Horticulture Research

We performed a screening to evaluate the responses to water deficit before the flowering stage in a panel of 31 genotypes composed of one commercial hybrid, one wild species, multiple ex-PVP (vintage) lines, several commercial heirlooms from the Northeast USA, Mexican landraces from hot and humid environments and genome edited lines with altered flowering and inflorescence traits. We characterized 18 different morphological, physiological and biochemical traits to assess the response to 40% water deficit. We observed diverse morphological, physiological and biochemical responses across the 31 genotypes screened, suggesting the presence of useful variation for breeding for drought tolerance in cultivated tomato. Interestingly, some heirlooms exhibited superior performance under drought, suggesting they can be used as donors to discover novel genes involved in drought responses. Unexpectedly, we found mutants in SlCLE9, a paralog of the stem cell regulator SlCLV3 known to co-regulate meristem proliferation in tomato, exhibited enhanced drought tolerance. Notably, the slcle9 mutant also conferred drought tolerance when used as rootstock with grafted scions from our reference cultivar M82, suggesting SlCLE9 influence root architecture and drought response. Consistent with this, we found SlCLE9 is transcriptionally upregulated in roots and leaves during drought stress, and exogenous application of SlCLE9 modifies root growth and response to drought. Altogether, our screening uncovered new potential trait donors for breeding against drought stress and describes a novel role for SlCLE9 in drought tolerance.

Plant pathogen genomes adapt across coding and non-coding regions in response to their hosts, environments, and disease management practices. Venturia inaequalis, the causal agent of apple scab, has evolved alongside its Malus host throughout apple domestication. We generated 17 high-quality genome assemblies, including the first chromosome-scale assembly of V. inaequalis, to define the species' complete gene content and investigate the role of structural variation in genome evolution. Together with a previously published scaffold-level reference, these assemblies were used to construct a gene-based pangenome containing 215,301 predicted protein-coding genes clustered into 13,240 orthogroups, 88.11% of which were core (73.86%) or soft-core (14.25%), 11.88% shell (present in 2-16 isolates), and 0.1% private, indicating a highly conserved gene repertoire. Virulence-associated effectors were significantly enriched in the soft-core and shell components, and accessory apoplastic effectors displayed elevated nucleotide diversity and nonsynonymous-to-synonymous substitution ratios (Ka/Ks) relative to core effectors, consistent with diversification. We further identified a putative accessory chromosome of variable size (23-132.6 kb) in European and U.S. isolates encoding genes with virulence function. A graph-based pangenome identified 38,799 non-redundant structural variants (SVs), largely driven by Gypsy LTR retrotransposons. We used the graph-based pangenome to genotype 136 globally distributed V. inaequalis isolates and identified variants differentiating populations associated with domesticated apple (Malus domestica) from those associated with its Central Asian wild progenitor, M. sieversii. Together, these resources establish a foundation for future studies of diversity, host adaptation, and genome evolution in V. inaequalis.

Bulk phloem flow is driven by pressure gradients generated by water drawn from the xylem, coupling source-sink transport with water status. Huanglongbing (HLB), a phloem-affecting bacterial disease of citrus, disrupts phloem transport, and causes canopy water deficit. Although improved water management can enhance HLB-affected tree health, the effects of HLB on water-driven source-sink relations are unknown. Fruits function as both carbon sink and water reservoir, but the role of fruit in regulating whole-tree water status remain poorly understood. We examined leaf-fruit water relations in HLB-affected citrus and evaluated how HLB exposure duration, fruit developmental stage, and source-sink manipulation shape these dynamics. Source-sink relations were manipulated in branches of symptomatic trees with long-term (four years) and recent (six months) HLB exposure. We girdled branches with a single fruit as the sink and defoliated at (0%, 50%, or 75%), and an ungirdled, non-defoliated branch served as control. We measured stomatal conductance, leaf hydraulic traits, leaf and fruit soluble sugars, diurnal fruit shrinkage (to estimate xylem backflow) and fruit water loss. Source-sink manipulation did not affect shoot total soluble sugar. HLB-exposure resulted in less negative osmotic potential, more negative turgor potential and reduced modulus of elasticity and relative water content at turgor loss point. HLB exposure also increased diurnal fruit shrinkage, with shrinkage responses to source-sink manipulation varying across fruit development stages. Collectively, these findings suggest that long-term HLB exposure promotes leaf acclimation to water deficits, however, high sink demand may diminish the leaf water status regulation at Stage II, when fruit sink carbon demand is highest.

