Host–pathogen co-evolution shapes resistance (R) proteins and their recognition of pathogen avirulence factors. However, little attention has been paid to naturally occurring genetic diversity in R genes. In this study, 12 Solanum bulbocastanum accessions from the Commonwealth Potato Collection were screened for resistance to Phytophthora infestans, identifying 11 resistant and one susceptible accession. Targeted enrichment sequencing of nucleotide-binding leucine-rich repeat (NLR) genes using RenSeq, followed by diagnostic RenSeq (dRenSeq) analysis, revealed that all accessions except 7650 contained Rpi-blb1/RB variants. Variants in accessions 7641 and 7648 were non-functional, while three novel functional variants were identified. Cloning and functional analysis of Rpi-blb1/RB variants assessed their recognition of the avirulence factor IPI-O1. Three variants were functional, conferring resistance to P. infestans. Variants in accessions 7644 and 7647 also recognized IPI-O4, confirmed in transgenic potatoes. Analysis of a non-functional variant in S. bulbocastanum accession 7648 identified amino acid Ser347 in the nucleotide-binding (NB-ARC) domain as critical for cell-death initiation following IPI-O1 recognition. Predictions from the FunFOLD2 protein–ligand interaction model suggested that Ser347 is essential for ATP binding, suggesting potential inhibition on pentameric resistosome assembly. Western blot analysis revealed that the mutation of Ser347 to Asn markedly compromises the Rpi-blb1/RB protein stability, and co-immunoprecipitation assay further confirmed that this mutation severely disrupts the self-association of CCNB, thereby preventing Rpi-blb1/RB activation. Consistently, substituting Asn347 with serine restored function, underscoring its key role in Rpi-blb1/RB activity. Cell biology experiments demonstrated that Rpi-blb1/RB relocalize to the plasma membrane in response to IPI-O1. This relocalization depends on Ser347, further supporting the idea that its mutation affects resistosome formation, impairing resistance. This study provides an in-depth functional analysis of natural Rpi-blb1/RB diversity, offering insights into NLR protein evolution and resistance mechanisms in potatoes.

Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus-dependent decision-making circuits. Unlike animals, plant memory is uniquely rooted in cellular, molecular, and biochemical networks, lacking specialized organs for these functions. Consequently, plants can effectively learn and respond to diverse challenges, becoming used to recurring signals. Artificial intelligence (AI) and machine learning (ML) represent the new frontiers of biological sciences, offering the potential to predict crop behavior under environmental stresses associated with climate change. Epigenetic mechanisms, serving as the foundational blueprints of plant memory, are crucial in regulating plant adaptation to environmental stimuli. They achieve this adaptation by modulating chromatin structure and accessibility, which contribute to gene expression regulation and allow plants to adapt dynamically to changing environmental conditions. In this review, we describe novel methods and approaches in AI and ML to elucidate how plant memory occurs in response to environmental stimuli and priming mechanisms. Furthermore, we explore innovative strategies exploiting transgenerational memory for plant breeding to develop crops resilient to multiple stresses. In this context, AI and ML can aid in integrating and analyzing epigenetic data of plant stress responses to optimize the training of the parental plants.

INOSITOL-REQUIRING ENZYME 1 (IRE1) is conserved in plants and mammals to regulate stress responses. Here, we found that TaIRE1 is involved in the unconventional splicing of cell membrane-localized TabZIP60 messenger RNA (mRNA), which results in a nucleus resident protein form (TabZIP60s), and enhanced heat stress tolerance. Transcriptome analysis together with binding element prediction revealed 121 high-confidence targets of TabZIP60s responsive to heat stress in wheat (Triticum aestivum), including heat shock protein genes. Interestingly, we found that an asparagine to glutamic acid substitution, located next to DNA-binding domain of TabZIP60s, results in reduced binding affinity and transcriptional activity to downstream targets, and this heat stress tolerance inferior allele was positively selected during modern wheat breeding programs in China, possibly due to their negative effects on yield potential. Finally, we showed that TaIRE1 is also responsible for the mis-cleavage of miR172 precursors, and consequently contribute to heat stress tolerance. To the best of our knowledge, this represents the first report showing that, like in mammals, IRE1 also regulates miRNA cleavage in response to heat stress in plants. Together, this coordinate control of two signaling pathways provides new insights into heat stress tolerance regulation in wheat.

