dynamics.

plant biology↗

bioRxiv2025

Molecular basis behind the isoprene emission diversity in Fagaceae

Plants emit a large amount of volatile organic compounds (VOCs) into the atmosphere, reaching approximately 109 tons of carbon per year. These biogenic VOCs exhibit significant chemical diversity, with terpenoids being the dominant group, and isoprene accounting for nearly half of the total biogenic VOCs. Due to its high chemical reactivity, isoprene has a strong impact on atmospheric quality and climate. Quercus species (Fagaceae) are known to be the main isoprene emitters in the Northern Hemisphere. However, isoprene synthase is unknown in the entire Fagaceae family. Notably, even within a single genus such as Quercus, both isoprene-emitting and non-emitting species are present, yet the molecular basis of this dichotomy remains unclear. Here, we report the identification of the IspS gene from the isoprene-emitting species Quercus serrata (QsIspS1) through seasonal transcriptome analysis and its detailed biochemical characterization. We also identified two genes with high sequence similarity to QsIspS1 in the genomes of non-emitting species: Q. glauca (QgIspS1-like) and Lithocarpus edulis (LeIspS1-like). We discovered mutations in these sequences that likely impair their function. Biochemical analysis revealed that QgIspS1-like is a monoterpene synthase, whereas LeIspS1-like is a pseudogene incapable of isoprene synthesis, explaining these plants inability to emit isoprene. Furthermore, site-directed mutagenesis revealed an amino acid that plays a pivotal role in the substrate and product specificities of isoprene synthase. Our findings provide new insight into the molecular mechanisms of isoprene emission diversity in Fagaceae.

biochemistry↗

bioRxiv2024

Modeling of transcriptomic variation among subgenomes in 25 accessions of common wheat reveals cis- and trans-regulation architectures

Common wheat is an allohexaploid plant, thus making it difficult to obtain homoeolog-distinguished transcriptome data. Lasy-Seq, a type of 3 RNA-seq, is efficient for obtaining homoeolog-distinguished transcriptomes and can thus overcome this measurement difficulty. This study obtained transcriptome data from the seedlings, second leaves, and root tips of 25 lines from mainly eastern transmitted area using Lasy-Seq. Roots and seedlings exhibited similar transcriptome profiles; however, they were different from those of the leaves. We determined the effects of subgenomes, lines and their interactions with leaves, roots, and seedlings on the expression levels of each homoeolog triad. Of the 19,805 homoeolog triads, 50.9-55.4%, 24.2-29.5%, and 7.7-9.0% showed significant effects on their expression levels from subgenome, line, and interaction, respectively. 51-55% and 24-30% have genetic variation in the cis- and trans-regulation. Hierarchical clustering and co-trans regulation network analysis of homoeolog triads revealed that the patterns of expression polymorphisms among the lines were shared in different genes. The triads in which the statistical model detected as line effects imply that expression variation between lines is caused by changes in a smaller number of common trans-factors. We assigned gene ontology (GO) terms of the Arabidopsis orthologs to wheat homoeolog triads via reciprocal BLAST between common wheat and Arabidopsis, thus improving the percentage of gene-assigned GO terms to all analyzed GO terms from 19.1% to 90.6%. GO term enrichment analysis revealed that GO terms related to each tissue type function were enriched in genes expressed in the leaves and roots. Our information provides fundamental knowledge for the future breeding of plants possessing complex gene regulatory networks such as common wheat.

plant biology↗

bioRxiv2024

Field-crop transcriptome models are enhanced by measurements in systematically controlled environments

Plants in the field respond to seasonal and diel changes in various environmental factors such as irradiance and temperature. We previously developed a statistical model that predicts rice gene expression from the meteorological data and identified the environmental factors regulating each gene. However, since irradiance and temperature (the two most critical environmental factors) are correlated in the field, it remains difficult to distinguish their roles in gene expression regulation. Here, we show that transcriptome dynamics in the field are predominantly regulated by irradiance, by the modelling involving diurnal transcriptome data from the 73 controlled conditions where irradiance and temperature were independently varied. The models prediction performance is substantially high when trained using field and controlled conditions data. Our results highlight the utility of a systematic sampling approach under controlled environments to understand the mechanism of plant environmental response and to improve transcriptome prediction under field environments.

plant biology↗

bioRxiv2024

Transcriptomic dynamics of petal development in the one-day flower species, Japanese morning glory (Ipomoea nil)

