Molecular Plant

The red/far-red sensing photoreceptor phytochrome B (phyB) governs multifaceted plant development and responses to light and temperature stimuli. PhyB photoconversion between red-absorbing, inactive Pr and far red-absorbing, active Pfr states, imparted by its covalently bound bilin chromophore, enables rapid switching and plasticity of phyB signaling activities. The phyBY276H variant (YHB) is photochemically inert but adopts a constitutively active Pfr-like structure regardless of light conditions, which becomes a versatile model to dissect phyB signaling mechanisms. Here, we conducted a large-scale EMS mutagenesis screen on YHB-expressing transgenic lines, mining intragenic suppressor mutations that would unveil critical residues for phyB structure-function relationships. Comparative analyses of 26 nonsense variants suggested modular organization of phyB overall structure and dispensability of the C-terminal HKRD domain for phyB signaling. Amongst fourteen novel and nine known loss-of-function missense variants identified herein, G284E was of particular interest for its fully suppressed constitutive activity in darkness and its restored photochemistry and light responsiveness. The G284E mutation was further tested to also nullify another constitutively active phyBY303V allele by eliminating chromophore attachment. P309L was the sole variant identified which fully suppressed YHB in both dark and light conditions. C402Y profoundly elicited YHB protein instability. Three variants G118R, C402Y and G538D markedly reduced chromophorylation levels of YHB. Although the chromophore binding site variant C357Y was a strong loss-of-function allele, it retained residual signaling activity with respect to PIF3 protein turnover in dark-grown seedlings, presumably due to its ability to noncovalently bind chromophore. Two tandem prolines (P799, P800) proved critical to YHB structural integrity/stability as well as signaling activity. In summary, these diverse variants shed new insights into multiple levels by which the YHB (and thereby phyB) signaling is initiated, tuned, and disseminated.

Salicylic acid (SA), a central hormone in plant immunity, is biosynthesized via a recently elucidated phenylalanine-derived pathway in most seed plants. This pathway requires benzyl alcohol as a key substrate for the formation of the SA precursor benzyl benzoate. However, how benzyl alcohol is produced in plants was unclear. Here, we identify a two-step conversion of benzoyl-CoA to benzyl alcohol via benzaldehyde in Nicotiana (N.) benthamiana. From a forward genetic screen for SA-deficient mutants, the and {beta} subunits of heterodimeric benzaldehyde synthase (BalS) involved in the conversion of benzoyl-CoA to benzaldehyde were found to be required for SA biosynthesis in N. benthamiana. Further reverse genetic analysis revealed that the NADPH-dependent benzaldehyde reductase (BalR1) acts downstream of BalS to convert benzaldehyde to benzyl alcohol. Interestingly, OsBalR1, but not OsBalS or OsBalS{beta}, is required for maintaining high basal SA levels in rice, suggesting the presence of redundant benzoyl-CoA-reducing activities or alternative biosynthesis routes for benzyl alcohol production. Together, this work defines the missing enzymatic steps in phenylalanine-derived SA pathway and provides insights into the evolutionary diversification of SA production strategies in plants.

Dendrobium officinale is a typical epiphytic orchid. We report the telomere-to-telomere (T2T) genome assembly for D. officinale, representing the first T2T reference genome within the Orchidaceae family. The assembly is anchored to 19 chromosomes and contains 38 complete telomeres and 15 characterized centromeres. We further generated haplotype-resolved assemblies of the autotetraploid genome, identifying 12,761 sets of tetra-allelic genes. Based on synonymous substitution analysis, we inferred that the autotetraploidization event occurred approximately 0.86 million years ago. A systematic analysis of the SWEET gene family across the genus Dendrobium revealed that the gene family size is shaped primarily by epiphytic types and environmental factors. In D. officinale from Langshan, eight SWEET genes were specifically expressed in roots, suggesting they may play specialized roles in the root mycorrhizal system, potentially contributing to the D. officinales ability to recruit and maintain fungal partners. Together, these resources provide valuable foundations for studies of orchid evolution, functional genomics, and molecular breeding.

