Drought is a major abiotic stress that poses a significant threat to plants. Basic leucine zipper (bZIP) transcription factors (TFs) are important for plant stress signal transduction. However, the specific functions and molecular mechanisms of bZIP TFs under drought stress are still unclear. In this study, a BpbZIP4 TF of Betula platyphylla (birch) that responds strongly to drought stress was identified. Transgenic birch plants with BpbZIP4 overexpression and RNA interference were developed for gain- and loss-of-function assays. Results from phenotypic, staining, and physiological analyses showed that BpbZIP4 significantly enhances drought resistance and promotes root growth in birch. A four-layer drought-responsive gene regulatory network (GRN) was constructed based on BpbZIP4 transgenic lines. Chromatin immunoprecipitation-polymerase chain reaction (ChIP-PCR) and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays verified the putative interactions among genes at different hierarchical levels, confirming the reliability of the GRN. TF-Centered Y1H, ChIP, and β-glucuronidase (GUS) assays revealed that BpbZIP4 regulates the expression of second-layer TFs in the GRN by binding to two novel elements and one photosynthesis-responsive element. Furthermore, six randomly selected second-layer GRN TFs (BpMYB61, BpBEL1, BpWOX4, BpbHLH100, BpZAT11, and BpHB17), when transformed into birch plants, significantly influence birch’s drought tolerance. These results indicate that BpbZIP4 regulates second-layer TFs, thereby hierarchically relaying signals to bottom-layer functional genes, engaging multiple biological pathways, and ultimately enhancing drought resistance in birch. Collectively, these findings clarify the drought regulatory mechanism of BpbZIP4 and identify additional key genes for breeding drought-resistant birch varieties.

The tender shoots of tea plant [Camellia sinensis (L.) Kuntze] contain characteristic flavor metabolites such as catechins, caffeine, and theanine, which are the raw materials for making various types of high-quality tea. The gene expression profiles with spatial information for tea shoots remain unclear, which has hindered the exploration of precise regulatory mechanisms of these characteristic metabolites in different cell types. Here, we provided a high-throughput analysis of the spatial gene expression of the tea shoot, including the apical bud, young leaf, and stem. The genome-wide expression pattern was delineated into nine representative spatial coexpression clusters, and cell type identification was achieved by integrating histological structures with marker gene annotation. The dynamic differentiation processes of cells in leaf and bud were revealed through the reconstruction of pseudotemporal trajectories, uncovering the coupling relationship between spatial organization and developmental progression. Gene Ontology enrichment analysis indicated that different clusters were enriched in functional pathways such as photosynthesis, cell wall construction, substance transport, and hormone response during differentiation, demonstrating their stage-specific expression throughout development. Additionally, we found that structural genes associated with the metabolism of catechins, theanine, and caffeine exhibited distinct spatial expression patterns across various tissues. Based on functional verification, we identified that the transcription factor gene CsTCP4 could positively regulate the biosynthesis of catechins and the hydrolysis of theanine. In conclusion, the spatial transcriptome atlas provides a foundational dataset for understanding gene expression heterogeneity in tea shoots and expands our understanding of the synergistic regulation of theanine and catechin metabolism in tea.

Genomic prediction (GP) in mango breeding faces challenges due to the species’ complex biology, long cycles, and limited reference populations. To accelerate genetic improvement, this study integrated data from diverse global populations to increase the reference population size. It included three mango collections reserved in Australia (225), USA (161), and China (224), totaling 610 individuals. Fruit weight (FW) and total soluble solids (TSS) were measured in multiple datasets, while several other traits were measured in specific datasets. We evaluated genetic diversity, performed genome-wide association studies (GWAS), and assessed GP accuracy using standard, genotype-by-environment (GxE), and multitrait models, both within and across collections. Findings revealed a highly admixed genetic structure, with faster linkage disequilibrium (LD) decay in the Chinese collection, indicating higher genetic diversity. Data integration significantly enhanced GWAS power, identifying 19 quantitative trait loci (QTLs) for FW and 9 for TSS. GxE models consistently achieved higher or comparable prediction accuracies for FW and TSS compared to the non-GxE models, especially when combining Australian and US collections. This was not the case when predicting into or from the Chinese collection, mostly due to differences in the phenotyping protocol. While single-trait models performed comparably to multitrait models in predicting new individuals (Cross-Validation: CV1), multitrait models significantly improved prediction accuracy in scenarios with incomplete phenotypic records (CV2). This study demonstrates that strategic global data integration significantly enhances GWAS power and GP accuracy in mango. This collaborative approach is crucial for developing more efficient and accelerated breeding programmes for mango and other perennial trees.

Plant architecture can directly impact on tomato (Solanum lycopersicum) fruit production. Our previous work has demonstrated an important role of microRNA156a (miR156a) in determining the lateral branches mainly by regulating SQUAMOSA PROMOTER BINDING PROTEIN LIKE 13 (SPL13) expression in tomato. However, the regulatory pathway by which the miR156a-SPL13 module regulates branching remains obscure. In this study, we examined the relationship between SPL13 and two other genes, BRANCHED1b (BRC1b) and DWARF (DWF), which have previously been known to regulate lateral branch development in tomato. Our findings indicate that SPL13 directly interacts with the promoters of BRC1b and DWF, enhancing BRC1b expression while inhibiting DWF expression, thereby finely regulating lateral branch development in tomatoes. Additionally, overexpression of BRC1b or knockout of DWF were found to rescue the increased lateral branch outgrowth phenotype of the spl13 mutant plants. Furthermore, brassinosteroid (BR) content was high in spl13 mutant plants, supporting the notion that SPL13 negatively regulates BR biosynthesis. These findings suggest that SPL13 serves as an activator of the BR signaling downstream gene BRC1b and a repressor of the BR biosynthesis gene DWF to regulate lateral branch outgrowth in tomato. One-sentence summary: The miR156a-targeted transcription factor SlSPL13 regulates plant architecture in tomato.

Fatty acid-derived volatile organic compounds (VOCs), especially C ₆ and C ₉ aldehydes and alcohols, are vital contributors to the fresh aroma of fruits. However, the specific volatiles responsible for this freshness and their biosynthetic regulatory mechanisms remain poorly characterized in litchi (Litchi chinensis Sonn.). In this study, we systematically characterized the VOC profiles of 24 representative litchi cultivars and identified four critical compounds- trans,cis-2,6-nonadien-1-ol, 1-hexanol, (E)-6-nonenal, and (E)-2-hexen-1-ol-as primary determinants of fresh-aroma variation. Weighted gene co-expression network analysis of the transcriptomic data, corroborated by RT-qPCR, revealed a strong positive correlation between the expression of LcLOX7 and the abundance of these key fresh-aroma volatiles. Functional characterization via LcLOX7 overexpression in litchi callus and tomato fruits validated its pivotal role in enhancing the biosynthesis of fatty acid-derived VOCs, specifically C ₉ volatiles. Subsequent in vivo and in vitro assays confirmed the direct transcriptional activation of LcLOX7 by two transcription factors (TF), LcARF17 and LcRAP2-4. The expression patterns of these TFs correlated with the accumulation of key fresh-aroma volatiles across different litchi cultivars and paralleled LcLOX7 expression during fruit ripening. Moreover, overexpression and silencing of LcARF17 or LcRAP2-4 in litchi callus validated their regulatory function in promoting C ₉ volatile synthesis. Our findings collectively support a regulatory model wherein the LcARF17/LcRAP2-4–LcLOX7 module orchestrates the biosynthesis of fresh aroma in litchi fruit. Notably, this study provides the first evidence that ARF transcription factor participates in the formation of fresh fruit aroma, thereby offering novel insights for the molecular breeding of flavor quality in fruit crops.

Kiwifruit plants are much damaged by several days of waterlogging stress. The effect can be a serious problem for the growers in the lowlands or plain areas where floods cannot be drained timely. Actinidia valvata is a polyploid species that has been widely used as waterlogging resistant rootstock in kiwifruit cultivation. Here we report haplotype-resolved chromosome-scale assemblies of an A. valvata male plant ‘DE’, defining two subgenomes, a diploid closely related to Actinidia polygama and an autotetraploid closely related to Actinidia macrosperma as their ancestral contributors, respectively, together to form an allohexaploid. Genome-wide comparisons of the assembled 174 pseudochromosomes with nine distinct Actinidia species revealed the genomic structure, phylogeny and duplication history of ‘DE’ genome. Evolutionary analyses suggest that it was formed ∼0.44 to 0.88 Mya and evolved by a recent alloploid addition to an autotetraploid ancestor. Annotation of sex determining genes ( SyGl and FrBy ) on Y chromosome unraveled that the chromosomal location and organization of sex determining region (SDR) are conserved to and share an identical lineage with A. polygama , the diploid ancestor. Comprehensive transcriptome analysis indicates that its enhanced waterlogging tolerance is due to the restricted activation of anaerobic survival genes and the consequence with prolonged carbohydrate supply to keep the root system quiescently alive under hypoxia. Our study provides valuable genomic resources and offers insights into the evolution and the underlying mechanism of enhanced waterlogging tolerance of A. valvata hexaploid.

Sucrose synthase (SUS) is a pivotal enzyme bridging primary carbon metabolism and secondary biosynthesis in plants. In Panax notoginseng , we demonstrate that sucrose synthase 1 (PnSUS1) serves as a metabolic bottleneck for saponin glycosylation by supplying UDP-glucose. PnWRKY38 was identified as a WRKY transcription factor whose expression correlated with both PnSUS1 and saponin accumulation. Overexpression of PnWRKY38 could up-regulate PnSUS1 expression by 3.5-fold, increase SUS enzyme activity by 2.8-fold, and elevate UDP-glucose pools by 68%. Consequently, the total content of ginsenosides Rg1, Rb1, and Rd rose by 2.1–2.4-fold. Conversely, PnSUS1 or PnWRKY38 suppression reduced UDP-glucose available and saponin biosynthesis by > 50%. Y1H and luciferase assays indicated that PnWRKY38 directly activated PnSUS1 expression by binding to W-box motifs in its promoter. These results not only illustrate the specific function that PnSUS1 executes in UDPG biosynthesis but also reveal a new WRKY transcriptional regulatory module regulating notoginsenosides production.

Trifolium pratense L. is a multifunctional crop of agronomic importance for forage, horticulture, and ecological restoration. However, the lack of a high-quality genome assembly and the limited representation of genetic diversity by a single reference have impeded its genetic research and molecular breeding. Here, we present the first telomere-to-telomere (T2T) gap-free genome for the diploid (2n = 2 x = 14) cultivarT. pratense cv. ‘Zhongtian No. 5’ (TpraZt5), assembled through an integrated sequencing strategy. The 390.94 Mb assembly demonstrates high quality, with a base accuracy > 98.5%, 98.1% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness, a long terminal repeat assembly index of 25.65, and a contig N50 of 52.95 Mb. We annotated 35 971 protein-coding genes and found repeat sequences accounting for 59.6% of the genome. The assembly resolved all seven centromeres and 14 telomeres, providing unprecedented insight into these complex genomic regions. We further constructed a 480.76 Mb pan-genome by integrating two additional accessions, which classified genes into core (70.2%), dispensable (25.3%), and private (4.5%) sets. Comparative genomic analyses identified 606 species-specific genes in TpraZt5 and uncovered extensive structural variations. Functional investigations revealed four species-specific genes and six contracted genes associated with isoflavonoid biosynthesis, two expanded chlorophyll a–b-binding proteins, and seven expanded auxin-related genes that may contribute to the high productivity of TpraZt5. Additionally, 44 Gypsy-type transposons within the zeatin biosynthesis pathway were identified as potential regulators of trifoliate leaf development. These genomic resources substantially improve structural annotation and functional characterization, providing vital tools for gene discovery and enhancing molecular breeding initiatives in red clover.

Glutamate synthase (GOGAT) is crucial for nitrogen metabolism and amino acid biosynthesis in tea plants, yet the post-transcriptional regulation of GOGAT remains unclear. This study identified miR1507c as a direct interactor of CsNADH-GOGAT, confirmed by DLR assays and 5′ RLM-RACE. Notably in tobacco, the relative luciferase activity in plants overexpressing CsNADH-GOGAT and co-expressing miR1507c + CsNADH-GOGATm3 (mutant) were significantly higher than in those co-expressing miR1507c + CsNADH-GOGAT. Overexpression of miR1507c also significantly suppressed the expression of CsNADH-GOGAT and endogenous NtNADH-GOGAT homologs. Leveraging lncRNA sequencing, we screened lncR12304.1 as a ceRNA that regulates CsNADH-GOGAT by competitively binding to miR1507c. Cytoplasmic co-localization (validated by FISH) and direct interaction (confirmed by DLR assays) between lncR12304.1 and miR1507c were established. RNA pull down-qPCR further demonstrated miR1507c binding to both lncR12304.1 and CsNADH-GOGAT. The regulatory axis lncR12304.1–miR1507c– CsNADH-GOGAT was substantiated in vivo: (i) in tea roots/shoots under varying nitrogen treatments and following miR1507c suppression using Antagomir, and (ii) in tobacco via transient co-overexpression. Collectively, our results demonstrate the establishment of this ceRNA network and its role in regulating glutamate and theanine biosynthesis.

The transcription factor BRASSINAZOLE-RESISTANT1 ( BZR1 ) plays a crucial role not only in plant responses to various biotic and abiotic stresses but also serves a critical function in plant growth and development. In this study, we analyzed the origin and evolution of the BZR family in plants. Then, we identified nine CaBZR1 genes from the pepper pan-genome and performed bioinformatics analyses. Through the integration of transcriptome data analysis with our prior bioinformatics findings, we have identified and selected a specific member of the CaBZR1 family, CaBZR1.2 , for further comprehensive investigation. We systematically investigated the biological function of CaBZR1.2 in pepper through classical reverse genetics approaches and subsequently identified proteins that interact with CaBZR1.2. After inhibiting the expression of CaBZR1.2 via virus-induced gene silencing (VIGS), the growth of pepper lateral branches was significantly suppressed, whereas heterologous overexpression of CaBZR1.2 increased lateral branch number in tomato. This result confirms the key role of CaBZR1.2 in the development of pepper lateral branches. Furthermore, protein–protein interaction assays confirmed that the Sucrose Nonfermenting 1-Related Protein Kinase 1 β subunit 2 (CaSnRK1 β 2) protein interacts with CaBZR1.2, with subsequent analyses revealing that these two proteins modulate pepper lateral branch development through a mutually antagonistic regulatory mechanism. This study reveals a novel mechanism by which CaBZR1.2 and CaSnRK1 β 2 coordinately regulate lateral branch development in pepper, providing candidate genes and a theoretical basis for the molecular breeding for pepper plant architecture.

Somatic embryogenesis is a crucial biotechnological approach for effectively addressing garlic variety degeneration and improving yield and quality. Previous studies have demonstrated that the long noncoding RNA 125175 (lncRNA125175) is specifically induced and expressed during somatic embryogenesis, and may act as an endogenous target mimic of AsmiR393h to participate in the regulation of somatic embryogenesis. On this basis, the present study systematically elucidated the functions of the lncRNA125175/AsmiR393h/ AsTIR1 regulatory module and its upstream transcriptional mechanism. First, transient expression assays in tobacco leaves and protoplast experiments in garlic suggested that lncRNA125175 served as a competing endogenous RNA (ceRNA) to sequester AsmiR393h, thereby attenuating its post-transcriptional cleavage of the target gene AsTIR1. Promoter analysis revealed that all core components of this module contain auxin cis-acting elements, and the promoter activities of lncRNA125175 and AsTIR1 are significantly induced by exogenous auxin, suggesting that this ceRNA network is precisely regulated by auxin signaling. Further weighted gene co-expression network analysis identified the auxin response factor AsARF16 as a key upstream regulator. Yeast one-hybrid and two-hybrid assays indicated that AsARF16 can directly bind to the promoter of lncRNA125175, and interact with the transcription factor AsWRKY31 and the auxin signaling factor AsIAA33 to form a transcriptional activation complex. In conclusion, this study uncovers a cascade pathway from auxin signal perception (the AsARF16 complex) to transcriptional activation (lncRNA125175), followed by post-transcriptional ceRNA regulation. It systematically clarifies the molecular mechanism underlying its precise regulation of garlic somatic embryogenesis, providing a critical theoretical basis for the targeted improvement in garlic regeneration efficiency and genetic transformation systems.

Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are revolutionizing precision genome editing and gene expression control in crop plants. While effective CRISPR-Cas applications traditionally rely on labor-intensive stable genetic transformation to deliver Cas nucleases and guide RNAs into plant cells, plant viruses have emerged as a faster and efficient alternative, a strategy known as virus-induced gene editing (VIGE). Cas12a, Class 2 Type V CRISPR nucleases, are an alternative to broadly used Cas9 for plant genome engineering. Both kind of nucleases offer precise editing, but some Cas12a unique features make them particularly well suited for VIGE. In this study, we first used a tobacco rattle virus vector to compare editing efficiency of various target sequences and CRISPR RNA (crRNA) architectures in Lachnospiraceae bacterium ND2006 Cas12a (LbCas12a)-expressing Nicotiana benthamiana plants, evaluating results in infected tissues and seeds. Next, we developed a tobacco etch virus (genus Potyvirus)-derived vector efficiently delivering crRNAs throughout the plant. This approach enabled generation of plants with all four edited alleles in the allotetraploid N. benthamiana through in vitro regeneration from infected leaves, and to produce edited non-infected progeny, although at a very low frequency. We then demonstrated the successful application of the potyviral vector for VIGE in agronomically important crops, such as tomato or cultivated tobacco. Finally, we replicated this design using two other potyviral vectors, turnip mosaic virus, and lettuce mosaic virus. Given the conserved biological properties among potyviruses, we believe these findings are broadly applicable to the largest genus of plant RNA viruses, significantly expanding the host range of the VIGE technology.

Although triploid poplars have larger cells and leaves than their diploid counterparts, the molecular mechanisms underlying this disparity remain elusive. Here, we found that PpnGATA8 and PpnGRF5 were significantly upregulated in triploid poplars through differential gene expression analysis between diploid and triploid poplars. Furthermore, through genetic transformation in poplar, it was found that both PpnGATA8 and PpnGRF5 positively regulated poplar cell size, resulting in increased leaf size and improved photosynthetic efficiency. RNA-sequencing of PpnGATA8-overexpressing poplars showed that PpnGATA8 promotes expression of PagGRF5 and PagXTH9. Yeast one-hybrid system, electrophoretic mobility shift assay, and dual-luciferase assay were employed to substantiate that PpnGATA8 directly regulated PagGRF5 and PagXTH9 expression. Meanwhile, PpnGRF5 positively regulates the expression of PagXTH9. Poplar protoplast cotransformation assays further proved that coexpression of PpnGATA8 and PpnGRF5 had the strongest effect on promoting PagXTH9 expression. Moreover, overexpression of PpnXTH9 also significantly increased poplar cell and leaf size. Therefore, GATA8, GRF5, and XTH9 formed a feed-forward regulatory loop to regulate plant cell size. Our results are of major significance for revealing the molecular regulatory mechanisms of plant cell size and leaf development, especially the genetic basis of giant variation in cells and leaves in polyploid plants.

DNA-binding with one finger (DOF) proteins are plant-specific transcription factors (TFs) that play critical roles in plant growth and development, including nitrogen metabolism, but the roles of these TFs in the nitrogen response of tomato ( Solanum lycopersicum) remain largely unexplored. Here, we show that overexpressing the DOF gene SlDOF3.4 enhanced the growth of tomato seedlings under low nitrogen (LN) conditions, resulting in longer roots and greater biomass accumulation. Multiple assays demonstrated that SlDOF3.4 interacts with another DOF family member, SlCDF4, and that both TFs bind to the promoters of the N-assimilation gene Glutamine synthetase ( SlGS) and the jasmonic acid (JA) biosynthesis gene Lipoxygenase ( SlLOXD), suggesting that SlDOF3.4 and SlCDF4 cooperatively regulate nitrogen assimilation and JA biosynthesis. In support of this notion, co-expressing SlCDF4 and SlDOF3.4 enhanced the binding activity of SlDOF3.4 to the SlGS and SlLOXD promoters in a dual-luciferase reporter assay. Under LN conditions, genes related to nitrogen assimilation and JA biosynthesis were markedly upregulated in SlDOF3.4-overexpressing and SlCDF4-overexpressing tomato plants. Knockout of SlCDF4 impaired plant growth under LN conditions, a phenotype that was partially alleviated by treatment with methyl jasmonate. These results provide insight into the roles of DOF TFs in nitrogen assimilation and JA biosynthesis in crops.

Flowering time is a critical trait in common bean ( Phaseolus vulgaris), influencing yield stability and geographical adaptation. While PvCOL2 and PvPHYA3 are known regulators under long-day (LD) conditions, we identified a third major locus through fine-mapping of the QTL DTF9.4/DTF9.5. Within this region, PvE1 ( Phvul.009G204600) emerged as a strong candidate, sharing sequence homology with the soybean E1 gene and acting as a transcriptional repressor of flowering. A naturally occurring 34-bp deletion in its 3′ UTR ( e1-del) was associated with early flowering and reduced photoperiod sensitivity. Expression analysis revealed that PvE1 displays a circadian rhythm under LD conditions, with a bimodal pattern peaking in the morning and early evening, resembling that reported for soybean E1. Phenotypic analyses of near-isogenic lines (NILs) confirmed that PvE1 delays flowering specifically under LD and also influences plant architecture, as e1 genotypes exhibited reduced plant height and node number. Functional dissection revealed that PvE1 and PvCOL2 act in partially redundant pathways to repress PvFT gene expression, with evidence of functional interaction. This regulatory module resembles that in soybean but shows species-specific divergence likely shaped by separate evolutionary paths. Genetic diversity analysis identified two rare PvE1 alleles, e1-del and e1-fs, both associated with earlier flowering when combined with col2 mutations, indicating additive effects and reduced photoperiod sensitivity. Although functional validation by transformation was not performed, the use of NILs provides robust genetic evidence of PvE1 activity. Together, these findings establish PvE1 as a conserved legume-specific floral repressor in common bean, with novel allelic variants that can be exploited to develop early-flowering, photoperiod-insensitive cultivars adapted to temperate and high-latitude regions.

Understanding the genetic control of fruit composition traits in interspecific grapevines ( Vitis spp.) is crucial when breeding new cultivars with desirable fruit chemistry. To address this, a genome-wide association study (GWAS) was conducted using 587 genotypes derived from three elite selections. This study spanned 3 years (2020–2022) and with phenotyping conducted at three different timepoints within each season for a total of nine phenotyping events focused on nine fruit traits. Several strong and stable quantitative trait locus (QTL) associations were identified on chromosomes 6, 16, and 17 across multiple phenotyping events for most sugar- and acid-related traits. Notably, putative sugar transporter genes Vitvi16g00860 and Vitvi16g00861 on chromosome 16, which facilitate the movement of sugars and K ⁺ ions across membranes, were found to be associated with all sugar and acid traits studied. Additionally, several QTLs on chromosomes 1–5, 7, 14, and 18 were identified for various fruit quality traits across different phenotyping events. We determined functional connections between traits and scrutinized candidate genes by utilizing gene ontology annotations for genes located near significant SNPs. We also highlighted the effect of different forms of phenotype (best linear unbiased predictions and unmodified) in suppressing certain QTL associations. This GWAS study focused on fruit quality in grapes, establishing a necessary knowledge base regarding the genetic architecture of these traits to aid molecular breeders in further improving them.

Downy mildew, caused by the biotrophic oomycete Hyaloperonospora parasitica, is one of the most devastating diseases affecting global Brassica production. Despite its significant impact, the molecular and cellular mechanisms underlying both compatible and incompatible interactions of H. parasitica and Brassica rapa remain poorly understood. In this study, we identified an H. parasitica RXLR effector, DM459, which demonstrates the ability to induce autophagy by targeting BraATG8i, a key component of autophagosome formation, as confirmed by multiple in vivo and in vitro assays. BraATG8i is a positive regulator of defense against downy mildew, which was determined by the BraATG8i overexpression and RNA interference in B. rapa. Furthermore, the effector DM459 interacts with BraATG8i as well as BraATG4, BraATG3, and BraATG7-core proteins required for autophagosome assembly. This interaction-enhanced autophagy contributed to elevated disease resistance. Moreover, pathogen inoculation or DM459 presence stimulated salicylic acid (SA) biosynthesis, which in turn activated BraATG8i expression and further elevated autophagy. Collectively, our results demonstrated that the effector DM459 triggers autophagy by directly targeting BraATG proteins and simultaneously activates SA signaling, which consequently enhances plant resistance to downy mildew.

Cowpea ( Vigna unguiculata) is a versatile legume crop providing a critical source of grain, vegetable and forage globally. Cultivated cowpea is classified into two main subspecies, subsp. sesquipedalis for fresh-pod vegetable and subsp. unguiculata for grain production. Here, we present two complete telomere-to-telomere (T2T) assemblies for the grain-type inbred lines HJD and vegetable-type FC6 through integrating PacBio HiFi reads, Oxford Nanopore ultralong reads, and Hi-C data. The T2T genomes demonstrated improved contiguity, completeness, and accuracy compared to existing genomes, revealing clear telomeric and centromeric features. Comparative analysis of the T2T genomes highlighted inversions underlying subspecies divergence in cowpea. Evolutionary analysis uncovered contraction of gene families related to symbiosis in HJD, consist with its reduced root nodules compared to FC6. Distribution and composition of tandem repeat arrays and transposable elements in centromeric regions were largely conserved in cowpea, but displayed pronounced variation among Phaseoleae. Furthermore, frequent shifts of centromeric locations coincided with inversions found in Phaseoleae. Overall, this study provides a set of fundamental resources for cowpea improvement and enhances our understanding of cowpea subspecies divergence and genome evolution in Phaseoleae.

Transposable elements constitute a large portion of plant genomes and, due to their ability to change their genomic localization, they largely contribute to genome evolution and adaptability. Miniature inverted-repeat transposable elements (MITEs), due to their small size and localization near genes, seem to be a major source of potential functional variability. Effects imposed by MITEs on the expression of associated genes through redistributing cis-regulatory elements have been postulated, but our knowledge in this area still remains limited. We showed that MITEs in the carrot genome are enriched with binding sites for LHY/RVE transcription factors (TFs). Experimental validation using DcLHY-DAP-seq not only confirmed the enrichment of DcLHY binding sites within MITEs but also demonstrated that elements from the DcTourist_15 family likely play a key role in redistributing these TF binding sites. We showed that insertional polymorphisms of DcTourist_15 correspond with changes in the expression of associated genes, both in control conditions and in response to heat stress. In addition to placing individual genes under the control of DcLHY/RVE TFs, DcTourist_15 copies were found in promoters of genes involved in sulfur metabolism and cysteine biosynthesis. The enrichment of rice MITEs in OsLHY binding sites suggests the phenomenon of MITE-driven rewiring of LHY/RVE regulation may be more widespread across the plant kingdom. Carrot MITEs, particularly those from the DcTourist_15 family, drive evolution of the carrot genome, especially in the context of stress responsiveness, as they possibly fine-tune gene expression by redistributing binding sites for TFs from the LHY/RVE family.

Ripening inducing factor (RIF) is a key NAC transcription factor (TF) regulating strawberry fruit ripening. Previous studies using RIF- RNAi and overexpression lines in Fragaria × ananassa and CRISPR knock-out lines in F. vesca have established the role of RIF in controlling ABA biosynthesis and signaling, cell wall remodeling, and secondary metabolism. In this study, we deciphered FaRIF’s transcriptional regulatory network by combining ChIP-seq-based identification of its direct targets with an analysis of FaRIF -RNAi transcriptome data. These analyses revealed FaRIF’s direct role in multiple aspects of strawberry fruit ripening, including the regulation of ripening-related TFs, phytohormone content and signaling, primary and secondary metabolism, and cell wall degradation. Additionally, using the TurboID-based proximity labeling approach, we have identified FaRIF interactors, including proteins involved in mRNA and protein homeostasis, as well as several NAC TFs. Among these, FaNAC021 and FaNAC034 were found to potentially cooperate with FaRIF to enhance the transcription of shared target genes. This integrative analysis, combining transcriptome analysis, in vivo ChIP-seq, and proximity labeling, broadens our understanding of FaRIF-mediated transcriptional networks and interaction partners, providing valuable insights into the molecular regulation of strawberry fruit ripening by this TF.

Hemsleya ellipsoidea (Xuedan) is a phylogenetically distinct medicinal species within the Cucurbitaceae family, notable for its ability to accumulate cucurbitacin IIa-a bioactive triterpenoid with potent anti-inflammatory and antibacterial activities. Here, we present a chromosome-scale reference genome for H. ellipsoidea , assembled using Oxford Nanopore, Illumina, and Hi-C sequencing technologies. The 535.68 Mb genome, with a contig N50 of 15.36 Mb, encodes 25 230 protein-coding genes across 14 pseudo-chromosomes, of which 63.85% comprise repetitive elements. Comparative genomic and phylogenomic analyses reveal that H. ellipsoidea diverged early (~84.7 MYA) from other cucurbits, maintaining several ancestral chromosomal segments but exhibiting lineage-specific rearrangements, reflecting an independent evolutionary trajectory without recent whole-genome duplication. Two conserved but functionally specialized biosynthetic gene clusters related to cucurbitacins formation were identified, suggesting coordinated regulation of triterpenoid metabolism. Integration of genomic and transcriptomic data enabled the reconstruction of the cucurbitacin IIa biosynthetic pathway and the identification of key structural enzymes and transcription factors. Distinct tissue-specific expression patterns further indicate root-localized synthesis and accumulation of cucurbitacin IIa. Collectively, this work provides the first high-quality genome of a medicinal Cucurbitaceae species and offers new insights into the chromosomal evolution, metabolic specialization, and adaptive diversification of H. ellipsoidea . The genomic resource also lays a foundation for functional genomics, metabolic engineering, and molecular breeding toward high-value triterpenoid production.

Circular RNAs (circRNAs) play important roles in plant stress responses, yet their dynamic regulation during stress remains unclear. This study elucidates a molecular mechanism whereby the grapevine U2 snRNP core component VvU2A′ enhances salt tolerance through a circRNA-mediated post-transcriptional network. We found that VvU2A′ expression is induced by salt stress and positively regulates salt tolerance in grapevine. CircRNA sequencing revealed 497 VvU2A′-regulated differentially expressed circRNAs, including downregulated VvcircHMA1. Mechanistic investigation revealed that VvcircHMA1 acts as a competitive endogenous RNA by sequestering VvmiR167b, thereby attenuating its cleavage activity on the target mRNA VvARF6. Functional analyses revealed that both VvcircHMA1 and VvARF6 negatively regulate salt tolerance, while VvmiR167b positively regulates it. Collectively, our study reveals a novel mechanism by which the splicing factor VvU2A′ enhances salt stress response through the VvcircHMA1-VvmiR167b- VvARF6 cascade, providing promising molecular targets for breeding salt-resistant grapevines.

Agriculture faces unprecedented challenges due to climate change, increasing food demand, and resource scarcity, which needs sustainable and innovative solutions. This review explores the emerging paradigm of holobiont biology (host and its microbiome as biological unit) in the context of emerging plant health challenges driven by global changes. We highlight three critical challenges: the rise of complex plant syndromes, the emergence and re-emergence of plant diseases, and the consequences of dysbiotic plant microbiomes. We discuss how microbiome-based strategies can enhance plant resilience, reduce reliance on agrochemicals, and foster sustainable agriculture. Integrating these strategies with advanced frameworks, such as holo-omics and machine learning, opens avenues for microbiome-based solutions to address agricultural challenges in the era of global changes, ensuring resilient crop systems and planetary health.

The control of fruit quality is of major scientific, nutritional, and commercial importance. In addition to being influenced by the intrinsic characteristics of each fruit species, fruit quality development is largely modulated by environmental factors. The environmental modulation of fruit quality primarily involves a signal transduction process that links environmental perception to the transcriptional or post-transcriptional regulation of key enzymes participating in fruit quality–associated metabolisms. Over the past decades, the effects of environmental factors on fruit quality traits have been extensively studied, and increasing attention has been directed toward elucidating the signaling mechanisms that govern this environmental modulation. However, knowledge in this research area has not yet been systematically summarized. In this review, we first provide an overview of the physiological and molecular bases underlying the modulation of fruit quality development by the three major environmental factors: water deficit, salinity, and temperature stresses. We then summarize recent advances in understanding the signaling mechanisms that mediate the environmental modulation of fruit quality development. Finally, we propose several perspectives to facilitate comprehension and guide future research endeavors.