Understanding the genetic architecture of ecophysiological traits related to carbon gain and water loss is crucial to develop cultivars tolerant to abiotic stresses and that maintain productivity in the context of climate change. This can be achieved both through experiments in the greenhouse on potted plants under controlled conditions and in the field. However, the stability of genetic determinism of ecophysiological traits across environmental conditions has rarely been evaluated. We studied a grapevine diversity panel grown both in a greenhouse and in the field, to investigate the impact of growing conditions on leaf ecophysiological traits related to leaf morphology, fluorescence, gas exchange and water use efficiency. The correlation structure between traits was conserved within each environment even though, for most traits, cultivars ranking was not conserved between both environments. However, a set of cultivars, sharing the same functioning pattern in terms of gas exchange and fluorescence in both environments, was identified. Single- and multi-environment Genome-Wide Association Studies (GWAS), based on a dense genotyping matrix, were used to dissect the genetic architecture of leaf traits. The Quantitative Trait Loci (QTLs) identified through single-environment analyses differed substantially from those detected using multi-environment ones. Multi-environment approaches highlighted shared QTLs across environments for gas exchange and fluorescence traits. Candidate genes associated with carbon- and water-related functions were further identified in these genomic regions. Despite the weak correlation between greenhouse and field trait values, combining both environments enabled the identification of robust genetic regions associated with ecophysiological traits of interest.

Although Cinnamomum includes globally important spice and medicinal plants, genome-scale knowledge of Cinnamomum species native to Japan remains limited. The Nansei Islands are an approximately 1,200-km-long archipelago located between the Pacific Ocean and the East China Sea and represent a key biogeographic region shaped by deep-sea barriers such as the Tokara and Kerama Gaps. Here, we integrated chloroplast and nuclear genome data generated in this study with public datasets to examine the phylogenetic relationships of four Cinnamomum species native to the Nansei Islands and ten related species. Chloroplast genomes showed no major structural differences among the four island species, whereas nuclear genome data resolved two distinct evolutionary lineages in the Nansei Islands: C. yabunikkei, C. x durifruticeticola, and C. daphnoides formed a distinct Nansei Islands lineage separate from Sri Lankan, Indonesian, and Taiwanese lineages, whereas C. sieboldii was placed in a Taiwanese lineage. Ancestry estimation indicated that C. x durifruticeticola and C. daphnoides share a common ancestral component, while C. sieboldii exhibited a single homogeneous ancestral component, suggesting reduced ancestral diversity after divergence from a Taiwanese lineage. These findings reveal previously unrecognized genomic differentiation among Japanese Cinnamomum species and suggest that deep-sea barriers, dispersal, and long-term isolation shaped their diversification.