Late blight pathogen Phytophthora infestans secretes numerous effectors to suppress plant immunity. However, little is known about their underlying biochemical mechanisms. Here we report that, in the host Nicotiana benthamiana, P. infestans core RXLR effector Pi17063 suppresses plant immunity by targeting the host plasma membrane and NbRab-G3 proteins, small GTPases of the Ras-related brain (Rab) family. Pi17063 functions as their specific GTPase-activating protein (GAP), driving them to the cytoplasm-localized guanosine diphosphate (GDP)-bound inactive state. Mutant analysis of the conserved Pi17063 arginine residues showed the essential role of its GAP activity for virulence contribution. All four NbRab-G3 subfamily members are positive immune regulators, and NbRab-G3c mutants lost the ability to switch between active and inactive states and showed compromised immune function. Consistent with this, both silencing and overexpression of an endogenous GAP, NbGYP, inhibited NbRab-G3c-mediated plant immunity. Our results revealed positive immune roles of host NbRab-G3 GTPases, the importance of their state balance, and the biochemical mechanism by which their functions are suppressed by a P. infestans effector, providing insights into understanding eukaryotic effector-mediated plant susceptibility.

Hidden hunger, caused by chronic micronutrient deficiencies, affects billions of people worldwide and remains a critical public health issue despite progress in food production. Biofortification offers a promising solution by enhancing nutrient levels within plant tissues through traditional breeding or advanced biotechnologies. Recent advancements in plant synthetic biology have significantly improved biofortification strategies, enabling precise and targeted nutrient enrichment. This mini-review outlines five core strategies in synthetic biology-based biofortification: overexpression of endogenous biosynthetic genes, introduction of heterologous biosynthetic pathways, expression of nutrient-specific transporters, optimization of transcriptional regulation, and protein (directed) evolution. Vitamin B₁ biofortification serves as a primary illustrative example due to its historical importance and ongoing relevance. Recent breakthroughs, particularly from Chinese research teams, are also highlighted. Together, these strategies offer transformative potential for addressing global nutritional challenges through precise, sustainable and innovative plant-based approaches.

Transcription factors (TFs) function as master regulators in multiple signaling pathways and govern diverse developmental and adaptive processes in plants. Some TFs identified in crop plants play critical roles in regulating yield through changes in plant architecture, including roots, stems, leaves, flowers, fruits, and grains. Although altering crop architecture can increase yields, the extent of yield enhancement is frequently hampered by diseases. Developing new crop varieties with improved yields and enhanced disease resistance remains challenging because immune system activation often impairs plant growth. Recently, approaches using TF engineering have made substantial progress in elevating both growth performance and disease resistance. However, most of these techniques rely on traditional transgenic methods. This review highlights discoveries in the last decade demonstrating improvements in growth performance, yield and immunity through TF engineering. We focus mainly on changes in plant architecture related to improved yield and disease resistance. We conclude with perspectives on the potential application of these discoveries for generating desirable crop traits by merging the most noteworthy biotechnology approaches, such as clustered regularly interspaced small palindromic repeats (CRISPR)/CRISPR-associated protein 9-mediated genome editing, with canonical molecular biology.

The SDS-sedimentation volume (SSV) is a critical indicator for assessing wheat gluten quality and is widely used when evaluating wheat processing quality. However, the molecular mechanisms regulating SSV remain poorly understood. In this study, we performed an analysis of quantitative trait loci (QTLs) for SSV using a recombinant inbred line (RIL) population derived from a cross between TAA10 and XX329, and identified four environmentally stable QTLs located on chromosomes 1D, 2D, 4D, and 6D. Among them, the effects of Qssv.cau-1D and Qssv.cau-6D were likely to be explained by genome variations at the Glu-D1 and Gli-D2 loci. We fine mapped Qssv.cau-2D to the candidate causal gene TaSED, encoding a nucleolar protein. Gene-edited TaSED knockout mutants (tased) had a lower SSV, while TaSED overexpression lines showed a higher SSV. We demonstrated that TaSED interacted with the transcription factor TaSPA to enhance its transcriptional activation activity of glutenin and gliadin, whose expression was downregulated in tased and upregulated in TaSED-OE plants, with corresponding differences in glutenin and gliadin content compared with the wild-type. A molecular marker sedTX was further developed based on a nonsynonymous mutation of the parents in TaSED that could be used to identify haplotypes with high SSV effectively. Our findings elucidate a molecular mechanism governing SSV and reveal valuable variants with promising applications for improving wheat quality.