Carotenoid accumulation underlies fruit color and nutritional quality in squash (Cucurbita pepo). One pair of dominant genes, B and L-2, have been long known to interact epistatically, substantially boosting carotenoid accumulation and producing intensely orange-fleshed fruit. However, their molecular identities and regulatory mechanism are unknown. Here, we show that B encodes a truncated H subunit of magnesium chelatase (CpCHLHB) and L-2 encodes a homolog of Arabidopsis Pseudo-Response Regulator 2 (CpAPRR2-A). Significantly, expression of phytoene synthase (CpPSY-A), which encodes the major rate-limiting enzyme in carotenoid biosynthesis, was dramatically upregulated in fruit of B/B L-2/L-2 plants compared with b/b L-2/L-2 or B/B l-2/l-2, showing that the B and L-2 interaction affects CpPSY-A transcription. A similar upregulation was also observed in Arabidopsis gun5 L-2 transgenic plants, where gun5 is a genetic mimic of the C. pepo B gene. The wild-type CpCHLHb physically interacted with CpAPRR2-A, attenuating the CpAPRR2-A-mediated activation of CpPSY-A. In contrast, the truncated CpCHLHB lost its ability to interact with CpAPRR2-A, enabling CpAPRR2-A to activate CpPSY-A and produce intensely orange fruit. These findings uncover the mechanism underlying the epistatic interaction through which B and L-2 act synergistically to boost carotenoid production, offering novel mechanistic insights and key targets for improving crop quality. One-sentence summarySynergistic epistasis between B and L-2 arises from loss of interaction between their encoded proteins, resulting in dramatically upregulating the key rate-limiting enzyme in carotenoid biosynthesis pathway to produce intensely orange-fleshed fruit in squash.

Oryza granulata Nees et Arn. ex Watt, a diploid wild rice (GG genome), possesses exceptional shade tolerance and is a key genetic resource for rice improvement. However, previous genome assemblies lacked continuity and completeness. Here we present a chromosome-scale reference genome of O. granulata using PacBio SMRT (113x), Hi-C (95x), and Illumina sequencing. The final assembly is ~764.24 Mb, with a scaffold N50 of ~59.32 Mb, and ~96.47% of the sequence anchored to 12 chromosomes. BUSCO completeness is ~98.6%. We annotated ~42,064 protein-coding genes, of which ~95.39% were functionally annotated, along with ~73.46% repetitive elements. The genome assembly and raw sequencing data are available at NGDC (PRJCA061980), NGDC GSA (CRA068332), and NGDC GWH (GWHISVE00000000.1). This high-quality genome will serve as a fundamental resource for evolutionary genomics, conservation biology, and breeding of shade-tolerant rice cultivars.

In nature, plants are subjected to multiple environmental stress factors simultaneously or sequentially. Recent studies revealed that when three or more stress factors impact a plant simultaneously (termed multifactorial stress combination; MFSC), plant survival declines, even if the intensity of each individual stress involved in the MFSC is low. We previously identified RAP2.3 as a key transcription factor (TF) required for Arabidopsis thaliana survival, specifically under a MFSC of salt+excess light+heat stress (i.e., S+EL+HS). Here we report that RAP2.3 is required for the expression of SIGMA3, a nuclear-encoded factor that directs plastid RNA polymerase to specific plastid promoters, and MYB51, a key stress response TF involved in glucosinolate metabolism and oxidative stress responses, specifically during a MFSC of S+EL+HS. Like rap2.3 mutants, myb51 and sig3 mutants display significantly low survival rate specifically under the MFSC of S+EL+HS. Based on MYB51 gene regulatory network analysis and characterization of jasmonic acid (JA) mutants, we further reveal that suppression of JA signaling could play an important role in promoting plant survival under conditions of S+EL+HS. Our findings uncover an additional layer of the response of plants to MFSC, as well as identify potential targets for breeding crops with enhanced tolerance to climate change.

Sacha inchi (Plukenetia volubilis L.) is an emerging woody oilseed crop prized for its high alpha-linolenic acid (ALA) content. Despite its nutritional and economic value, the lack of high-quality genomic resources has hindered genetic improvement and the elucidation of its unique polyunsaturated fatty acid and lipid biosynthetic pathways. In this study, we report a high-quality, chromosome-scale genome assembly of sacha inchi with a total length of 710.62 Mb, integrated from Illumina, PacBio, and chromosome conformation capture (Hi-C) technology. The genome harbors 37,570 protein-coding genes, and 379.86 Mb (53.45%) of repetitive sequences. Phylogenomic analysis reveals that sacha inchi diverged from its closest relative Ricinus communis, [~] approximately 36.2 million years ago. Comparative genomics indicates that sacha inchi experienced only ancient whole genome duplication events. To elucidate the mechanisms governing ALA biosynthesis and triacylglycerol (TAG) accumulation in sacha inchi seeds, we performed temporal transcriptome profiling across six seed development stages. Our findings demonstrate that high TAG content is primarily driven by the sustained expression of biosynthetic genes and low activity of degradation genes during mid-to-late seed development. Notably, while genes encoding stearoyl-ACP desaturases (SADs) maintain the precursor pool, the expression of genes encoding fatty-acid desaturase 2 (FAD2) and fatty-acid desaturase 3 (FAD3) is positively correlated with the final accumulation of C18:2 and C18:3 fatty acids. We also identified lncRNAs as potential epigenetic regulators of these key pathways. This high-quality genome provides a critical foundation for elucidating the molecular mechanisms of seed growth and development in sacha inchi.

Flavonoids are important specialized metabolites that contribute to plant pigmentation, stress adaptation, and nutritional value. In banana, a major global staple crop, their accumulation is highly tissue-specific, with very low levels in the edible pulp, and the mechanisms underlying this spatial distribution remain unclear. Here, integrative transcriptomic and metabolomic analyses across vegetative and reproductive tissues reveal that light-responsive regulatory networks control tissue-specific flavonoid biosynthesis. We identified a B-box transcription factor MaBBX21 as a key positive regulator of flavonoid biosynthesis. Its overexpression enhances flavonoid accumulation, whereas knockdown leads to a reduction in flavonoid levels in banana. Mechanistically, MaBBX21 interacts with MaHY5 and directly activates anthocyanin biosynthesis genes (MaDFR2 and MaANS). It also regulates metabolic flux by binding to the MaWRKY23 promoter, promoting flavonol biosynthesis through activation of MaFLS1 while partially repressing the anthocyanin branch. In addition, MaBBX21 introduces an epigenetic layer by activating the histone acetyltransferase MaGCN5, increasing H3K9 acetylation at target promoters, including MaDFR2, MaANS, and MaBBX21 itself, thereby forming a positive feedback loop. Functionally, MaBBX21 overexpression enhances flavonoid accumulation, ROS scavenging, and tolerance to heat and UV-B stress, whereas knockdown lines show reduced metabolite levels and increased stress sensitivity. Collectively, these results define a MaBBX21-MaWRKY23/MaGCN5 regulatory axis that integrates transcriptional regulation, and chromatin modification to control flavonoid biosynthesis, providing a foundation for improving nutritional quality and stress resilience in banana.

O_LIWhether gymnosperm FLAGELLIN-SENSING 2 (FLS2) orthologues are functional receptors and whether their flg22-recognition spectra have already diversified remain unclear, despite the central role of FLS2 in flagellin perception in angiosperms. C_LIO_LIHere, we identified two gymnosperm FLS2 orthologues, GbFLS2 from Ginkgo biloba and PtFLS2 from Pinus tabuliformis, and analysed their function using transient and stable expression in the Nicotiana benthamiana fls2 mutant, in planta cross-linking assays, AlphaFold3 modelling and structure-guided mutagenesis. C_LIO_LIBoth receptors restored flg22Pst-triggered reactive oxygen species production and MAPK activation, physically associated with flg22Pst, and required conserved residues for flg22Pst recognition. In stable transgenic plants, both receptors mediated flg22Pst-triggered PTI outputs and flg22Pst-induced resistance to Pseudomonas syringae. PtFLS2 additionally mediated responsiveness to flg22Rso and enhanced resistance to Ralstonia solanacearum, whereas GbFLS2 retained a typical flg22Pst-recognition profile. C_LIO_LIThese findings provide direct evidence that gymnosperm FLS2 orthologues can function as bona fide flagellin receptors in a heterologous angiosperm background, and further suggest that diversification in flg22 recognition had already emerged within gymnosperms. C_LI

Polyploidization plays a fundamental role in plant evolution and crop domestication. However, due to the high similarity of genomic sequences between some homologous or homeologous chromosomes, the assembly of some polyploid genomes is extremely difficult, frequently resulting in erroneous assemblies, such as sequence chimeras and sequence collapse. The genus Brachypodium is an important model system for the study of polyploidy in grasses. However, high-quality reference genomes are still lacking for its complex polyploid perennial species. In this study, we developed a bioinformatic pipeline for the accurate assembly of high-quality reference genomes at the chromosomal level for two representative perennial Brachypodium species with conflicting collapsed segments, the allotetraploid B. phoenicoides (2n = 4x = 28) and the autohexaploid B. boissieri (2n = 6x = 48). We developed an innovative methodology (CollapsedChrom) that uses depth-of-read profiling and relies on prior karyotypic information to systematically detect and rescue collapsed regions. This depth-sensitive curation strategy successfully recovered 328.9 Mb and 195.8 Mb of previously collapsed sequences in the genomes of B. phoenicoides and B. boissieri, respectively. Comprehensive quality assessments demonstrated the high quality of our final assemblies. Our chromosomal-level assemblies fully capture the genomic architectures of these species. These robust genomic resources overcome long-standing challenges in polyploid assembly and provide an essential foundation for future research on the evolutionary dynamics, subgenomic interactions, and functional biology of complex polyploid plant genomes.

Plant amino acids function as both pathogen nutrients and essential drivers of systemic immunity. The regulation of amino acid homeostasis through transporters is a essential for mounting a robust and coordinated immune response in plants during pathogen infection. Using systems biology and integrative network science, we investigated bacterial virulence in Arabidopsis. By comparing gene coexpression networks of effector-triggered susceptibility (ETS) and pattern-triggered immunity (PTI), we uncovered a plant amino acid-related processes specifically linked to ETS. Integrating time-series transcriptomics, protein-DNA interactions, and mathematical simulations, we identified ANAC046 as a transcriptional regulator of amino acid processes during ETS. Single-cell RNA-Seq revealed that amino acid transporters are primarily expressed in companion and mesophyll cells, while functional validation confirmed ANAC046s roles in promoting susceptibility. Further integration of transcriptome and interactome data showed that amino acid-related genes interact with key immune hub proteins. Network topology analysis enabled the characterization of seven additional genes involved in plant defense. To support community-wide research, we developed MIData, an open-access platform for pre-analyzed Arabidopsis networks. Together, our findings demonstrate the power of systems-level approaches in uncovering hierarchical regulatory mechanisms underlying plant susceptibility to bacterial pathogens.

Hi-C data is commonly used for reference-free de novo scaffolding. However, with the rapid increase in high-quality reference genomes, reference-guided workflows are now more practical for assembling large numbers of target genomes without relying on costly and labor-intensive Hi-C sequencing. Recently, a pangenome graph-based haplotype sampling algorithm was introduced to generate personalized graphs for target genomes. Such graphs have strong potential as references for reference-guided contig scaffolding. Here, we present noHiC, a reference-guided scaffolding pipeline supporting key steps of plant contig scaffolding. A distinctive feature of noHiC is the nohic-refpick script, generating a best-fit synthetic reference (synref) from a pangenome graph that is genetically close to the target contigs. This enables the integration of genetic information from many references (up to 48 in our tests) without using them separately during scaffolding. Synrefs showed advantages over highly contiguous conventional references in reducing false contig breaking during reference-based correction. Additionally, nohic-refpick can be combined with fast scaffolders (ntJoin) to rapidly produce highly contiguous assemblies using synrefs derived from pangenome graphs. The noHiC pipeline, used alone or in combination with ntJoin, can generally produce assemblies that are structurally consistent with public Hi-C-based or manually curated genomes. The pipeline is publicly available at https://github.com/andyngh/noHiC. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/712436v1_ufig1.gif" ALT="Figure 1"> View larger version (9K): org.highwire.dtl.DTLVardef@40bd8forg.highwire.dtl.DTLVardef@5d2bbborg.highwire.dtl.DTLVardef@e214a3org.highwire.dtl.DTLVardef@b90b06_HPS_FORMAT_FIGEXP M_FIG C_FIG

Grapevines (Vitis) belonging to grape family (Vitaceae) are symbolic fruit crops pivotal to human civilization. The evolutionary history of grapevines divergent from other Vitaceae plants remains mysterious, requiring a family-wide whole-genome phylogenomic analysis. Here, we conduct chromosome-level phylogenomics to investigate the origin and evolution of grapevines using 29 genome assemblies of five genera Vitis, Parthenocissus, Ampelopsis, Tetrastigma, and Cissus, 27 of which are newly released in this study. Phylogenomic and macrosynteny analysis unanimously support Ampelopsis as a sister lineage to Parthenocissus, placing both closer to Vitis, with introgression and incomplete lineage sorting contributing to these relationships. Ancestral genome reconstruction delineates the major chromosome rearrangement events in Vitaceae karyotype evolution, highlighting the conserved karyotype in Vitis and the extensive karyotypic reorganization in Tetrastigma and Cissus. Pan-3D genome analysis highlights the contributions of structural variants (SVs) to the variation of A/B compartments and topologically associated domains (TADs), revealing a strong purifying selection of SVs at TAD boundaries. We further demonstrate that Helitron transposons drive the expansion and expression regulation of NLR immune-receptor genes in Vitis. Importantly, we discovered an NLR gene VbRpv35 from wild grapevine V. bellula resistant to downy mildew (DM), whose heterologous expression in V. vinifera confers enhanced DM resistance. Taken together, we provide phylogenomic insight into the origin and evolution of grapevines and valuable resources for grapevine improvement and understanding angiosperm evolution.

Grain oil content and composition are complex quantitative traits that shape cereal grain quality and nutritional value. Sorghum (Sorghum bicolor), a heat- and drought-adapted C crop essential for global food and feed security, remains insufficiently characterized with respect to grain lipidome diversity and its genetic architecture. Here, we integrated population-scale whole-grain lipidomics with genome-wide association studies (GWAS) in 266 sorghum accessions. Lipidome profiling revealed extensive natural variation in triacylglycerols (TAGs), accompanied by coordinated shifts in phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs), explaining 87% of population-level differences in total grain oil. Lipidome-wide GWAS identified approximately 1.6 million significant variant-trait associations and resolved 55 loci linked to plastidial fatty acid synthesis, TAG assembly, lipid transport, and membrane remodeling. These loci, many undetected in previous GWAS of bulk oil content, demonstrated the increased mapping resolution achieved through lipidomics. Integration with metabolic gene clusters revealed significant enrichment of lipid-associated variants within terpene and saccharide-terpene biosynthetic clusters, indicating coordinated genetic regulation between central lipid metabolism and specialized metabolic pathways. Variants within these clusters explained more than 50% of the variance in measured grain oil content and exhibited additive effects of favorable alleles. Haplotype analyses further identified 27 elite sorghum accessions and 12 linked markers for marker-assisted improvement of sorghum grain oil. These findings elucidate the multilayered genetic architecture of sorghum grain lipid diversity and showcase the value of large-scale lipidomics integrated with GWAS for accelerating C crop grain quality improvement.

Chromosome number variation and structural reorganization are key drivers of plant evolution, yet their genomic basis remains unclear due to incomplete representation of repetitive regions in existing assemblies. The Linum genus exhibits exceptional karyotypic diversity (n = 7-43), providing a powerful system to investigate chromosome evolution. Here, we generated near telomere-to-telomere (T2T) genome assemblies for four species, including cultivated flax (L. usitatissimum cv. CDC Bethune; n = 15), its wild progenitor (L. bienne; n = 15), and two related species (L. decumbens and L. grandiflorum; n = 8). Together with published genomes of L. lewisii (n = 9) and L. tenue (n = 10), these enabled reconstruction of chromosome evolution across six lineages. Phylogenomic analyses revealed a shared ancestral whole-genome duplication (WGD) associated with the n = 9 karyotype, followed by lineage-specific WGDs and divergent diploidization. The transition from n = 8 to the derived n = 15 flax lineage not only occurred without chromosome length expansion, but also with genome size reduction, indicating extensive internal restructuring. Comparative analyses showed that this restructuring was associated with lineage-specific expansion of a single DNA transposon family (TE_00003234; hAT), which is highly enriched in expansive pericentromeric regions that are characterized by low gene density and nucleotide diversity, suppressed recombination, segregation distortion, and extensive synteny disruption, unlike the LTR retrotransposon-rich pericentromeres typical of most plant genomes. These findings support a model in which lineage-specific DNA transposon expansion is associated with remodeling of pericentromeric architecture and large-scale chromosome restructuring following polyploidization.

O_LIBetacyanins are red pigments characteristic of Caryophyllales and show considerable structural diversity, yet the enzymatic basis underlying 6-O-glucosylated betacyanins such as gomphrenin I has remained unclear. In particular, how alternative glucosylation patterns contribute to betacyanin diversification is poorly understood. C_LIO_LIHere, we identified cyclo-DOPA glucosyltransferases from Basella alba and Gomphrena globosa and examined their roles in gomphrenin I biosynthesis using transient expression assays and tobacco BY-2 cell systems. Phylogenetic analyses, structural modelling and site-directed mutagenesis were employed to investigate their functional and structural characteristics. C_LIO_LIBacDOPA5/6GTs catalysed both 5-O- and 6-O-glucosylation of cyclo-DOPA, leading to the production of betanin and gomphrenin I, whereas GgcDOPA6GT specifically mediated gomphrenin I formation. These enzymes belong to distinct subclades within the cDOPA-GT family, and mutational analyses demonstrated essential roles for conserved histidine residues and an -helical region adjacent to the catalytic site. C_LIO_LIThermal stability analyses further showed that gomphrenin I is more thermally stable than betanin, likely due to the formation of an intramolecular hydrogen bond. Together, these results reveal an additional cDOPA6GT-mediated route for gomphrenin I biosynthesis and provide insight into the diversification and functional specialization of betacyanins, linking the position of glucosylation to pigment stability and biochemical properties. C_LI

Flexible developmental programs enable plants to customize their organ size and cellular composition. In leaves of eudicots, the stomatal lineage produces two essential cell types, stomata and pavement cells, and plants can adjust the total numbers and ratios of these cell types in response to external cues. Central to this flexibility is the stomatal lineage-initiating transcription factor, SPEECHLESS (SPCH). Here we explore the mechanisms underlying SPCHs involvement in environmental response. Using multiplexed CRISPR/Cas9 editing of SlSPCH cis-regulatory sequences in tomato, we identified variants with altered stomatal development responses to drought, light and temperature cues. By creating and live-cell tracking translational reporters of SlSPCH and its paralogues SlMUTE and SlFAMA, we revealed the corresponding cellular events that lead to the environmental change-driven responses in stomatal production and leaf form. Plants bearing the novel reporters and SlSPCH variants are powerful resources for fundamental and applied studies of tomato resilience in response to climate change.

Brassinosteroids (BRs) are key regulators of plant growth and have been implicated in suppressing glucosinolates (GSLs) biosynthesis in Brassicaceae species, including Arabidopsis thaliana. However, the molecular mechanism linking BR signaling to transcriptional control of the aliphatic GSL pathway remains unclear. Here, we provide genetic and molecular evidence that the BR-responsive transcription factor BZR1 negatively regulates aliphatic GSL biosynthesis through interaction with TOPLESS (TPL) family corepressors and the histone deacetylase HISTONE DEACETYLASE 19 (HDA19). The gain-of-function mutant bzr1-1D exhibited reduced accumulation of aliphatic glucosinolates (GSLs), whereas disruption of TPL family genes (tpl, tpr1, tpr4) or HDA19 resulted in elevated GSL levels, supporting a repressive role for the BZR1-associated complex in the regulation of GSL biosynthetic gene expression. Furthermore, we uncover a functional connection between ABA and BR signaling in this process. The ABA-responsive transcription factor ABI5 reduces the expression of UBP12 and UBP13, which encode deubiquitinases known to influence BZR1 stability. Genetic and transcriptional analyses indicate that ABI5-mediated attenuation of the UBP12/13-BZR1 pathway contributes to enhanced aliphatic GSL accumulation under ABA treatment. Collectively, our findings delineate a regulatory framework linking ABA and BR signaling pathways and suggest that modulation of the UBP12/13-BZR1 module by ABI5 integrates growth and defense responses by fine-tuning aliphatic GSLs biosynthesis in Arabidopsis. One sentence summaryan ABA signaling factor, ABI5 acts to suppress expression of brassinosteroids (BR) hormone signaling genes like UBP12, UBP13, and BZR1 to promote biosynthesis of defensive secondary metabolites, glucosinolates (GSLs) in Arabidopsis.

Iron (Fe) is an essential micronutrient for plant growth, and the hormone auxin is a key regulator of developmental processes, including root gravitropism. Here, we investigated the molecular mechanisms underlying the crosstalk between iron nutrition and auxin-mediated root growth in Arabidopsis thaliana. Phenotypic analysis revealed that iron deficiency strongly shaped root system architecture and root gravitropism, and these phenotypes were exacerbated in the iron uptake mutant irt1-1. Genetic analysis revealed that iron deficiency did not aggravate the gravitropic defect of the pin2 mutant, eir1-4, suggesting that iron availability modulates root gravitropism through a PIN2-dependent pathway. Further transcriptomic analysis confirmed that iron deficiency significantly altered the expression of numerous genes related to the auxin pathway, providing molecular evidence for the observed physiological connection. Collectively, this study revealed that iron availability regulates root gravitropic growth by modulating PIN-mediated auxin transport and distribution, providing insights into how plants integrate nutritional cues with developmental programs. Graphical abstract A brief descriptionIron modulates auxin transport and root tip distribution by regulating PIN2 protein, thereby mediating root gravitropism in Arabidopsis. Public summaryO_LIIron nutrition specifically regulates root gravitropism and architecture in Arabidopsis. C_LIO_LIIron deficiency disrupts local auxin homeostasis in root tips and impairs asymmetric distribution in response to gravity. C_LIO_LIIron deficiency stress significantly reduces the abundance of PIN2 protein in root tip cells and disrupts its polar localization pattern on the plasma membrane, thereby precisely modulating polar auxin transport by interfering with the vesicle trafficking and recycling efficiency of PIN2. C_LIO_LIRNA-seq results showed that iron deficiency induced differential expression of multiple auxin-related genes, indicating that iron nutrition affects root development through the auxin pathway. C_LI

Plants are continuously exposed to a myriad of DNA-damaging agents, including environmental cues such as sunlight. At the cellular level, plants respond to DNA damage by activating DNA damage response (DDR) pathways, in which chromatin remodelers play an important role. Among them, the evolutionary conserved INO80 complex (INO80c) has been shown in Arabidopsis to play a key role in DDR, notably by positively regulating Homologous Recombination (HR). Arabidopsis EIN6 ENHANCER (EEN) is the homolog of Yeast INO EIGHTY SUBUNIT 6 and interacts with the N-terminal region of INO80 in the INO80c. Using plant phenotyping, cellular and molecular biology, and third-generation sequencing technology we investigated how INO80 and EEN regulate plant development and genome integrity. We uncovered new roles for INO80 and EEN in plant growth and for INO80 in fine tuning endoreduplication. In addition, linear genome analysis revealed an important and unexpected function for the INO80-EEN complex in preventing Protein Coding Genes (PCGs) from structural rearrangements in somatic tissue and upon exposure to UV-B. Therefore, our results shed new light on the previously overlooked roles of INO80 and EEN in protecting genome integrity at PCGs.