Boron toxicity constrains grapevine (Vitis) production in irrigated arid and semi-arid regions, yet most available rootstocks are sensitive to excessive boron. Although underutilized Vitis species may harbor sources of adaptation, the genetic basis of natural variation in boron exclusion remains poorly understood, limiting the development of boron-tolerant rootstocks. We screened 267 wild Vitis accessions representing 16 species for their ability to limit leaf boron accumulation under excess boron conditions. Leaf boron concentration varied 190-fold among accessions and was highly heritable (entry-mean H^2 = 0.71). Its correlation with stomatal conductance was modest (r = 0.34), indicating that transpiration rate explained only a small proportion of the variation in leaf boron accumulation. Leaf boron was correlated with leaf chloride (r = 0.36), but their largely non-overlapping association profiles supported distinct genetic control. Genome-wide association analysis identified a suggestive association on chromosome 11. Independent quantitative trait locus mapping in a full-sib F1 population (n = 158) derived from Longii-9018 (V. acerifolia) x GRN3 (commercial rootstock) identified qBEx11.1 in the same syntenic region on chromosome 11, which explained 19.5% of the phenotypic variance. Positional candidate genes near the association peak included a pectinesterase and a MATE efflux transporter, suggesting roles for cell wall modification and membrane transport. Leaf spectral reflectance was associated with leaf boron concentration in both populations, particularly at visible and red-edge wavelengths, indicating potential for high-throughput phenotyping. Together, these findings identify qBEx11.1 as a priority locus for boron exclusion and support integrated genetic and spectral approaches for breeding boron-tolerant grapevine rootstocks.

Drought stress severely limits tree growth and survival, a problem intensifying under climate change due to the rising frequency of extreme weather events. Identifying genetic variants that modulate drought stress responses and enhance resilience is therefore of great interest for developing climate-adapted trees. While the MADS-box transcription factor AGL16 has been implicated in drought responses and stomatal regulation in herbaceous species, the function of its homolog in woody perennials remains largely unexplored. Here, we investigate the role of PtaAGL16 in the poplar hybrid Populus tremula x P. alba. We generated CRISPR/Cas9 knockout lines of PtaAGL16 in the poplar clone INRA 717-1B4. Plants were subjected to a severe drought stress regime followed by a re-watering recovery phase. Morphological and physiological traits, including growth, stomatal conductance, shoot vitality, and stomatal density, together with stress-associated metabolites and drought-responsive gene expression, were analyzed. All agl16 knockout lines exhibited significantly reduced drought-induced damage compared to the wild-type. While the wild-type suffered extensive defoliation and persistent stem necrosis, the knockout lines retained higher shoot vitality and resumed growth after re-watering, including the formation of new leaves. Consequently, vitality in the knockout lines reached up to 86%, compared to only 34% in the wild-type. This improved resilience was accompanied by reduced persistent oxidative membrane damage, as indicated by lower MDA levels after recovery. These findings indicate that the disruption of PtaAGL16 is associated with enhanced drought resilience in a woody perennial species and highlight its potential as a genetic target for improving climate adaptation in fast-growing forest trees.

Petal coloration is a key ornamental trait in Cyclamen persicum Mill. and is closely associated with anthocyanin composition and relative accumulation, yet the major anthocyanins and candidate molecular factors associated with color variation remain unclear. In this study, anthocyanin profiling and transcriptome analysis were integrated to investigate three Cyclamen materials with distinct petal colors, BXK, FXK, and SHXK. Anthocyanin profiling showed clear separation among the three materials, indicating that petal color divergence was associated with differences in anthocyanin composition and relative abundance. Petunidin-, peonidin-, delphinidin-, malvidin-, and cyanidin-related derivatives exhibited distinct accumulation patterns. Transcriptome analysis revealed marked transcriptional divergence, with phenylpropanoid and flavonoid biosynthesis repeatedly enriched across comparisons, whereas isoflavonoid and flavone and flavonol biosynthesis were enriched in selected comparisons. Mapping differentially expressed genes onto the anthocyanin biosynthetic pathway revealed branch-specific expression patterns of structural genes, including CHS, F3H/F3'H, F3'5'H, DFR, and ANS. Notably, Cluster-26256.0, annotated as a putative anthocyanidin synthase gene, showed a progressive increase in expression from BXK to FXK and SHXK, consistent with increasing petal pigmentation. Several DFR-related transcripts also showed relatively high expression in SHXK. Co-expression analysis linked key anthocyanins, structural genes, and transcription factors, while qRT-PCR generally confirmed RNA-seq trends. These results suggest that late anthocyanin biosynthesis, particularly ANS-related transcriptional variation, may contribute to dark red petal coloration. This study provides a metabolite-transcript framework for Cyclamen petal coloration and identifies ANS-related genes as priority candidates for future functional studies and flower-color breeding.