Transcription activator-like effectors (TALEs) mimic eukaryotic transcriptional activators and translocate into host plant cells via the bacterial type III secretion system (T3SS) during pathogenic interactions. They play a crucial role in disease development by regulating host genes. Despite this, the regulatory mechanisms by which TALEs control OsWRKY transcription factors (TFs) remain poorly understood. In this study, we show that two TALEs from Xanthomonas oryzae pv. oryzae (Xoo) individually modulate two OsWRKY TFs, resulting in increased susceptibility and reduced host defense. Specifically, Xoo1219 and Xoo2145 activate the expression of OsWRKY104 and OsWRKY55, respectively, through direct interactions. OsWRKY104 increases the susceptibility to Xoo by activating OsSWEET11 and OsSWEET14, while OsWRKY55 suppresses host defense against Xoo by directly regulating OsWRKY62. These findings suggest that TALEs hijack the host's OsWRKY TFs to create a favorable environment for bacterial survival.

In recent decades, research on model organisms has significantly increased our understanding of core biological processes in plant science. However, this focus has created a substantial knowledge bottleneck due to the limited phylogenetic and ecological spectrum covered. Gymnosperms, especially conifers, represent a molecular and ecological diversity hotspot among seed plants. Despite their importance, research on these species is notably underrepresented, primarily due to a slower pace of investigation resulting from a lack of community-based resources and databases. To fill this gap, we developed the P(inus)ra(diata)-G(ene)E(xpression) (Pra-GE)-ATLAS, which consists of several tools and two main modules: transcriptomics and proteomics, presented in this work for the forestry commercial and stress-sensitive species Pinus radiata. We have summarized and centralized all the available information to provide a comprehensive view of the gene expression landscape. To illustrate how applications of the database lead to new biological insights, we have integrated multiple regulatory layers across tissues and stressors. While stress favors the retention of small introns, harmonized alternative splicing analyses reveal that genes with conifers' iconic large introns tend to be under constitutive regulation. Furthermore, the degree of convergence between stressors differed between regulatory layers, with proteomic responses remaining highly distinctive even through intergenerational memory tolerance. Overall, the Pra-GE-ATLAS aims to narrow the distance between angiosperms and gymnosperms resources, deepening our understanding of how characteristic pine features have evolved. Pra-GE-ATLAS DB is available at: http://pra-ge-atlas.valmei.es.

Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂) is known to be an instrumental anionic phospholipid in governing pollen germination and pollen tube growth. However, the precise functions and regulatory mechanisms of PI(4,5)P₂ in pollen polarity establishment and germination remain poorly understood. Our previous studies demonstrated the pivotal involvement of Arabidopsis formin homology 5 (AtFH5)-dependent vesicle trafficking in polarity establishment of pollen. Here, we observed that PI(4,5)P₂ accumulated and oscillated at the prospective germination site, a process closely associated with the rotational movement of AtFH5-labeled vesicles. Disruption of the mobility of AtFH5-labeled vesicles, either through AtFH5 mutation or pharmacological treatment, significantly perturbed the accumulation of PI(4,5)P₂ at the plasma membrane. Subcellular localization and genetic analysis revealed that two phosphatidylinositol 4-phosphate 5-kinases, AtPIP5K1 and AtPIP5K4, are essential for PI(4,5)P₂ oscillation at the germination site prior to pollen germination. Furthermore, we found that the dynamics of AtPIP5K4 depended on the mobility of AtFH5-labeled vesicles and reduced PI(4,5)P₂ in turn disturbed the attachment of AtFH5-labeled secretory vesicles to the plasma membrane. In conclusion, these findings collectively highlight the reciprocal regulation of AtFH5-labeled secretory vesicles and PI(4,5)P₂ oscillations at the plasma membrane, providing critical insights into the molecular mechanism underlying polarity establishment during pollen germination.

Plants have evolved a sophisticated chemical defense network to counteract pathogens, with phenolamides and salicylic acid (SA) playing pivotal roles in the immune response. However, the synergistic regulatory mechanisms of their biosynthesis remain to be explored. Here, we identified a biosynthetic gene cluster on chromosome 2 (BGC2) associated with the biosynthesis of phenolamide and SA, wherein the key component SlEPS1 exhibits dual catalytic functions for the synthesis of phenolamides and SA. Overexpression of the key component SlEPS1 of BGC2 in tomato enhanced resistance to the bacterial pathogen Pst DC3000, whereas knockout plants were more susceptible. Exogenous applications of SA and phenolamides revealed that these two compounds act synergistically to enhance plant resistance. Notably, during tomato domestication, a disease-resistant allele of SlEPS1, SlEPS1^HapB, was subject to negative selection, leading to a reduction in phenolamide and SA levels and compromised disease resistance in modern varieties. Moreover, the SlMYB78 directly regulates the BGC2 gene cluster to enhance phenolamide and SA biosynthesis, modulating resistance to Pst DC3000. Our study employed multi-omics approaches to describe the synergistic regulation of phenolamide and SA biosynthesis, offering new insights into the complexity of plant immune-related metabolism.

