Plant Communications最新文献

Molecular phylogenetics elucidates the evolution and divergence of green plants by analyzing sequence data from diverse sources. Notably, phylogenetic reconstruction based on mitochondrial genes often shows incongruence with results from nuclear and chloroplast genes. Although the uniparental inheritance and conservatively retained protein-coding genes of mitochondrial genomes inherently exclude certain confounding factors that affect phylogenetic reconstruction-such as hybridization and gene loss-the use of mitochondrial genomes for phylogeny and divergence-time estimation has remained limited. Here, we assembled a comprehensive dataset of 565 mitochondrial genomes representing all major lineages of green plants. Applying multiple partitions and phylogenetic models, our mitochondrial-based phylogenies support paraphyly in both bryophytes and charophytes, place hornworts (Anthocerotaceae) as sister to all tracheophytes, and recover stoneworts (Charophyceae) as sister to land plants. We systematically evaluated the influence of factors in mitochondrial coding sequences, including GC-content heterogeneity and codon-usage bias. Furthermore, by rigorously testing seven dating strategies, we assessed the impact of confounding elements affecting divergence-time estimates, such as fossil calibration number and prior settings, as well as rate heterogeneity among sites and across lineages. Our dating analyses support a Neoproterozoic origin (crown age) of land plants and a Triassic origin of angiosperms, consistent with nuclear evidence. In conclusion, we emphasize the importance of exploring alternative partitioning strategies and addressing among-lineage heterogeneity in both phylogenetic and dating analyses, with extended sampling and careful data pruning to minimize systematic error in phylogenetic inference.

With rising living standards, consumers' demand for color diversity and nutritional quality in tomato products has increased. Flavonoids are a key determinant of peel color and nutritional value in tomato fruit, where their biosynthesis is controlled by various phytohormones, including brassinosteroids (BRs). However, the underlying mechanism by which BR regulates flavonoid biosynthesis remains unclear. Here, we show that exogenous BRs suppress flavonoid accumulation, whereas reduced endogenous BR levels in RNAi lines of SlCYP90B3, a rate-limiting BR biosynthetic gene, result in increased flavonoid content in the fruit peel. We further demonstrate that BRI1-EMS-suppressor1 (SlBES1), a basic helix-loop-helix transcription factor essential for BR signaling, not only regulates fruit firmness but also represses flavonoid accumulation by directly binding to the promoters of the flavonoid biosynthetic genes SlCHS1, SlCHS2, and SlF3'H. Additionally, SlBES1 modulates a hierarchical transcriptional cascade by repressing the expression of SlMYB12, further suppressing flavonoid biosynthesis. Moreover, the homologous transcription factor brassinazole-resistant1 (SlBZR1) enhances SlBES1-mediated repression of flavonoid accumulation. Specifically, SlBES1 predominantly inhibits flavonoid biosynthesis, whereas SlBZR1 primarily enhances carotenoid pathway activity. Notably, variation in SlBES1 is correlated with flavonoid content during tomato domestication. Collectively, these results highlight a novel role for SlBES1 as a negative regulator of flavonoid biosynthesis, offering potential strategies for flavonoid biofortification in tomato.

Most extant angiosperms belong to Mesangiospermae (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). Resolving the evolutionary relationships among these five lineages is essential for understanding the early diversification of angiosperms. However, the rapid early diversification of angiosperms within a short geological period complicates the untangling of phylogenetic relationships among these Mesangiospermae lineages. Here, we used 177 publicly available angiosperm genomes to reconstruct the phylogeny of Mesangiospermae using multiple orthology inference approaches, character coding schemes, and data filtering criteria. We further investigated the potential causes of phylogenetic discordance and inferred phylogenetic networks to explore reticulation events among the five Mesangiospermae lineages. Coalescent simulation analyses suggested that a combination of incomplete lineage sorting and hybridization could explain the extensive discordance among nuclear genes in the Mesangiospermae backbone. Cytonuclear discordance was also observed among the five Mesangiospermae lineages, likely resulting from ancient hybridization. Furthermore, systematic errors in species network inference cannot be excluded. Our findings indicate that deep phylogenetic discordances among the five Mesangiospermae lineages are shaped by multiple factors, particularly pervasive ancient hybridization.

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is critical for plant photosynthesis and essential for enhancing tolerance to oxidative stress. However, the precise mechanisms by which plants regulate HPPD in response to oxidative stress remain largely unknown. Here, we show that Arabidopsis thaliana HPPD (AtHPPD) undergoes a previously uncharacterized post-translational modification-phenylalanine hydroxylation-in response to excessive hydroxyl radicals (·OH), thereby mediating oxidative stress tolerance. Biochemical analyses revealed that this hydroxylation impairs the normal function of AtHPPD, accelerating its degradation. We further identified PUB11 as a key interactor of AtHPPD. Both in vitro and in vivo assays demonstrated that this interaction is enhanced under oxidative stress, promoting ubiquitination and facilitating rapid AtHPPD degradation via the 26S proteasome to maintain reactive oxygen species homeostasis. Overall, this work uncovers a novel mechanism by which plants balance photosynthetic efficiency with the repair of oxidative damage, identifies key processes in oxidative stress regulation, and provides a foundation for breeding crops with improved resilience to abiotic stress.