Amaranthus tricolor is a climate-resilient orphan crop whose betalain pigments contribute to nutritional quality and stress tolerance. However, breeding efforts have traditionally relied on field yield trials due to the limited availability of genomic information and genetic resources. To address this gap, we first used the Illumina and PacBio sequencing platforms to assemble a novel reference genome of A. tricolor, using the Japanese cultivar Bayam. By combining this reference genome with a core collection developed in our previous study, we aimed to identify genomic regions associated with pigmentation-related traits across winter and summer seasonal environments. Betalains are antioxidant phytonutrients that contribute to abiotic stress tolerance, making the regulation of their biosynthesis under heat stress particularly relevant for developing climate-resilient crops such as A. tricolor. As a result, ATR1.0CH03_5131103, which is associated with ATR1.0ch03g000565, was identified under the winter seasonal environment. Meanwhile, transcriptomic profiles in this study revealed that ATR1.0ch03g000565 was differentially expressed under both control and heat stress conditions, suggesting that it may be associated with the regulation of CYP76AD1 expression under optimal conditions. Under the elevated-temperature treatment, transcript levels of CYP76AD1 and 5GT decreased in Am087, coinciding with lower betacyanin-dominated absorbance indices. cDOPA-like homologs were upregulated; however, pigmentation-related absorbance remained reduced. Further molecular experiments, such as CRISPR-Cas9 knockouts or overexpression studies, are necessary to validate the regulatory mechanisms of CYP76AD1 and 5GT under heat stress.

Pectobacterium, a member of the soft rot Pectobacteriaceae (SRP), can cause highly destructive soft rot and blackleg diseases on many important crop and other host plants, particularly potato (Solanum tuberosum). Pectobacterium and its sister genus Dickeya have common virulence strategies, yet a highly diverse "open" pangenome containing many unique and hypothetical proteins. Here, we used randomly-barcoded transposon insertion-site sequencing (RB-TnSeq) on six Pectobacterium species to identify genes involved in bacterial survival and growth in potato tubers, as well as in minimal media conditions containing different single carbon sources. The strains evaluated varied broadly in genomic content as well as host plant and year of isolation. We focused on identifying conditionally essential genes across all strains tested, as well as genes that were important for growth in one or few of the tested strains. These results highlight the importance of many common genes involved in metabolism and maintaining cellular homeostasis, as well as shared and rare virulence traits including polygalacturonate catabolism, genes involved in polysaccharide biosynthesis, immunity proteins, and (for P. brasiliense) self-tolerance of the antibiotic carbapenem. This large dataset of conditionally essential genes, generated across Pectobacterium species during soft rot infection of the agriculturally important plant host potato, can serve as a rich dataset for further hypothesis generation and identification of important and/or novel in planta fitness factors.

Pseudomonas species include important plant pathogens responsible for substantial agricultural losses. Although CRISPR-INTEGRATE has been applied for genome engineering in medically relevant Pseudomonas, its utility in plant-pathogenic Pseudomonas has not been established. Here, we demonstrate CRISPR-INTEGRATE, an RNA-guided Tn7-like transposition system that enables targeted chromosomal integration without double-strand breaks or host-dependent homologous recombination, across three plant-pathogenic Pseudomonas backgrounds. Targeted disruption of hrpJ, hrcC, and gacA was confirmed by PCR and Sanger sequencing and resulted in distinct phenotypes, including impaired type III secretion-associated virulence and hypersensitive response, altered colony morphology and biofilm formation, and reduced motility. We further coupled CRISPR-INTEGRATE with Cre-lox recombination to excise a ~40-kb prophage-associated region from the P. syringae pv. tomato DC3000 chromosome. Genomic characterization identified a 33.45-kb predicted prophage within this region, putative attL/attR sites sharing an identical 14-bp core sequence, an orthologous empty locus containing a candidate attB site, and conserved prophage-associated gene organization across P. syringae genomes. Deletion of the region altered bacterial growth and increased susceptibility to phage infection, with the strongest effect observed for phage Plaza, while having no detectable effect on the tested plant virulence phenotypes. Together, these findings establish CRISPR-INTEGRATE as a portable genome-engineering platform for plant-pathogenic Pseudomonas and demonstrate its utility for functional interrogation of individual genes and large accessory genomic elements.