Deep learning-based genomic prediction (DL-based GP) has shown promising performance compared to traditional GP methods in plant breeding, particularly in handling large, complex multi-omics data sets. However, the effective development and widespread adoption of DL-based GP still face substantial challenges, including the need for large, high-quality data sets, inconsistencies in performance benchmarking, and the integration of environmental factors. Here, we summarize the key obstacles impeding the development of DL-based GP models and propose future developing directions, such as modular approaches, data augmentation, and advanced attention mechanisms.

Pollen hydration, germination, and tube growth are vital processes for the successful fertilization of flowering plants. These processes involve complex signaling pathways. Reactive oxygen species (ROS) generated in apoplast involves signaling for the cell wall expansion during tube growth, however molecular regulators are less known. We identified pollen-specific receptor-like kinase (OsPRK) family genes from rice (Oryza sativa), which have conserved leucine-rich repeat (LRR) and kinase domains. To understand the function of these genes, we produced single and triple mutations for OsPRK1, OsPRK2, and OsPRK3 using the clustered regularly interspaced palindromic repeats (CRISPR/Cas9) system. Among these mutants, triple knockout (KO) lines (osprk1/2/3) exhibited the male-sterile phenotype with normal vegetative growth and floret formation. Through cytological analysis, we confirmed that the reduced seed fertility was due to defects in pollen hydration and germination with low ROS accumulation. This defect of pollen germination was partially recovered by treatment with exogenous H₂O₂. We also confirmed that OsPRKs could interact with the LRR extension protein. Our results suggest that rice PRKs redundantly play a role in ROS signaling for pollen hydration and germination, and fertility can be controlled by exogenous application.

Silicon (Si) plays a crucial role in plant growth, development, and stress tolerance. However, in some consumable plant products, such as fruits, Si deposition leads to the formation of a white powdery layer known as bloom, which diminishes glossiness and consumer appeal. Despite its significance, the genetic basis of bloom formation remains largely unexplored. Here, we identified a unique cucumber backbone parent line exhibiting bloomless fruit, which was designated bloomless cucumber 1 (bec1). Map-based cloning of the bec1 locus revealed that BEC1, harboring a natural C-to-T variation at the 754th base of its coding region, is a strong candidate gene for the bloomless trait. Functional validation through gene-editing mutants and BEC1::BEC1-GFP transgenic lines confirmed that BEC1, encoding a Si efflux transporter, is responsible for bloom formation. Mutation of BEC1 impaired Si uptake, thereby preventing the deposition of Si on the surface of glandular trichomes and resulting in bloomless fruits. Additionally, Si deficiency in BEC1 mutants compromised resistance to Corynespora cassiicola and chilling stress. Interestingly, grafting bec1 scions onto bloom rootstocks restored the Si accumulation and stress resistance, while maintaining bloomless phenotype. Overall, our findings elucidate the role of BEC1 in bloom formation and provide a valuable genetic target for breeding bloomless cucumber with enhanced stress resilience.

Sex chromosomes have evolved independently in numerous lineages across the Tree of Life, in both diploid-dominant species, including many animals and plants, and the less studied haploid-dominant plants and algae. Strict genetic sex determination ensures that individuals reproduce by outcrossing. However, species with separate sexes (termed dioecy in diploid plants, and dioicy in haploid plants) may sometimes evolve different sex systems, and become monoicous, with the ability to self-fertilize. Here, we studied dioicy-monoicy transitions in the ancient liverwort haploid-dominant plant lineage, using three telomere-to-telomere gapless chromosome-scale reference genome assemblies from the Ricciaceae group of Marchantiales. Ancestral liverworts are believed to have been dioicous, with U and V chromosomes (chromosome 9) determining femaleness and maleness, respectively. We confirm the finding that monoicy in Ricciocarpos natans evolved from a dioicous ancestor, and most ancestrally U chromosomal genes have been retained on autosomes in this species. We also describe evidence suggesting the possible re-evolution of dioicy in the genus Riccia, with probable de novo establishment of a sex chromosome from an autosome (chromosome 5), and further translocations of genes from the new sex chromosome to autosomes. Our results also indicated that micro-chromosomes are consistent genomic features, and may have evolved independently from sex chromosomes in Ricciocarpos and Riccia lineages.

