Biology subjects

Kudoh, H.

Publications and source records attributed to Kudoh, H..

11 recordsLinked to original sources

bioRxiv2026

Circadian entrainment to environmental cues in a natural plant population

Circadian clocks coordinate physiology, development and behaviour with cycles of day and night, which contributes to organismal fitness. For this to occur, the circadian clock must be aligned with the natural daily fluctuations in the environmental conditions. Here, we investigated under natural conditions the role of environmental cues in adjusting the circadian clock, and how this affects clock outputs. By combining novel field-based experimentation in a natural plant population with genome-wide analysis and machine-learning strategies for data interpretation, we inferred that temperature cues change circadian timing under natural conditions. We inferred that low temperature cues can shift circadian phase under naturally fluctuating conditions, and that there are seasonal changes in the effects of temperature upon circadian entrainment. We also identified extensive circadian modulation of temperature responses under field conditions. Therefore, plasticity of circadian timing under natural conditions allows flexible responses of both the clock and its outputs to environmental stimuli.

plant biology↗

bioRxiv2025

Conserved gene- and network-level thermal memory intervals in two divergent perennial crucifers in nature

Some biological responses persist long after the initial stimulus has disappeared--a phenomenon known as cellular memory. In its long-term form, cellular memory often reflects interactions between cis-acting chromatin states and diffusible trans-acting regulators, which are experimentally difficult to separate in vivo. A key challenge is to develop a quantitative framework that captures cellular memory length even without prior mechanistic knowledge. The FLOWERING LOCUS C (FLC) gene illustrates this problem and opportunity: a Polycomb/Trithorax cis-acting chromatin switch at FLC produces bistable ON/OFF transcriptional states, while trans-acting factors such as VIN3 and FT modulate transitions between those states. In laboratory studies, FLC memory is classically viewed as persistence of repression or activation after the inducing signal disappears; field studies additionally show that FLC integrates fluctuating temperatures over past intervals, revealing time-integrative mode of memory. To quantify such long-term effects systematically, we formalized the thermal memory interval (TMI), the time window of past environmental cues that best predicts current gene expression--as a transferable metric. We applied TMI to the VIN3-FLC-FT module in two perennial Brassicaceae with divergent life histories: Arabidopsis halleri subsp. gemmifera, an established ecological model, and Eutrema japonicum, introduced here to identify features generalizable beyond a single species. Using long-term expression and meteorological data, TMIs distinguished spring versus autumn FLC states and revealed distributed memory across the VIN3-FLC-FT network, with intervals from 1-150 days, extending previously reported FLC timescales. While TMIs require dense time-series data and do not by themselves reveal molecular mechanism, they offer a robust, quantitative, and generalizable framework: TMIs can be extended to other genes and to alternative environmental or physiological variables, enabling direct, comparative quantification of cellular memory across genes, species, and contexts.

molecular biology↗

bioRxiv2025

H3K4me2 orchestrates H2A.Z and Polycomb repressive marks in Arabidopsis

The dimethylation of histone H3 lysine 4 (H3K4me2) plays an important role in developmental phase transitions in plants, such as regeneration from the callus and the initiation of flowering. H3K4me2 in plants is correlated with transcriptionally repressed states, which can be accounted for by transcription-coupled active H3K4me2 demethylation, but the converse molecular pathway by which H3K4me2 represses transcription remains largely unexplored. Here, we show that H3K4me2 colocalizes with the facultatively repressive marks H2A.Z, H2A ubiquitination (H2Aub), and H3K27me3 in the gene body. Our genetic analyses reveal that H3K4me2 functions upstream but not downstream of these repressive marks. Interestingly, in genes with diurnal H3K4me2 oscillation, H3K4me2 oscillates in antiphase with transcription but in phase with H2A.Z. In addition, the genetic manipulation of H3K4me2 affects the oscillating profiles of H2A.Z, suggesting the efficient relay from H3K4me2 to H2A.Z. Notably, the diurnal oscillation of H2Aub is much weaker than that of H2A.Z despite the overall similarity in their distributions. These results suggest that H3K4me2 orchestrates H2A.Z and H2Aub with distinct dynamics. Our findings reveal that plants employ H3K4me2 to transmit transcriptional cessation into repressive chromatin states.

genetics↗

bioRxiv2024

Machine learning models reveal environmental and genetic factors associated with the plant circadian clock

