Molecular Plant最新文献

The molecular regulatory mechanisms underlying spike development critically influence grain yield of wheat (Triticum aestivum L.) but remain incompletely understood. Using spatial transcriptomic analysis with single-cell resolution, we comprehensively mapped the spatiotemporal transcriptome across five key stages of wheat spike development. Our approach enabled the identification and annotation of nine distinct cell types, revealing the spatiotemporal distribution of hormonal and metabolic signaling pathways across multiple cell populations. Notably, we observed variations in biosynthesis and response signaling patterns among key phytohormones, particularly cytokinin and auxin, and demonstrated that the rachis cell population serves a crucial role in nutrient and energy supply during spike morphogenesis. The analysis of pseudotime and RNA velocity revealed cell populations with distinct differentiation states, highlighting the potential influence of spikelet primordium base cells on lateral organ development and grain number determination. By integrating snRNA-seq data from the W3.5 stage, gene regulatory relationships and GWAS data from public databases, we constructed a co-expression regulatory network for wheat spike development and identified a key gene module that regulates multiple spike-related traits. Subsequent investigations characterized the heterogeneous subpopulations of spikelet primordium base cells, identifying a novel gene cluster substantially regulates grain number per spike. Based on spatial transcriptomics data, we have developed a publicly accessible online platform (http://www.wssed.com/) that allows users to interactively query and visualize spatiotemporal gene expression patterns during wheat spike development. Overall, this study provides a comprehensive molecular framework for early spike development in wheat, offering valuable genetic resources and public data for functional genomics research. This information may hold significant implications for breeding efforts aimed at optimizing spike architecture and enhancing grain yield potential in wheat.

The gaseous hormone ethylene plays a key role in regulating plant growth and stress responses. Although Ca²⁺ has long been implicated in ethylene signaling, the identity of molecules controlling Ca²⁺ permeability has remained elusive. Here we show that Arabidopsis subfamily I ethylene receptors ETR1 and ERS1, as well as their homologs across the green lineage, are Ca²⁺ permeable. We found that simultaneous disruption of ETR1 and ERS1 markedly attenuates ethylene-induced elevation in cytosolic Ca²⁺ concentrations in Arabidopsis seedlings, and that both proteins exhibit Ca²⁺ permeability in the Xenopus laevis oocyte system and two additional heterologous expression systems. Moreover, we showed that homologs of ETR1 from eight land plant and algal species also exhibit Ca²⁺ permeability, suggesting an evolutionarily conserved function. We further demonstrate ethylene enhances the Ca²⁺ permeability of ETR1 and its homologue from the charophyte Klebsormidium flaccidum, and a mutation to disrupt ethylene binding (Cys65Ser) abolishes the ethylene influence. These findings uncover a previously unrecognized yet conserved role of ethylene receptors as Ca²⁺-permeable channels in the green lineage, with broad implications for Ca²⁺ signaling in plant development and environmental adaptation.

Centromeres are indispensable for accurate chromosome segregation, but are subject to rapid sequence turnover while maintaining conserved functions -- a paradox in genome evolution. To unravel this paradox, we integrated over 400 fully resolved centromeres from 17 diploid angiosperms spanning 180 million years of divergence, along with 1,000+ pan-genomic assemblies, resequencing datasets, and congeneric whole-genome sequences. Our study shows that angiosperm centromere organization is determined by lineage-specific combinations of satellite repeat and transposable element (TE), which in turn shape distinct epigenetic landscapes and evolutionary trajectories within centromeres. In particular, TE insertion patterns are found to be one key driver of structural diversification and positional shift of centromeres in angiosperms. Intriguingly, population-level analyses uncovered considerable plasticity in centromere sequences within species, with satellite repeats acting as focal points of evolutionary change and displaying species-specific heterogeneity patterns. Temporal reconstructions across congeneric species revealed the emergence and subsequent differentiation of centromeric repeats, outlining a dynamic continuum from gradual sequence diversification to complete turnover during speciation over time, often accompanied by karyotype reorganization. By integrating intra- and inter-species comparisons, we propose a unifying framework in which centromere innovation is governed by a delicate interplay between genome evolution, chromosomal shuffling and selection constraints, resulting in phylogenomic signatures of centromere-driven speciation.

Root immunometabolism: balancing defense and accommodation Plant health depends on balanced immune defense and microbial accommodation. As constant contact zones, roots must exclude pathogens while fostering beneficial symbionts. Classical, leaf-based immunity models fail to capture the spatial and metabolic complexity of roots, which contain functionally distinct zones and cell types with diverse immune sensitivities and responses (Tsai et al., 2023). Unlike broad immune responses in leaves, root defense is often confined to a few neighboring cells where cellular damage signals coincide with microbial cues. This localized activation likely prevents excessive immunity that could disrupt root development or beneficial colonization (Tsai et al., 2023), shaping microbiome assembly by determining which taxa persist in specific root niches. Beyond immunity, metabolic cues also influence niche formation, collectively defining the physicochemical landscape that selects specific microbial consortia (Loo et al., 2024). Microbial effector proteins from both pathogens and mutualists act individually or cooperatively to reprogram host immune and metabolic pathways, modulating compatibility and plant health. This integrated regulation, known as immunometabolism, is well established in animals, where defined metabolic pathways govern immune cell fate and function. In plants, immunometabolic control is emerging as a conceptual frontier, with host transporters, receptors, and microbial effectors increasingly recognized as key modulators along the mutualism-pathogenesis continuum. Central to this molecular dialogue are extracellular and intracellular signaling metabolites, or infochemicals, produced by both plants and microbes. These small molecules coordinate immune-metabolic states and shape community composition, with purine-derived signals and iron-mediated redox exchanges representing conserved regulatory axes across plant and animal systems (Dangol et al., 2019; Dunken et al., 2024). Together, these cross-kingdom principles offer conceptual and practical leverage for predictive microbiome engineering. Because this opinion piece spans immunity, metabolism, and microbial ecology, INFOBOX 1 defines key terms to establish a shared conceptual framework.

Histone methylation is involved in a wide range of biological regulation in plants, and conducted by three major components including methyltransferases, demethylases, and histone readers. Compared to the other two components, research on histone readers is relatively limited. In this study, we demonstrate that OsSHH5 functions as an H3K9me1 reader to regulate rice disease resistance, tillering, and grain yield. Loss of OsSHH5 significantly enhances both grain yield and disease resistance. Mechanistically, OsSHH5 recruits the H3K9 methyltransferase SGD733 and binds to H3K9me1, thereby maintaining H3K9me1 enrichment and facilitating gene silencing. In leaves, OsSHH5 interacts with the transcriptional factor HPY1 to target the resistance-related genes OsWAKg52 and OsWRKY81, maintaining their H3K9me1 levels and suppressing multiple PAMP-triggered immunity (PTI) responses, which ultimately reduces rice disease resistance. In tiller buds, OsSHH5 interacts with the transcriptional factor TCP19 to target the tillering-related gene OsNGR5, maintaining its H3K9me1 enrichment and inhibition of tillering, leading to reduced yield. Collectively, these findings reveal that OsSHH5 plays a vital role in integrating immune response, tillering and grain yield in rice. It will provide new insights into the function of histone readers and offers a new strategy to improve rice yield and disease resistance.