Maize (Zea mays L.) growth and yield are severely limited by drought stress worldwide. Stomata play crucial roles in transpiration and gas exchange and are thus essential for improving plant water-use efficiency (WUE) to help plants deal with the threat of drought. In this study, we characterized the maize dsd1 (decreased stomatal density 1) mutant, which showed defects in stomatal development, including guard mother cell differentiation, subsidiary cell formation and guard cell maturation. DSD1 encodes the basic helix-loop-helix transcription factor INDUCER OF CBF EXPRESSION b (ZmICEb) and is a homolog of ICE1 in Arabidopsis (Arabidopsis thaliana). DSD1/ZmICEb is expressed in stomatal file cells throughout stomatal development and plays a conserved role in stomatal development across maize and Arabidopsis. Mutations in DSD1/ZmICEb dramatically improved drought tolerance and WUE in maize and reduced yield losses under drought conditions. Therefore, DSD1/ZmICEb represents a promising candidate target gene for the genetic improvement of drought tolerance in maize by manipulating stomatal density.

Diverse heterotic groups have been developed in China over several decades, but their genomic divergences have not been systematically studied after improvement. In this study, we performed Maize6H-60K array of 5,822 maize accessions and whole-genome re-sequencing of 150 inbred lines collected in China. Using multiple population structure analysis methods, we established a genetic boundary used to categorize heterotic groups and germplasm resources. We identified three chloroplast–cytoplasmic types that evolved during adaptation to diverse climatic environments in maize through phylogenetic and haplotype analyses. Comparative analyses revealed obvious genetic differences between heterotic groups and germplasm resources at both the chloroplast and nuclear genome levels, especially in the unique heterotic groups HG1 and HG2, which exhibited distinct regionality and genetic uniqueness. The divergent differentiation of heterotic groups from germplasm resources was driven by differential selection in specific genomic regions. Genome-wide selective sweep analysis identified core selected regions and candidate selected genes associated with traits between heterotic groups, highlighting that stress response- and plant defense-related genes were selected for environmental adaptation across a broad latitudinal range in China. Meanwhile, a genome-wide association study analysis provided evidence that core selected genes served as an important candidate gene pool with a potential role in genetic improvement. Gene exchanges among heterotic groups, which avoided the predominant heterotic patterns as much as possible, occurred to achieve population improvement during modern maize breeding. This study provides insights into the population differentiation and genetic characteristics of heterotic groups, which will facilitate the utilization of germplasm resources, the creation of novel maize germplasm, and the optimization of heterotic patterns during future maize breeding in China.

Successful reproduction depends on the stable germination and growth of the pollen tubes (PT). However, the molecular mechanisms involved in rice PT growth and development remain largely unknown. In a previous study, microarray transcriptome analysis identified 627 genes preferentially expressed in the tricellular and germinating pollen of rice (i.e., Oryza sativa ssp. japonica). To elucidate key genes involved in the gene transfer process facilitated by male gametophytes, we systematically screened T-DNA lines containing disrupted sequences that corresponded to these 627 genes and analyzed the genotypes of heterozygote progeny from 107 T-DNA-indexed lines covering 105 genes. We found that 42 lines exhibited a distorted segregation ratio among the wild-type (WT), heterozygote (HT), and homozygote (HM) genotypes, which deviated from the expected Mendelian ratio of 1:2:1 (WT:HT:HM). Further characterization using CRISPR/Cas9 mutants revealed that knockout mutants of certain genes that exhibited segregation distortion in the T-DNA insertion region were completely sterile. Moreover, even when T-DNA insertion lines followed Mendelian segregation patterns, sterility could be induced by simultaneously mutating functionally redundant genes, thereby overcoming genetic compensation. Interestingly, although some T-DNA insertion lines exhibited segregation ratios approximating 1:1:0, the corresponding CRISPR/Cas9 mutants produced homozygous seeds and showed partial sterility. Partial sterility suggests that despite mutant pollen grains being less competitive than WT pollen, they retain their fertilization potential under relaxed competition from WT pollen. Beyond mutant-based analysis, transcriptomic profiling of sterile mutant lines provided additional insight into the regulatory relationship between key germination regulators and the 105 target genes studied here. Overall, this study demonstrates the effectiveness of a multi-pronged strategy to accelerate the identification of defective phenotypes using mutant studies and provides valuable genetic resources for inducing novel male sterility in rice.