The circadian clock of plants contributes to their survival and fitness. However, understanding clock function at the transcriptome level and its response to the environment requires assaying across high resolution time-course experiments. Generating these datasets is labour-intensive, costly and, in most cases, performed under tightly controlled laboratory conditions. To overcome this barrier, we have developed ChronoGauge: an ensemble model which can reliably estimate the endogenous circadian time of plants using the expression of a handful of time-indicating genes within a single time-pointed transcriptomic sample. ChronoGauge can predict a plants circadian time with high accuracy across unseen Arabidopsis bulk RNA-seq and microarray samples, and can be further applied across samples in non-model species, including field samples. Finally, we demonstrate how ChronoGauge can be applied to test hypotheses regarding the response of the circadian transcriptome to specific genotypes or environmental conditions.

plant biology↗

bioRxiv2024

Parallel rapid phenotypic differentiation along climatic gradients in multiple introduced lineages of an alien plant species

Widespread plant species are faced with various climatic gradients and undergo clinal differentiation. Alien species which have been introduced repeatedly can be used to investigate the parallel processes of clinal differentiation during their range expansions. Cardamine hirsuta L. has been unintentionally introduced to Japan at least three times and has become widely distributed across Japan. To elucidate the processes of clinal differentiation, we conducted a common garden experiment using three lineages of C. hirsuta (North, East, and West). We tested for phenotypic differentiation among and within the lineages, and for a common pattern of clinal variations in phenotypic traits. We detected differentiations of flowering phenology and body size within and among the lineages. The East lineage showed delayed flowering phenology and larger mass, whereas the West lineage showed rapid flowering phenology and smaller mass. In addition, three patterns of variation between climate factors in seed source habitats and phenotypic traits were detected in all three lineages: higher temperature was related to earlier flowering and lower leaf number at the start of flowering, and more hours of sunshine were related to shorter flowering period. These patterns imply independent and parallel differentiations in the three lineages. These results suggest that analyses of distinct lineages allow repeated observations of differentiation processes and rapid responses of species during successful distribution in new environments.

ecology↗

bioRxiv2022

PlantServation: time-series phenotyping using machine learning revealed seasonal pigment fluctuation in diploid and polyploid Arabidopsis

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers, but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software to analyze field images, where the plant shape, color, and background vary over months. We estimated the anthocyanin contents of small individuals of four Arabidopsis species using color information and verified the results experimentally. We obtained >4 million plant images over three field seasons to study anthocyanin fluctuations. We found significant effects of past radiation, coldness, and precipitation on the anthocyanin content in the field. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation pipeline facilitates the study of plant responses to complex environments termed "in natura."

plant biology↗

bioRxiv2022

Circadian and environmental signal transduction in a natural population of Arabidopsis

Plants sense and respond to environmental cues during 24 h fluctuations in their environment. This requires the integration of internal cues such as circadian timing with environmental cues such as light and temperature to elicit cellular responses through signal transduction. However, the integration and transduction of circadian and environmental signals within plants growing in natural environments remains poorly understood. To gain insights into the 24 h dynamics of environmental signalling in nature, we performed a field study of signalling from the nucleus to chloroplasts in a natural population of Arabidopsis halleri. Using advanced modelling approaches to interpret the data, we identified that the circadian clock and temperature are key regulators of this pathway under natural conditions. We identified potential time-delay steps between pathway components, and diel fluctuations in the response of the pathway to temperature cues that are reminiscent of the process of circadian gating. This approach of combining studies of gene expression in the field with modelling allowed us to identify the dynamic integration and transduction of environmental cues, in plant cells, under naturally fluctuating diel cycles.

plant biology↗

bioRxiv2022

A chronotype effect: circadian-period variation underlies the local adaptation of photoperiodism in the short-day plant Lemna aequinoctialis.

Phenotypic variation is the basis for trait adaptation via evolutionary selection.1, 2, 3 However, the driving forces behind the quantitative trait variations remain unclear owing to their complexity at the molecular level.4, 5, 6 This study focused on the natural variation of the free-running period (FRP) of the circadian clock because FRP is a determining factor of the internal clock phase (chronotype), which is responsible for physiological timing during a day.7 Although natural variations in FRP have been widely reported,8, 10, 11 few studies have shown the association between FRP and adaptive temporal traits. As a clock-dependent physiological process, photoperiodism is a typical target of local adaptation.12, 13 Lemna aequinoctialis in Japan is a paddy-field duckweed exhibiting a latitudinal cline of critical day-lengths (CDLs) for short-day flowering.14 To investigate the relationship between FRP and CDL, we collected 72 strains of L. aequinoctialis within a latitudinal range between 31.5{degrees}N to 43.8{degrees}N. We found a significant correlation (P = 7.5E-8) between FRPs and locally adaptive CDLs, confirming that the variation in FRP-dependent chronotypes underlies geographically differentiated photoperiodism. Diel transcriptome analysis revealed that the induction timing of a florigen gene is key for connecting chronotypes to photoperiodism at the molecular level. Based on these results, we propose a fundamental rule concerning the "chronotype effect" in evolution: the variation of FRP functions as a resource for the variation of temporal traits. This study highlights the adaptive significance of FRP variation and provides a reason for the maintenance of FRP variation in natural populations.