Various aspects of Japanese morning glory (Ipomoea nil) petals, such as color, pattern, shape, flower opening time, and senescence, have been extensively studied. To facilitate such studies, transcriptome data were collected from flower petals at 3-h intervals over 3.5 days; the data was collected from 72 h before and 12 h after flower opening, accounting for 29 timepoints. Data analysis revealed substantial transcriptomic changes before and after flower opening. The expression patterns of cell division marker genes indicated that cell division practically stops at approximately 48 h before flower opening. Furthermore, the increased expression of genes encoding transporters for sugars, amino acids, nucleic acids, and autophagy-related genes was observed after flower opening, indicating the translocation of nutrients from senescing petal cells to other developing tissues. Correlations were found between the temporal expression patterns of the three transcriptional regulators and expression patterns of different sets of structural genes within the anthocyanin biosynthesis pathway, indicating differential reliance on each regulator for the activation of specific structural genes. Furthermore, clock genes were identified. Three copies of the clock gene ELF3 did not exhibit circadian rhythms, potentially allowing I. nil to adapt to high-latitude regions. The temporal transcriptome data and interactive database (https://ipomoeanil.nibb.ac.jp/fpkm/) offer valuable insights into gene expression dynamics, periodicity, and correlations and provide a crucial resource for further research on I. nil and other plant species.

plant biology↗

bioRxiv2024

Simulation study of factors affecting the accuracy of transcriptome models under complex environments

Characterization of molecular responses in real and complex field environments is essential for understanding the environmental response of plants. Field transcriptomics, i.e. modelling large amounts of transcriptomic and meteorological data, is the most comprehensive method of studying gene expression dynamics in complex environments. However, it is not clear what factors influence the accuracy of field transcriptome models. In this study, a novel simulation system was developed. Using the system, we performed a large-scale simulation to reveal the factors affecting the accuracy of the models. We found that the factors that had the greatest impact on the accuracy are, in order of importance, the expression pattern of the gene, the number of samples in the training data, the diurnal coverage of the training data, and the temperature coverage of the training data. Validation using actually measured transcriptome data showed similar results to the simulations. Our simulation system and the analysis results will be helpful for developing efficient sampling strategies for training data and for generating simulated data for benchmarking new modelling methods. It will also be valuable to dissect the relative importance of various factors behind transcriptome dynamics in the real environment. Key messageNovel simulation system revealed how prediction accuracy of field transcriptome was affected by number and diversity of training data

plant biology↗

bioRxiv2024

Identification of new resistance QTL regions in loquat cultivar Champagne against Pseudomonas syringae pv. eriobotryae group C

Loquat canker, caused by Pseudomonas syringae pv. eriobotryae, is a bacterial disease that infects loquat (Eriobotrya japonica) and has been reported in several countries. Three pathotypes, A, B, and C, have been reported in Japan. The loquat cultivar Champagne is resistant to the loquat canker group C and possesses a qualitative trait governed by a recessive homozygous pse-c gene located on Linkage Group 3 (LG3), and quantitative traits located at unidentified loci. In this study, we identified novel quantitative trait loci (QTL) regions for resistance to group C in this cultivar. A seedling population with Tanaka (Pse-c/Pse-c) crossed with Champagne (pse-c/pse-c) was tested. The genetic map of Champagne includes a total of 1,016 SNP markers mapped across 17 LGs, covering a total distance of 1,301 cM and an average marker density of 1.4 cM/locus. In addition to minor potential QTLs, the major QTL for resistance to loquat canker group C was detected in the upper region of LG14, with the QTL contributing 6.9% to the disease index. The results of this study open new possibilities for resistance breeding against this disease. Highlights.A total of 1,016 SNP markers were mapped on a linkage map consisting of 17 linkage groups with a total distance of 1,301 cM. QTL analysis revealed a novel resistance QTL region in Champagne against loquat canker group C in the upper part of the LG14. The identified QTLs in this study provide new possibilities for resistance breeding in loquat.

plant biology↗

bioRxiv2023

The Arabidopsis katamari2 Mutant Exhibits a Hypersensitive Seedling Arrest Response at the Phase Transition from Heterotrophic to Autotrophic Growth

