Language：English   Publishing type：Research paper (scientific journal)  

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1371/journal.pgen.1005597

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1111/j.1365-313X.2008.03510.x

Language：English  

DOI： 10.7554/eLife.88456

PubMed

Language：English   Publisher：New Phytologist  

DOI： 10.1111/nph.19995

Web of Science

Scopus

PubMed

Language：English  

DOI： 10.1093/pcp/pcae079

Web of Science

PubMed

Language：English   Publisher：Nature Communications  

NLR family proteins act as intracellular receptors. Gene duplication amplifies the number of NLR genes, and subsequent mutations occasionally provide modifications to the second gene that benefits immunity. However, evolutionary processes after gene duplication and functional relationships between duplicated NLRs remain largely unclear. Here, we report that the rice NLR protein Pit1 is associated with its paralogue Pit2. The two are required for the resistance to rice blast fungus but have different functions: Pit1 induces cell death, while Pit2 competitively suppresses Pit1-mediated cell death. During evolution, the suppression of Pit1 by Pit2 was probably generated through positive selection on two fate-determining residues in the NB-ARC domain of Pit2, which account for functional differences between Pit1 and Pit2. Consequently, Pit2 lost its plasma membrane localization but acquired a new function to interfere with Pit1 in the cytosol. These findings illuminate the evolutionary trajectory of tandemly duplicated NLR genes after gene duplication.

DOI： 10.1038/s41467-024-48943-5

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Scopus

PubMed

Language：English   Publisher：Current Opinion in Plant Biology  

Recent population genomic studies in plants have shed new light on natural epigenetic variation by identifying key genetic determinants, “trans modifiers,” that influence epigenetic states genome-wide and their interplay with environmental factors. Here, we review this progress by focusing on the epigenetic control of transposition and life-cycle transitions to highlight the ecological consequences of this genetic architecture and its evolutionary significance. This knowledge provides new opportunities to address long-standing questions about the establishment of environment-associated epigenetic variation and its relevance in adaptation.

DOI： 10.1016/j.pbi.2023.102409

Web of Science

Scopus

PubMed

Language：English   Publishing type：Research paper (scientific journal)  

DOI： https://doi.org/10.7554/eLife.88456.1

Publisher：eLife  

The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly-constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation.

DOI： 10.7554/eLife.88456.1

Scopus

Language：English  

DOI： 10.1038/s41598-023-29850-z

Web of Science

PubMed

DOI： 10.35848/1347-4065/ac971e

Web of Science

Language：English   Publishing type：Research paper (scientific journal)  

Plants have evolved to time their leafing, flowering and fruiting in appropriate seasons for growth, reproduction and resting. As a consequence of their adaptation to geographically different environments, there is a rich diversity in plant phenology from temperate and tropical climates. Recent progress in genetic and molecular studies will provide numerous opportunities to study the genetic basis of phenological traits and the history of adaptation of phenological traits to seasonal and aseasonal environments. Integrating molecular data with long-term phenology and climate data into predictive models will be a powerful tool to forecast future phenological changes in the face of global environmental change. Here, we review the cross-scale approach from genes to plant communities from three aspects: the latitudinal gradient of plant phenology at the community level, the environmental and genetic factors underlying the diversity of plant phenology, and an integrated approach to forecast future plant phenology based on genetically informed knowledge. Synthesizing the latest knowledge about plant phenology from molecular, ecological and mathematical perspectives will help us understand how natural selection can lead to the further evolution of the gene regulatory mechanisms in phenological traits in future forest ecosystems.

DOI： 10.1111/nph.17897

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1371/journal.pone.0119724

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1371/journal.pone.0083720

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1093/molbev/mst103

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.phytochem.2012.11.023

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1093/pcp/pcq185

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1104/pp.109.148031

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1271/bbb.90443

Event date： 2022.12

Language：English  

Venue：淡路   Country：Japan  

The epigenome, in a particular variation of DNA methylation profiles across individuals, has long been of interest as a modifier of the genetic code, with “mutations” reflecting past environments, stochastic events, or genetic regulation. To address this question, we dissected the genetic effects on CG methylation over transposable elements as an inherited epigenetics mark. Through GWAS approaches with natural populations of Arabidopsis thaliana, we discovered that CG methylation variation around pericentromeric regions is significantly affected by a genetic variant of a major trans-modifier conserved from mammals to plants. In this presentation, we will discuss a feature of the genetic basis of CG methylation.

Event date： 2021.12

Language：English  

Venue：Virtual   Country：Japan  

The epigenome, in particular variation of DNA methylation profiles across individuals, has long been of interest as a modifier of the genetic code, with “mutations” reflecting past environments, stochastic events, or genetic regulation. To address this issue, we dissected an inherited epigenetics mark, mCHG methylation, using conditional GWAS approaches in Arabidopsis thaliana. Our study revealed the genome-wide mCHG levels largely share the variation with de novo methylation and are under the control of major trans-modifiers, including the key regulators CMT2, CMT3, MIR823A, and a novel regulator JMJ26 that specifically regulated RdDM-targeted TEs.

Event date： 2020.12

Language：English   Presentation type：Symposium, workshop panel (public)  

Venue：オンライン   Country：Japan  

Transposable element (TE) is one of the major drivers in genome evolution. The ‘selfish mobile elements’ distributing over the genome are considered to influence genome organization, such as genome size, recombination rate, and chromatin structures. Therefore, many species have evolved genome defense system to control TE activities by epigenetic regulation for genome stabilization. DNA cytosine methylation (DNA methylation), a typical epigenetic mark, plays an important role in TE silencing and heterochromatin formation. In plants, it occurs in three sequence contexts: CG, CHG, and CHH (where H is A, T, or C). The latter does not allow direct inheritance of methylation during DNA replication due to lack of symmetry, and methylation must therefore be re-established every cell generation. Genome-wide association studies (GWAS) have shown that CHROMOMETHYLASE2 and NRPE1 as the largest subunit of RNA polymerase V are major determinants of genome-wide patterns of TE CHH methylation. Methylation at TEs targeted by the RNA-directed DNA methylation (RdDM) pathway is unaffected by CMT2 variation, but is strongly affected by variation at NRPE1, which is largely responsible for the longitudinal cline in this phenotype. In contrast, CMT2-targeted TEs are affected by both loci, which jointly explain 7.3% of the phenotypic variation (13.2% of total genetic effects). There is no longitudinal pattern for this phenotype, however, because the geographic patterns appear to compensate for each other in a pattern suggestive of stabilizing selection.