ecology↗

bioRxiv2019

Altered stomatal patterning accompanies a trichome dimorphism in a natural population of Arabidopsis

Trichomes are large epidermal cells on the surface of leaves that are thought to deter herbivores, yet the presence of trichomes can also negatively impact plant growth and reproduction. Stomatal guard cells and trichomes have shared developmental origins, and experimental manipulation of trichome formation can lead to changes in stomatal density. The influence of trichome formation upon stomatal development in natural populations of plants is currently unknown. Here, we show that a natural population of Arabidopsis halleri that includes hairy (trichome-bearing) and glabrous (no trichomes) morphs has differences in stomatal density that are associated with this trichome dimorphism. We found that glabrous morphs had significantly greater stomatal density and stomatal index than hairy morphs. One interpretation is that this arises from a trade-off between the proportions of cells that have trichome and guard cell fates during leaf development. The differences in stomatal density between the two morphs might have impacts upon environmental adaptation, in addition to herbivory deterrence caused by trichome development.

plant biology↗

bioRxiv2019

Fine-scale ecological and transcriptomic data reveal niche differentiation of an allopolyploid from diploid parents in Cardamine

Polyploidization, or whole genome duplication, is one of the major mechanisms of plant speciation. Allopolyploids (species that harbor polyploid genomes originating from hybridization of different diploid species) have been hypothesized to occupy a niche with intermediate, broader, or fluctuating environmental conditions compared with parental diploids. It remains unclear whether empirical data support this hypothesis and whether specialization of expression patterns of the homeologs (paralogous gene copies resulting from allopolyploidization) relates to habitat environments. Here, we studied the ecology and transcriptomics of a wild allopolyploid Cardamine flexuosa and its diploid parents C. hirsuta and C. amara at a fine geographical scale in their native area in Switzerland. We found that the diploid parents favored opposite extremes in terms of soil moisture, soil carbon-to-nitrogen ratios, and light availability. The habitat of the allopolyploid C. flexuosa was broader compared with those of its parental species and overlapped with those of the parents, but not at its extremes. In C. flexuosa, the genes related to water availability were overrepresented among those at both the expression level and the expression ratio of homeolog pairs, which varied among habitat environments. These findings provide empirical evidence for niche differentiation between an allopolyploid and its diploid parents at a fine scale, where both ecological and transcriptomic data indicated water availability to be the key environmental factor for niche differentiation.Significance statement Polyploidization, or whole genome duplication, is common in plants and may contribute to their ecological diversification. However, little is known about the niche differentiation of wild allopolyploids relative to their diploid parents and the gene expression patterns that may underlie such ecological divergence. We detected niche differentiation between the allopolyploid Cardamine flexuosa and its diploid parents C. amara and C. hirsuta along water availability gradient at a fine scale. The ecological differentiation was mirrored by the dynamic control of water availability-related gene expression patterns according to habitat environments. Thus, both ecological and transcriptomic data revealed niche differentiation between an allopolyploid species and its diploid parents.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2019

Seasonal stability and dynamics of DNA methylation in plants in a natural environment

Organisms survive in naturally fluctuating environments by responding to long-term signals, such as seasonality, by filtering out short-term noise. DNA methylation has been considered a stable epigenetic mark but has also been reported to change in response to experimental manipulations of biotic and abiotic factors. However, it is unclear how they behave in natural environments. Here, we analyzed seasonal patterns of genome-wide DNA methylation at a single-base resolution using a single clone from a natural population of the perennial Arabidopsis halleri. The genome-wide pattern of DNA methylation was primarily stable, and most of the repetitive regions were methylated across the year. Although the proportion was small, we detected seasonally methylated cytosines (SeMCs) in the genome. SeMCs in the different contexts showed distinct seasonal patterns of methylation. SeMCs in CHH context were detected predominantly at repetitive sequences in intergenic regions. Additionally, we found that CHH methylation within AhgFLC locus showed a seasonal pattern that was negatively associated with changes in gene expression. Gene-body CG methylation (gbM) itself was generally stable across seasons, but the levels of gbM were positively associated with seasonal stability of RNA expression of the genes. These results suggest the existence of two distinct aspects of DNA methylation in natural environments: sources of epigenetic variation and epigenetic marks for stable gene expression.

plant biology↗