Young seedlings use nutrients stored in the seeds to grow and acquire photosynthetic potential. This process, called seedling establishment, involves a developmental phase transition from heterotrophic to autotrophic growth. Some membrane-trafficking mutants of Arabidopsis thaliana (Arabidopsis), such as the katamari2 (kam2) mutant, exhibit growth arrest during seedling development, with a portion of individuals failing to develop true leaves on sucrose-free solid medium. However, the reason for this seedling arrest is unclear. In this study, we show that seedling arrest is a temporal growth arrest response that occurs not only in kam2 but also in wild-type Arabidopsis; however, the threshold for this response is lower in kam2 than in the wild type. A subset of the arrested kam2 seedlings resumed growth after transfer to fresh sucrose-free medium. Growth arrest in kam2 on sucrose-free medium was restored by increasing the gel concentration of the medium or covering the surface of the medium with a perforated plastic sheet. Wild-type Arabidopsis seedlings were also arrested when the gel concentration of sucrose-free medium was reduced. RNA sequencing revealed that transcriptomic changes associated with the rate of seedling establishment were observed as early as 4 days after sowing. Our results suggest that the growth arrest of both kam2 and wild-type seedlings is an adaptive stress response and is not simply caused by the lack of a carbon source in the medium. This study provides a new perspective on an environmental stress response under unfavorable conditions during the phase transition from heterotrophic to autotrophic growth in Arabidopsis.

plant biology↗

bioRxiv2023

Genome-wide neighbor effects predict genotype pairs that reduce herbivory in mixed planting

Genetically diverse populations can increase plant resistance to natural enemies. Yet, beneficial genotype pairs remain elusive due to the occurrence of both positive and negative effects of mixed planting on plant resistance, called associational resistance and susceptibility. We used genome-wide polymorphisms of the plant species Arabidopsis thaliana to identify genotype pairs that enhance associational resistance to herbivory. By quantifying neighbor interactions among 199 genotypes grown in a randomized block design, we predicted that 823 of the 19,701 candidate pairs could reduce herbivory through associational resistance. We planted such pairs with predicted associational resistance in mixtures and monocultures and found a significant reduction in herbivore damage in the mixtures. Our study highlights the potential application to assemble genotype mixtures with positive biodiversity effects.

ecology↗

bioRxiv2023

Hybridization and its impact on the ontogenetic allometry of skulls in macaques

The role of hybridization in morphological diversification is a fundamental topic in evolutionary biology. However, despite the accumulated knowledge on adult hybrid variation, how hybridization affects ontogenetic allometry is less well understood. Here, we investigated the effects of hybridization on postnatal ontogenetic allometry in the skulls of a putative hybrid population of introduced Taiwanese macaques (Macaca cyclopis) and native Japanese macaques (M. fuscata). Genomic analyses indicated that the population consisted of individuals with varying degrees of admixture, formed by male migration from Japanese to Taiwanese macaques. For overall skull shape, ontogenetic trajectories were shifted by hybridization in a nearly additive manner, with moderate transgressive variation observed throughout development. In contrast, for the maxillary sinus (hollow space in the face), hybrids grew as fast as Taiwanese macaques, diverging from Japanese macaques, which showed slow growth. Consequently, adult hybrids showed a mosaic pattern, i.e., the maxillary sinus is as large as that of Taiwanese macaques, while the overall skull shape is intermediate. Our findings suggest that the transgressive variation can be caused by prenatal shape modification and non-additive inheritance on regional growth rates, highlighting the complex genetic and ontogenetic bases underlying hybridization-induced morphological diversification.

evolutionary biology↗

bioRxiv2023

Detecting and validating influential organisms for rice growth: An ecological network approach

How to achieve sustainable food production while reducing environmental impacts is a major concern in agricultural science, and advanced breeding techniques are promising for achieving such goals. However, rice is usually grown under field conditions and influenced by surrounding ecological community members. How ecological communities influence the rice performance in the field has been underexplored despite the potential of ecological communities to establish an environment-friendly agricultural system. In the present study, we demonstrate an ecological-network-based approach to detect potentially influential, previously overlooked organisms for rice (Oryza sativa). First, we established small experimental rice plots, and measured rice growth and monitored ecological community dynamics intensively and extensively using quantitative environmental DNA metabarcoding in 2017 in Japan. We detected more than 1000 species (including microbes and macrobes such as insects) in the rice plots, and nonlinear time series analysis detected 52 potentially influential organisms with lower-level taxonomic information. The results of the time series analysis were validated under field conditions in 2019 by field manipulation experiments. In 2019, we focused on two species, Globisporangium nunn and Chironomus kiiensis, whose abundance was manipulated in artificial rice plots. The responses of rice, namely, the growth rate and gene expression patterns, were measured before and after the manipulation. We confirmed that, especially in the G. nunn-added treatment, rice growth rate and gene expression pattern were changed. In the present study, we demonstrated that intensive monitoring of an agricultural system and the application of nonlinear time series analysis were helpful to identify influential organisms under field conditions. Although the effects of the manipulations were relatively small, the research framework presented here has future potential to harness the ecological complexity and utilize it in agriculture. Our proof-of-concept study would be an important basis for the further development of field-basis system management.

ecology↗

bioRxiv2022

Apoplast-localized β-Glucosidase Elevates Isoflavone Accumulation in the Soybean Rhizosphere