Understanding how grafts form has fascinated scientists for over a century, and numerous transcription regulators involved in wound healing, callus formation, and grafting have been identified in model plants. However, the genetic architecture underlying grafting traits remains poorly characterized. To address this gap, we aimed to identify quantitative trait loci (QTLs) associated with grafting success rates and grafting-related traits (including callus formation, mechanical strength of the graft union, and post-grafting growth) in a grapevine rootstock mapping population, Vitis berlandieri x V. rupestris. Although no QTLs were identified for grafting success rate, QTLs were identified for component traits revealing a genetic architecture that would have remained hidden when considering grafting success as a single composite phenotype. By integrating QTL and transcriptome data, we identified regulators potentially mediating grafting-related traits. We then showed that one transcription factor that regulates callus formation and grafting in Arabidopsis potentially has a similar role in grapevine by silencing with exogenous double-stranded RNAs and that exogenous application of methyl jasmonate increases callus development at the graft interface. Candidate transcriptional regulators located within QTLs and evidence from gene silencing and hormone treatments suggest the conservation of regulatory mechanisms underlying wound-induced callus formation across plant species.

Genotype-by-environment interactions can complicate plant breeding because genetic effects may vary across weather regimes, locations, and years. Although genomic prediction models can use dense marker data to predict complex crop traits, they often provide limited information about how marker relevance changes across environmental conditions. This study introduces a graph-based framework for estimating environment-associated marker rankings from multi-environment crop trial data. We introduce an attention-based graph neural network that jointly represents SNP markers and weather-based environment vectors as interacting nodes and is designed to learn environment-associated marker rankings from supervised yield data. The model is trained using yield prediction as the supervised objective, and the learned marker-level attention signals are aggregated to estimate marker rankings overall and within groups of similar environments. We evaluate the framework on two genotype-by-environment datasets. In both datasets, we examine whether learned marker rankings are stable across independent training runs and determine the overlap between high-ranked markers and external GWAS references. In a maize dataset with data from 212 different site-years, we rank markers separately within each weather-defined environment cluster and define a global marker set as the markers shared across all clusters. This provides a structured way to examine how marker rankings vary across weather-defined groups and which markers remain important across environments. We further encode each weather variable with a separate LSTM combined by attention, which makes the contribution of individual weather variables readable, and compare the resulting variable ranking against an independent SHAP-based attribution. Genes located near the top-ranked markers are also examined for functional enrichment. Overall, the results suggest that graph-based, environment-conditioned marker attribution may complement genomic prediction as an exploratory tool for studying context-dependent genomic signals in multi-environment trials.

The mechanisation of agriculture has achieved major increases in labour productivity but has also led to an erosion of agrobiodiversity. Neglected and underutilized crops such as common buckwheat (Fagopyrum esculentum Moench) offer the potential to diversify food production systems but require major genetic improvement to compete with established crops. Although target traits for breeding such as more homogeneous ripening, reduced height, larger seeds and higher and more stable yields are well known, large-scale and field-based phenotyping data of diverse common buckwheat accessions across multiple environments are still scarce. Here, we tested the agronomic performance of a common buckwheat germplasm collection consisting of 170 accessions of diverse origin. The collection was tested at seven year-sites, and 19 agronomic traits related to phenology, growth habit and yield were assessed. Most traits showed high repeatability (0.31 < R2 < 0.98) and heritability (0.45 < H2 < 0.97), indicating genetic control of these traits. Coefficients of variation ranged between 6.19% and 46.15%, showing the high phenotypic diversity within the collection. By combining multiple traits, distinct ideotypes for different roles in the crop rotation were investigated, and accessions with promising agronomic profiles identified. Genome-wide association studies revealed marker-trait associations for 18 traits, allowing the identification of putative candidate genes influencing these traits such as a putative GRF-INTERACTING FACTOR associated with flowering time and biomass production. Our results show that the collection offers vast phenotypic diversity that can be exploited for the development of improved varieties tailored to meet specific agronomic purposes. The efficient utilization of these genetic resources should be supported by the application of genomics-based breeding approaches. The development of genetic markers and search for putative candidate genes mark important steps towards the establishment of efficient breeding schemes. Thus, these genomic resources provide a foundation for accelerating the genetic improvement of common buckwheat and developing agronomically competitive varieties.

Caraway (Carum carvi L., 2n = 2x = 20) is a medicinal and aromatic plant of the Apiaceae family valued for its essential oil with the major terpenoids carvone and limonene. While the essential oil content represents an important quality trait, low seed shattering and high thousand-grain weight (TGW) are key determinants of seed yield. As molecular tools remain scarce within Apiaceae breeding beyond carrot, we conducted a QTL mapping for these seed-related traits using two previously established F2 populations (Effective N(P1) = 236; N(P2) = 266). In P1 with the non-shattering maternal parent Rekord, QTL mapping revealed at least one shattering locus on LG03 (PVE: 9.9%). In addition, loci associated with essential oil (LG08, 10.5% PVE) and TGW (LG09, 11.1% PVE) were detected. In P2, we identified six essential-oil loci (LG02-06, LG10; combined PVE: 49.2%), with five loci affecting both carvone and limonene, and one (LG03) exclusively limonene. Additionally, a major QTL for TGW mapped to LG02 (PVE: 15.6%). For stalk attachment rate one minor QTL was detected (LG07, 8.5% PVE), while no QTL co-localized with the major shattering locus. To pave the path towards fine-mapping, we designed and validated 26 diagnostic PACE markers covering five key QTLs.

Cassava produces starch-filled tubers which are a crucial food source for many people, especially in Africa. This plant species is famous for drought tolerance and resilience, but changing conditions due to climate change require genetic improvements to ensure sustainable cassava cultivation. In this context, a comprehensive understanding of the genetic basis responsible for a variety of traits is beneficial. Here, we present insights into the anthocyanin metabolism, responsible for coloration and protection of cassava structures during stress. Intraspecific variation in the transcriptional control of the anthocyanin biosynthesis was characterized through comparative genomics and phylogenetic analyses. A member of the R2R3-MYB transcription factor family, orthologous to crucial activators of anthocyanin biosynthesis in other plant species, was identified as a genetic hotspot for pigment accumulation capacity between cultivars. Orthologs of this gene appeared absent from three cassava cultivars without pronounced anthocyanin pigmentation, while being present in cultivars known for anthocyanin formation. This discovery corroborates previous reports about the importance of transcriptional regulators in the intraspecific diversity of anthocyanin pigmentation.

Lipolytic enzymes play critical roles in plant development, growth, and stress responses. In oat (Avena sativa), they are of particular interest because lipid hydrolysis contributes to rancidity and reduced grain quality, yet little is known about genomic variation in oat lipolytic enzymes. Here, we investigated genomic and expression diversity of the GDSL-esterase/lipase gene family using pangenome, transcriptome, and genome-wide association analyses. Across 22 A. sativa and two A. sterilis genome assemblies, we identified 7,775 GDSL genes (~324 per assembly), revealing wide conservation of ancestral orthologs alongside extensive copy-number variation among homoeologs and paralogs. Transcriptome profiling across 20 genotypes and six tissues demonstrated preferential expression in embryo and root, with tissue-specific patterns highlighting candidates for specific functions, such as seed lipid metabolism. Associations with structural variants further uncovered candidate mutations underlying expression variation among accessions. Comparisons of cultivated and wild oat detected loci with signatures of breeding-based selection, suggesting that GDSL genes have contributed to diversification of the cultivated gene pool. Using 629 whole-genome sequenced accessions, we also identified associations between GDSL regions and agronomic traits, particularly plant height and effective tiller number. Several regions showed patterns consistent with selection, highlighting candidate loci for further investigation of agronomic variation. Together, our results reveal substantial genomic and transcriptional diversity within the oat GDSL gene family and identify candidate genes and genomic regions for improving seed quality and agronomic performance. More broadly, our study demonstrates how pangenomic resources can be used to investigate gene-family diversity and function in complex polyploid crops.

