Plant respiratory burst oxidase homologs (Rbohs) contribute to the production of reactive oxygen species, which are crucial defense signals in plants. However, the regulation of rice (Oryza sativa) OsRboh homeostasis has remained unclear. In this study, we reported that overexpression of OsRbohB confers resistance to Magnaporthe oryzae and Xanthomonas oryzae pv. oryzae. Mechanistically, the calcium-dependent protein kinase OsCPK4 interacts with and phosphorylates OsRbohB at Ser322 and Ser326, thereby reducing immune responses. OsRbohB phosphomimic modifications at these 2 sites disrupt OsRbohB-mediated disease resistance. Moreover, the RING-type E3 ubiquitin ligase OsRING142 interacts with and ubiquitinates OsRbohB at Lys266, targeting it for degradation by the 26S proteasome pathway and compromising the immune response. Overexpression of OsRbohBK266R further increased resistance compared with OsRbohB overexpression plants. Remarkably, phosphorylation at OsRbohB facilitates OsRING142-mediated ubiquitination and degradation of OsRbohB. OsRbohBK266R×S2A overexpression plants with reduced ubiquitination and phosphorylation levels of OsRbohB exhibit stronger resistance against M. oryzae. Overall, our study highlights the critical role of Rbohs in broad-spectrum resistance and demonstrates that phosphorylation and ubiquitination synergistically fine-tune Rboh protein stability and immunity.

Gene duplication is a major source of evolutionary innovation, enabling the emergence of novel expression patterns and functions. Leveraging single-cell genomics, we investigated the transcriptional and cis-regulatory landscapes of duplicated genes in cultivated soybean (Glycine max), which has undergone 2 rounds of whole-genome duplication. Our analysis revealed extensive diversity of transcriptional profiles within and across tissues among duplicated gene pairs. Within-tissue divergence was largely attributable to genetic variation in their associated accessible chromatin regions (ACRs), where cis-regulatory elements reside, whereas cross-tissue divergence was more likely shaped by dynamics in ACR chromatin accessibility profiles across tissues. Distinct duplication mechanisms also likely give rise to different types of cis-regulatory variants, contributing variably to transcriptional divergence. By comparing ACRs associated with gene sets derived from 2 rounds of whole-genome duplication and sharing a common ancestral gene, we found that most ACRs retained one or multiple corresponding duplicated sequences in which mutations gradually accumulated over time, while a subset likely arose de novo. Finally, we traced the evolution of cell-type-specific expression and cell-type-specific ACRs within duplicated gene sets, illustrating a powerful framework for identifying candidate regulatory regions driving cell-type-specific expression. Collectively, our findings highlight the important role of cis-regulatory evolution in shaping transcriptional divergence in a spatiotemporal manner, uncovered with the resolution of single-cell genomics.

The angiosperm seed life cycle encompasses three broad phases-embryogenesis, maturation, and germination. Seed maturation is particularly critical, bridging embryo development and germination while enabling accumulation of nutrient reserves and acquisition of traits like desiccation tolerance, essential for survival in diverse environments. While embryogenesis and germination in Arabidopsis thaliana are known to follow an hourglass-like phylotranscriptomic pattern (with higher gene expression conservation in the mid-stages), the transcriptomic landscape of seed maturation and the complete seed life cycle remain unexplored. Using publicly available RNA-seq data, we generated transcriptome age index and transcriptome divergence index profiles of all three phases of the Arabidopsis seed life cycle, revealing a reverse hourglass-like phylotranscriptome pattern. Seed maturation exhibited increased expression of younger genes with divergent expression patterns compared to embryogenesis and germination, which was conserved in other dicots and monocots. Tissue-specific analyses revealed that, in monocots, the endosperm has increased expression of younger genes during maturation. We found that, similar to pollen development, seed maturation is a pivotal phase enabling the expression of young, rapidly evolving genes. We propose the "out of the seed" hypothesis, where seed maturation serves as a landscape for expressing new genes and promoting functional specialization.

Nickel hyperaccumulation is an extreme adaptation to ultramafic soils observed in more than 500 plant species. However, our understanding of the molecular mechanisms underlying the evolution of this trait remains limited. To shed light on these mechanisms, we have generated a high-quality genome assembly of the metal hyperaccumulator Noccaea caerulescens. We then used this genome as reference to conduct comparative intraspecific and interspecific transcriptomic analyses using various accessions of N. caerulescens and the non-accumulating relative Microthlaspi perfoliatum to identify genes associated with nickel hyperaccumulation. Our results suggest a correlation between nickel hyperaccumulation and a decrease in the expression of genes involved in defense responses and the regulation of membrane trafficking. Surprisingly, these analyses did not reveal a significant enrichment of genes involved in the regulation of metal homeostasis. However, we found that the expression levels of selected metal transporter genes, namely NcHMA3, NcHMA4 and NcIREG2, are consistently elevated in N. caerulescens accessions hyperaccumulating nickel. Furthermore, our analyses identified frameshift mutations in NcIRT1 associated with the loss of nickel hyperaccumulation in a few accessions. We further showed that the expression of a functional NcIRT1 in the roots of the La Calamine accession increases nickel accumulation in shoots. Our results demonstrate that NcIRT1 participates in nickel hyperaccumulation in N. caerulescens. They also suggest that nickel hyperaccumulation is an ancient trait in N. caerulescens that has evolved from the high and constitutive expression of several metal transporters, including NcIREG2, and that the trait was subsequently lost in a few accessions due to mutations in NcIRT1.

Bryophytes are a promising source of bioactive compounds, offering a natural alternative to conventional anticancer drugs known for their cytotoxicity. This article highlights potent anticancer agents such as Marchantin A, Phytol, Perrottetin E, Phenanthrene, and Prenylated bibenzyls, which have demonstrated significant efficacy in inhibiting and destroying various cancer cell lines.

The ability for stress to modify development is common in plants yet how external cues determine phenotypic outputs and developmental responses is not fully understood. Here, we uncovered a ZINC FINGER OF ARABIDOPSIS THALIANA14 (ZAT14) transcription factor whose expression was enhanced in differentiating xylem through its positive regulation by VASCULAR RELATED NAC-DOMAIN PROTEIN7 (VND7) yet decreased in root tips through its negative regulation by PLETHORA2 (PLT2) in Arabidopsis (Arabidopsis thaliana). Mutating ZAT14 and its closely related homologs, ZAT5, ZAT14L and ZAT15, disrupted vascular patterning and inhibited xylem differentiation indicating that ZATs are important for xylem formation. A transcriptome analysis of zat triple and quadruple mutants found that many cell wall-related genes were differentially expressed. In particular, ten expansin genes were repressed by ZATs and several were direct targets of the ZATs. We uncovered that salinity repressed ZAT14, ZAT14L and ZAT15 vascular expression, whereas zat mutants improved salinity tolerance, decreased xylem differentiation and reduced cell death mediated by salt. Furthermore, expansin mutants decreased salinity tolerance and increased xylem differentiation under salinity stress. We propose that ZATs are key regulators of programmed cell death that promote xylem formation, yet upon salinity stress, ZATs are repressed to inhibit cell death and improve salt tolerance, thus modifying developmental outputs in response to stress.

The Green Revolution (GR) dramatically increased the yield of bread wheat (Triticum aestivum L.); however, whether and how GR reshaped the wheat root system remains largely unknown. Here, a large-scale transcriptomic and phenotypic investigation was performed on seedling roots of 406 worldwide bread wheat accessions, and this analysis revealed differences in the transcriptomes and phenotypes between landraces and modern cultivars. The GR allele Reduced height (Rht)-D1b was the main genetic factor driving this phenotypic diversity, and it conferred a significantly larger seedling root to modern cultivars by increasing cell length and root meristem size. In this case, the translational reinitiation of TaRht-D1 underlies the genetic effects of Rht-D1b. In contrast, another GR allele, Rht-B1b, has no significant effect on root-related traits, although both alleles have similar genetic effects on reducing plant height. This unexpected effect of Rht-D1b on root systems, coupled with its effect on plant height, contributes to a substantially larger root-shoot ratio in modern wheat cultivars. These findings reveal previously overlooked benefits of GR alleles in modern wheat cultivars and provide clues for their future application in enhancing the seminal root system.

The nuclear basket (NB) is a key peripheral structure of the nuclear pore complex (NPC) that plays essential roles in eukaryotic mRNA surveillance and export, chromatin organization, and gene expression regulation. However, the architectural and functional mechanisms of plant NB remain poorly characterized. Here, we combined proximity labeling with fluorescence imaging to examine NUP50c, a paralog of NUP50 in Arabidopsis thaliana. Unlike its nucleoplasmic paralogs NUP50a/b, NUP50c localizes specifically to the NB at the nuclear periphery. Structural analysis revealed that NUP50c contains conserved α-helices that mediate its interaction with the β-sheets of NUP82, enabling its NPC anchoring. AlphaFold-Multimer modeling and protein-protein interaction assays using yeast and Nicotiana benthamiana confirmed the formation of an evolutionarily conserved NUP50c-NUP82-NUP136 complex in Arabidopsis, Oryza sativa, and Solanum lycopersicum. Notably, simultaneous disruption of NUP50c with NUP136 or with both NUP82 and NUP136 resulted in developmental defects and enhanced stress responses, accompanied by altered transcript profiles, and pronounced nuclear mRNA retention. These findings establish NUP50c as a bona fide NB component that cooperates with NUP82/NUP136 to mediate mRNA export and regulate gene expression, advancing our understanding of the assembly and function of the NB in plants.

The decision to flower in chrysanthemum (Chrysanthemum morifolium) is controlled by the photoperiod imposed by the outside environment along with endogenous gibberellin levels. Small peptides have broad and critical functions throughout the plant life cycle, but whether and how small peptides are involved in photoperiod- and gibberellin-dependent regulation of flowering remain unclear. Here, we demonstrate that a GIBBERELLIC ACID-STIMULATED TRANSCRIPT (GAST) peptide family member, CmGAST1, promotes flowering in chrysanthemum by interacting with SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9), a key regulator of flowering in the age-dependent pathway. CmGAST1 expression was induced under short-day photoperiods and by gibberellin treatment. In addition, we show that a negative regulator of GA signaling GIBBERELLIC ACID INSENSITIVE (GAI) interacts with CALMODULIN 7 (CAM7), a key factor in calcium signaling, and the resulting CmCAM7-GAI complex directly suppresses CmGAST1 expression. Notably, short-day photoperiods induce the accumulation of bioactive gibberellins and Ca2+ in the shoot apex, thereby inhibiting CmGAI and CmCAM7, respectively, and releasing their inhibition of CmGAST1 expression. We propose that the peptide CmGAST1 integrates gibberellin and calcium signals, coordinating the photoperiod and aging pathways to accelerate chrysanthemum maturation and flowering.

Diversity in plant specialized metabolites plays critical roles in plant-environment interactions. In longer evolutionary scales, e.g. between families or orders, this diversity arises from whole-genome and tandem duplication events. Less is known about the evolutionary patterns that shape chemical diversity at shorter scales, e.g. within a family. Utilizing the aliphatic glucosinolate pathway, we explored how the genes encoding the terminal structural modification enzyme GSL-OH evolved across the Brassicaceae and the genomic processes that control presence-absence variation of its products (R)-2-hydroxy-but-3-enyl and (S)-2-hydroxy-but-3-enyl glucosinolate. We implemented a phylo-functional approach to functionally validate GSL-OH orthologs across the Brassicaceae and used that information to map the genomic origin and trajectory of the locus. This uncovered a complex mechanism involving at least 3 ancestral loci with extensive gene loss across all species, creating unequal retention across the phylogenetic relationships. Convergent evolution in enantiomeric specificity was observed, where several independent species had tandem duplicates that diverged toward producing the R or S enantiomers. To explore potential biological differences between the enantiomers, we performed Trichoplusia ni larval choice assays and tested resistance against Botrytis cinerea in a detached leaf assay. We found that plants with the S-enantiomer were more susceptible to B. cinerea infection than to T. ni larval herbivory, while plants with the R-enantiomer seemed more susceptible to T. ni larval herbivory when compared to B. cinerea. Ultimately, we observed recurrent GSL-OH loss, uncovered a complex origin story for the gene, and measured the bioactivity of the enzyme's metabolic products.

Melon (Cucumis melo L.) is a globally important fruit crop, but progress in molecular breeding has been hampered by limited functional dissection of genes associated with agronomic traits. Therefore, we developed a comprehensive genome resource based on the C. melo ssp. agrestis accession 13C. This resource includes a complete telomere-to-telomere genome assembly, including accurate quantification of 45S rDNA copy number in melon, a transcriptome atlas from 31 tissue samples, a phenotypically diverse EMS-induced mutant library and a stable transformation system. By sequencing 1,125 M2 families, we identified about 660,000 variants, which cover 97.33% of the annotated gene space. Leveraging these integrated resources, we identified and functionally characterized several key genes, including CLAVATA3 INSENSITIVE RECEPTOR KINASES 2 (CmCIK2), which regulates carpel number; PARA-AMINOBENZOIC ACID SYNTHASE (CmACDS), a central regulator of folate biosynthesis; and a mutant allele of the known gynoecious gene WIP DOMAIN PROTEIN 1 (CmWIP1). In addition, we discovered a specific EMS-induced variant in the fruit ripening regulator CmNAC-NOR, and further validated its function by generating targeted mutants. The CmNAC-NOR mutants exhibited delayed fruit ripening, thus providing a valuable resource for improving ripening traits in agrestis accessions. To facilitate broader utilization, we developed the Melon Information Resource, available at https://zhanglab.qau.edu.cn/melon/index.php, an integrated platform housing 13C comprehensive genome resources and associated convenient analysis tools. This unified and accession-specific resource offers unprecedented opportunities to accelerate gene discovery and trait improvement in melon through functional genomics and molecular breeding.