Plant specialized metabolites (PSMs) are often stored as glycosides within cells and released from the roots with some chemical modifications. While isoflavones are known to function as symbiotic signals with rhizobia and to modulate the soybean rhizosphere microbiome, the underlying mechanisms of root-to-soil delivery are poorly understood. In addition to transporter-mediated secretion, the hydrolysis of isoflavone glycosides in the apoplast by an isoflavone conjugate-hydrolyzing {beta}-glucosidase (ICHG) has been proposed but not yet verified. To clarify the role of ICHG in isoflavone supply to the rhizosphere, we have isolated two independent mutants defective in ICHG activity from a soybean high-density mutant library. In the ichg mutants, the isoflavone contents and composition in the root apoplast and root exudate significantly changed. When grown in a field, the lack of ICHG activity considerably reduced isoflavone aglycone contents in roots and the rhizosphere soil, although the transcriptomes showed no distinct differences between the ichg mutants and WTs. Despite the change in isoflavone contents and composition of the root and rhizosphere of the mutants, root and rhizosphere bacterial communities were not distinctive from those of the WTs. Root bacterial communities and nodulation capacities of the ichg mutants did not differ from the WTs under nitrogen-deficient conditions, either. Taken together, these results indicate that ICHG elevates the accumulation of isoflavones in the soybean rhizosphere but is not essential in isoflavone-mediated plant-microbe interactions.

plant biology↗

bioRxiv2022

Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes)

Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared to other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between two rockfishes, Sebastes schlegelii and S. trivittatus, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in two reciprocal backcross populations. Markers showing either of the two types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between two backcross families and two developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage-specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldanes rule in terms of hybrid inviability does not hold. Additionally, QTL mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, including agouti-signaling protein 1 (asip1) and melanocortin 1 receptor (mc1r), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step towards a comprehensive understanding of speciation and morphological diversification of rockfishes.

evolutionary biology↗

bioRxiv2022

Genome sequence of 12 Vigna species as a knowledge base of stress tolerance and resistance

Harnessing plant genetic resources including wild plants enables exploitation of agronomically unfavorable lands to secure food in the future. The genus Vigna, family Fabaceae, consists of many species of such kind, as they are often adapted to harsh environments including marine beach, arid sandy soil, acidic soil, limestone karst and marshes. Here we report long-read assemblies of 12 Vigna species, achieving 95% or higher BUSCO scores. The comparative analyses discovered a new class of WUSCHEL-related homeobox (WOX) transcription factor superfamily that are incorporated into LTR retrotransposons and have dramatically amplified in some species of the genus Vigna. Except WOX transcription factors, however, gene contents are highly conserved among Vigna species with few copy number variations. On the other hand, transcriptome data provided some insights that transcriptional alterations played more important roles in evolution of stress tolerance in the genus Vigna. The whole genome sequences presented in this study will facilitate understanding genetic mechanisms of stress tolerance and application for developing new crops that are adapted to unfavorable environments.

genomics↗

bioRxiv2022

Diversity of sex chromosomes in Sulawesian medaka fishes

Recent genetic and genomic studies have revealed tremendous diversity in sex chromosomes across diverse taxa. Although theoretical studies predict that sex chromosome evolution can drive the evolution of sexual dimorphism, empirical studies are still limited. A taxonomic group that shows diversity in both sex chromosomes and sexual dimorphism provides excellent opportunity to investigate the link between the evolution of sex chromosomes and sexual dimorphism. The medaka fishes (family Adrianichthyidae) exhibit both rapid sex chromosome turnovers and diversification of sexually dimorphic traits. In the present study, we investigated the sex chromosomes of 13 Oryzias species from Sulawesi, Indonesia, that have diversified in sexual dichromatism. Using pooled sequencing we found sex chromosomes in 9 species that all had XY systems, with a few species being possibly modified by multiple loci. Seven species (O. woworae, O. asinua, O. wolasi, O. matanensis, O. celebensis, O. hadiatyae, and O. dopingdopingensis) share linkage group (LG) 24 as sex chromosomes; however, they differed in the length and magnitude of sequence divergence between the X and Y chromosomes. The sex chromosome of O. eversi was LG4, which has not been reported as a sex chromosome in any other medaka species. In O. sarasinorum, LG16 and LG22 are associated with sex. Although LG16 was found to be sex-linked in another medaka species previously examined, the sex-determining regions did not overlap. Frequent turnovers and the great diversity of the sex chromosomes make Sulawesian medaka species a model system for investigating the roles of sex chromosome evolution in the diversification of sexual dimorphism.

evolutionary biology↗