Phospholipases are major regulators of lipid-dependent signaling and play crucial roles in plant immunity. Rice (Oryza sativa) phospholipase C4 (OsPLC4) is a major functional enzyme in the rice phospholipase family that regulates intracellular Ca²⁺ levels. Here we show that OsPLC4 translocates primarily to the plasma membrane in a Ca²⁺-dependent manner, with its C2 domain functioning as a membrane trafficker. Transient expression of OsPLC4 and its truncated variants triggers cell death and immune responses in plants. During effector-triggered immunity (ETI) in rice, OsPLC4 expression and Ca²⁺ influx are specifically and strongly induced in response to avirulent Magnaporthe oryzae. Upon infection, the rice Osplc4 knockout mutant (ΔOsplc4) exhibits substantially reduced Ca²⁺, reactive oxygen species (ROS), and Fe³⁺ accumulation, as well as diminished lipid peroxidation and hypersensitive response (HR) cell death. Complementation of ΔOsplc4 can fully restore Ca²⁺-mediated ferroptotic cell death. OsPLC4 expression also activates HR cell death and the expression of defense-related genes such as OsRbohB, OsMEK2, OsMPK1, and OsPAL1 during avirulent M. oryzae infection. The Ca²⁺ chelator ethylene glycol-bis(2-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) substantially inhibits Ca²⁺, ROS, and Fe³⁺ accumulation and HR-related cell death in rice, whereas the Ca²⁺ influx enhancers trifluoperazine hydrochloride (TFP) and acibenzolar-S-methyl (ASM) strongly induce Ca²⁺-mediated ferroptotic cell death. Additionally, OsPLC4 overexpression triggers cell death and immune responses in Arabidopsis. Collectively, our findings demonstrate that OsPLC4 acts as a downstream target of resistosome activation and sustains the co-elevation of Ca²⁺ and ROS levels during rice ETI, thereby promoting Ca²⁺-mediated, lipid ROS-dependent ferroptotic cell death. These results establish OsPLC4 as a key regulator of Ca²⁺-dependent plant immunity.

In the current context of climate change, there is a need to develop more sustainable agrifood strategies. As an alternative to the intensive use of chemically synthesized fertilizers and pesticides that pollute water and impact biodiversity, there is a growing interest in using beneficial microbes as biostimulants and/or bioprotection agents. However, their implementation in agriculture remains a challenge due to highly variable outcomes and benefits. Furthermore, there are major knowledge gaps about the molecular mechanisms that regulate different plant-microbe interactions. In the present review, we summarize current knowledge on the molecular mechanisms that control different beneficial plant root-microbe interactions; namely, arbuscular mycorrhiza, the rhizobium-legume symbiosis, ectomycorrhiza, and fungal and bacterial endophytic associations. This includes the signaling pathways required for recognition of microbes as beneficial, the metabolic pathways that provide nutritional benefits to the plant, and the regulatory pathways that modulate the extent of symbiosis establishment depending on soil nutrient availability and plant needs. Our aim is to highlight the main common mechanisms, as well as knowledge gaps, in order to promote the use of microbes, either individually or in consortia, within the framework of a sustainable agriculture that is less dependent on chemicals and more protective of biodiversity and water resources.

Bulked segregant analysis (BSA) is a widely used method for identifying genomic loci associated with traits of interest in crops. However, conventional BSA is limited by its reliance on phenotype-driven bulk sampling, which restricts its scalability and confines its applicability to single-trait analysis. This study introduces a novel method, reverse BSA-QTLseq, which uses genotype-driven bulk reconstruction through bioinformatics, enabling the simultaneous mapping of multiple traits from the same genotypic dataset. Reverse BSA-QTLseq uses a two-step strategy-low-resolution genotyping of the entire population followed by high-resolution sequencing of selected bulks-enabling cost-effective identification of genetically divergent lines to enhance the discovery of quantitative trait loci (QTLs). Using a bread wheat recombinant inbred line (RIL) population as a case study, we mapped loci associated with heading date and plant height , confirming approximately 95% of known QTLs, including both dwarfing genes (e.g., Rht-B1 and Rht-5) and flowering-time regulators (e.g., Vrn-A1), and identified novel QTLs and candidate loci with strong phenotypic effects. The phased genotyping strategy maximized genetic distance in the initial sampling, facilitating the in silico reconstruction of trait-specific contrasting bulks. Integration of transcriptional profiles from the parental lines of the RIL population, from which the bulks were derived, aided in identifying candidate genes and regulatory networks underlying the variation of traits such as photoperiod response, nutrient transport, and stress adaptation. The versatility and potential for data reuse offered by the proposed method represent a significant advancement in QTL mapping, with broad implications for marker-assisted breeding and selection programs. Future integration of transcriptomic and epigenomic data is expected to further enhance the power of reverse BSA-QTLseq, accelerating genetic improvement in crops.