Avena barbata, a wild oat species within the genus Avena, is a widely used model for studying plant ecological adaptation due to its strong environmental adaptability and disease resistance, serving as a valuable genetic resource for oat improvement. Here, we phased the high-quality chromosome-level genome assembly of A. barbata (6.88 Gb, contig N50 = 53.74 Mb) into A (3.57 Gb with 47,687 genes) and B (3.31 Gb with 46,029 genes) subgenomes. Comparative genomics and phylogenomic analyses clarified the evolutionary relationships and trajectories of A, B, C and D subgenomes in Avena. We inferred that the A subgenome donor of A. barbata was Avena hirtula, while the B subgenome donor was probably an extinct diploid species closely related to Avena wiestii. Genome evolution analysis revealed the dynamic transposable element (TE) content and subgenome divergence, as well as extensive structure variations across A, B, C, and D subgenomes in Avena. Population genetic analysis of 211 A. barbata accessions from distinct ecotypes identified several candidate genes related to environmental adaptability and drought resistance. Our study provides a comprehensive genetic resource for exploring the genetic basis underlying the strong environmental adaptability of A. barbata and the molecular identification of important agronomic traits for oat breeding.

The development of a single and multiplex gene editing system is highly desirable for either functional genomics or pyramiding beneficial alleles in crop improvement. CRISPR/Cas12i3, which belongs to the Class II Type V-I Cas system, has attracted extensive attention recently due to its smaller protein size and less restricted canonical “TTN” protospacer adjacent motif (PAM). However, due to its relatively lower editing efficiency, Cas12i3-mediated multiplex gene editing has not yet been documented in plants. Here, we fused four 5′ exonucleases (Exo) including T5E, UL12, PapE, ME15 to the N terminal of an optimized Cas12i3 variant (Cas12i3-5M), respectively, and systematically evaluated the editing activities of these Exo:Cas12i3-5M fusions across six endogenous targets in rice stable lines. We demonstrated that the Exo:Cas12i3-5M fusions increased the gene editing efficiencies by up to 12.46-fold and 1.25-fold compared with Cas12i3 and Cas12i3-5M, respectively. Notably, the UL12:Cas12i3-5M fusion enabled robust single gene editing with editing efficiencies of up to 90.42%–98.61% across the six tested endogenous genes. We further demonstrated that, although all the Exo:Cas12i5-5M fusions were capable of multiplex gene editing, UL12:Cas12i3-5M exhibited a superior performance in the simultaneous editing of three, four, five or six genes with efficiencies of 82.76%, 61.36%, 52.94%, and 51.06% in rice stable lines, respectively. Together, we evaluated different Exo:Cas12i3-5M fusions systemically and established UL12:Cas12i3-5M as the more robust system for single and multiplex gene editing in rice. The development of an alternative robust single and multiplex gene editing system will enrich plant genome editing toolkits and facilitate pyramiding of agronomically important traits for crop improvement.

NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1), the receptor for salicylic acid (SA), plays a central role in the SA-mediated basal antiviral responses. Recent studies have shown that two different plant RNA viruses encode proteins that suppress such antiviral responses by inhibiting its SUMOylation and inducing its degradation, respectively. However, it is unclear whether targeting NPR1 is a general phenomenon in viruses and whether viruses have novel strategies to inhibit NPR1. In the present study, we report that two different positive-sense single-stranded RNA (+ssRNA) viruses, namely, alfalfa mosaic virus (AMV) and potato virus X (PVX); one negative-sense single-stranded RNA (−ssRNA) virus (calla lily chlorotic spot virus, CCSV); and one single-stranded DNA virus (beet severe curly-top virus, BSCTV) that also encode one or more proteins that interact with NPR1. In addition, we found that the AMV-encoded coat protein (CP) can induce NPR1 degradation by recruiting S-phase kinase-associated protein 1 (Skp1), a key component of the Skp1/cullin1/F-box (SCF) E3 ligase. In contrast, the BSCTV-encoded V2 protein inhibits NPR1 function, probably by affecting its nucleocytoplasmic distribution via the nuclear export factor ALY. Taken together, these data suggest that NPR1 is one of the central hubs in the molecular arms race between plants and viruses and that different viruses have independently evolved different strategies to target NPR1 and disrupt its function.

Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early-Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably co-occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co-occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups.