Plant Communications最新文献

Plant species adapting to complex environments will experience contrasting selection pressures that drive the expansion and contraction of different gene families. However, few studies have investigated simultaneous genomic responses to such diverse selection. Here, we generate a high-quality genome assembly for the hemiparasitic plant Thesium ramosoides, the first for the largest genus in the Santalales, and explore the genomic basis underlying the evolution of parasitism and alpine adaptation. Unlike many other parasitic plants, the Thesium genome has not experienced additional rounds of whole genome duplication, making it particularly tractable for studying gene family evolution. Our analyses reveal the significant loss of photosynthesis-related genes and the contraction of biotic defense gene families, likely reflecting adaptation to a hemiparasitic lifestyle and to reduced pathogen pressure at high altitudes. The absence of key root hair development genes correlates with the degenerate root hair phenotype observed in this species. Furthermore, hallmarks of high-altitude adaptation include the expansion of gene families involved in responses to hypoxia. Notably, expansions of gene families associated with meristem development are consistent with the presence of below-ground crown buds that can enable rapid regeneration after mountain fires. Unexpectedly, we detected tandem duplication and diversification in the strigolactone receptor gene D14 that regulates secondary shoot formation, but not in its ancestral paralog KAI2 that mediates seed germination stimulated by the smoke-derived compound karrikin. This indicates divergent mechanisms of signaling for fire adaptation across different parasitic plant lineages. By analyzing time-series transcriptomic data, we propose a post-fire "defense-first, repair-later, recovery-last" model, where resources are reallocated from immediate defense to rapid repair and finally to long-term recovery to explain the adaptation of T. ramosoides to fire-prone habitats. Our study provides critical insights into the complex and contrasting genomic dynamics driving adaptation to multiple co-occurring selection pressures.

The climate crisis poses a critical challenge to agriculture, with freshwater scarcity becoming a major constraint on crop production. Harnessing halophytic adaptations for growth in saline environments offers a promising path for neodomestication of salt-tolerant crops. Distichlis spp. (saltgrass)-a genus of dioecious, halophytic C4 grasses in the PACMAD clade-thrives in extreme saline conditions, making it a compelling species to understand salinity tolerance and adaptation. Here, we present high-quality phased genome assemblies of four Distichlis genets, revealing an allotetraploid genome (576-610 Mb) with two highly syntenic but degenerate subgenomes, each exhibiting over 30% gene loss across orthologous pairs. Comparative genomic analyses uncovered a novel chromosome fusion event differentiating D. spicata (2n=40) and D. stricta (2n=38), highlighting a chromosomal rearrangement differentiating the species. Population genomic analysis of 364 genets across 35 populations demonstrated strong geographic differentiation and confirmed D. stricta as a distinct species. Additionally, we identified a 7 Mb B chromosome in two genets, displaying common features shared with B chromosomes in other species. Using k-mer analyses of sex-typed populations, we identified an 8 Mb sex-determining region in female genets with 24 candidate genes, confirming that Distichlis has a ZW-type sex determination. Expression profiling of plants under extreme (seawater-level) salinity revealed key salt-tolerance genes that are also implicated in drought resilience, suggesting an overlapping genetic basis for these stress responses. These genomic resources establish a foundation for neodomestication of saltgrass as a climate-resilient crop for saline agroecosystems and enhance our understanding of genome evolution in halophytic grasses.

WD40 proteins form β-propeller structures essential for plant development and signaling; however, their complete domain architecture is often missed due to high sequence divergence. Here, we reannotated 117 plant genomes and found that many WD40 genes contain fewer than the canonical seven domains, raising questions about their functionality as complete WD40 proteins. Structure-based modeling of 17,369 WD40-only genes without the other associated domains revealed 41,379 additional WD40 domains that were entirely missed by sequence-based annotation but required for forming stable β-propeller structures. Despite being annotated as partial, two rice genes with sequence-invisible domains formed complete β-propeller folds and were critical for pollen development. CRISPR-Cas9 knockouts showed that OsWD40-31 is required for pollen tube elongation, while OsWD40-169 is necessary for pollen germination. Disruption of the sequence-invisible domains reduced binding affinity to key reproductive regulators, PME1 and Lipase3, as confirmed by structural interaction modeling, yeast two-hybrid assays, and co-immunoprecipitation assays. Residue substitution further revealed that WD40 domain stability depends on hydrogen bonding residues not captured by sequence conservation, explaining why many functional domains elude sequence-based detection. These findings highlight a fundamental disconnect between sequence conservation and structural integrity, establishing a structure-guided framework for uncovering hidden domain architectures in complex, repeat-rich gene families across plant genomes.

Plant-derived natural products offer a rich source of therapeutic agents. However, sustainable and high-yield production remains a grand challenge. We engineered Salvia miltiorrhiza hairy roots to produce taxadiene, a key precursor for the anticancer drug paclitaxel, and protopanaxadiol, a precursor for ginsenosides. We have successfully established the heterologous expression of two key biosynthetic genes, taxadiene synthase from Taxus wallichiana and protopanaxadiol synthase from Panax notoginseng, enabled the production of taxadiene and protopanaxadiol, respectively. Our strategy combined multiple approaches to enhance terpenoid production, including genome editing to redirect metabolic flux by eliminating a competing GGPP sink (via SmCPS1 disruption), transcriptional reprogramming through SmWRKY61 overexpression to enhance terpenoid precursor pathways (MVA/MEP), and cultivation optimization. This holistic approach yielded 65.17 ± 5.25 mg/kg FW taxadiene in batch cultures, while the protopanaxadiol yield reached 50.04 ± 2.94 mg/kg DW without optimization. These results highlight the potential of this platform for industrial-scale production. Our findings demonstrate that S. miltiorrhiza hairy roots can serve as a robust and scalable platform to produce valuable plant-derived compounds. This work paves the way for future metabolic engineering efforts to achieve cost-effective and sustainable production of high-value natural products using medicinal plant systems, addressing critical supply bottlenecks for pharmaceutical compounds.

Jasmonate (JA) is a pivotal phytohormone balancing defense and growth processes to orchestrate plant survival based on external conditions. While JA-mediated resistance against biotic and abiotic threats offers promising avenues for crop improvement, its concurrent growth suppression poses a fundamental challenge in agricultural practices. This review synthesizes recent advances in understanding of JA-mediated growth-defense trade-off (GDT), with a special focus on innovative strategies to decouple JA-induced defense from growth inhibition, including expanding photosynthetic capacity, rewiring JA signaling, optimizing rapid JA bursts and degrading targeted protein via subtype-selective JA agonists. We further propose future research directions to advance the field of transcending JA-mediated GDT in crops, such as fine-tuning chloroplast functionality, manipulating DAMPs signaling as well as remodeling JA regulators. By integrating these insights, we provide strategic frameworks for fundamentally re-engineering the JA pathways to develop plants with more resilience and sustained productivity.

Traditional sugarcane breeding, reliant on phenotypic selection, is being transformed by genomic tools. However, the crop's highly polyploid genome and significant genotype-by-environment interactions (G×E) pose challenges that conventional models cannot adequately address. While the Integrated Genomic-Environmic Prediction (iGEP) framework provides a viable path forward, its application to a complex clonal crop like sugarcane requires profound extension. This review provides the first comprehensive roadmap for implementing iGEP in sugarcane, systematically addressing its unique biological constraints, and synthesizes a tailored "Three-Model" computational framework (Genetic, Environmental, Phenotypic) to decode polyploid allelic dosage, quantify high-resolution environmental drivers via "isoenvironment" design, and predict clonal performance. Furthermore, we detail the extension of artificial intelligence (AI) and iGEP models to leverage clonal propagation, optimize multi-trait selection, and overcome perennial ratoon dynamics. Finally, we present a phased roadmap to build an AI, outlining a transformative path from digitization to synthetic design. By bridging cutting-edge predictive analytics with the distinctive biology of sugarcane, this work establishes a new paradigm for accelerating genetic gain in this vital crop and offers a transferable strategy for other species with complex genomes.

Short summary: ArtemisiaDB is a comprehensive, interactive multi-omics database designed to accelerate Artemisia annua research. It integrates curated genomic, transcriptomic, and metabolomic data alongside specialized modules for transcription factors, CRISPR design, and gene-metabolite correlation. This platform provides a critical resource for exploring the regulatory mechanisms governing artemisinin biosynthesis to advance plant metabolic engineering.