Groundnut (Arachis hypogaea) is an important oilseed crop, and its production is severely affected by drought worldwide. Improving the drought-tolerance of groundnut without compromising its agronomic traits is a major challenge for researchers. Here, a meta-transcriptome analysis identified tandemly duplicated G{beta} subunits (AhG{beta}1 and AhG{beta}3) as early signaling genes under water deficit conditions. Heterotrimeric G-protein {beta}-subunit is a major signaling element that can regulate diverse responses in plants. Heterologous complementation studies in Arabidopsis G{beta} mutant (agb1-2) demonstrated evolutionary conservation of AhG{beta} function, while the transgenic overexpression and RNAi knockdown in groundnut established AhG{beta}1 as a positive regulator of plant growth, yield, and drought tolerance. Integrated transcriptomic, transcription factor regulatory network, and metabolomic analyses demonstrated that AhG{beta}1 coordinates drought-responsive transcriptional and metabolic reprogramming characterized by suppression of cell wall-associated processes and activation of phenylpropanoid, flavonoid, and isoflavonoid biosynthesis. This reprogramming resulted in enhanced accumulation of antioxidant flavonoids, including quercetin and rutin, reduced ROS accumulation, and improved drought tolerance. Furthermore, exogenous application of these flavonoids enhanced drought recovery, highlighting their role as protective downstream metabolites. Collectively, our findings establish AhG{beta}1 as a conserved regulator linking early G-protein signaling with transcriptional and metabolic reprogramming to maintain redox homeostasis during drought stress and identify promising molecular and metabolic targets for improving drought resilience in groundnut.

Mitochondrial genomes of angiosperms are unusual due to their large size, low gene content, and high structural variation. In the palm family (Arecaceae), mitochondrial architecture is highly dynamic, characterized by expansive sizes, fragmentation, and extensive recombination activity. This biological complexity presents a significant bioinformatic challenge, especially since only three complete palm mitochondrial genomes are publicly available to date. Here, we present the complete mitochondrial genome sequence for the Amazonian palm Euterpe precatoria, assembled de novo using PacBio HiFi long-read sequencing data. The assembly required extensive manual curation and graph tracing to resolve a complex recombination topology. The final resolved sequence spans 1,268,308 base pairs and is supported by a mean read coverage depth estimated at 746X. Annotation revealed a high degree of structural complexity, including 177 total gene features corresponding to 76 unique genes. This gene set includes 41 unique protein-coding genes (56 features), 32 unique tRNA genes (118 features), and three unique rRNA genes, reflecting the characteristic gene duplication and fragmentation documented in Arecaceae. The complete mitochondrial genome sequence is publicly available and provides a high-quality resource for understanding the mechanisms of plant mitochondrial genome expansion and structural evolution.

FLS2-mediated perception of the bacterial flagellin epitope flg22 is frequently compromised by pathogen sequence variation, and Val14-containing Xanthomonas flg22 variants remain unrecognized by multiple characterized expanded-recognition FLS2 homologues. Using AlphaFold 3-based structural screening of 256 natural FLS2 homologues against the flg22 epitope from Xanthomonas campestris pv. campestris (flg22Xcc), we identified sunflower HaFLS2-1 as the top structural candidate and experimentally validated its recognition through biochemical and immune-response assays. We then used ligand-proximal HaFLS2-1 residue states as a donor reference for iterative engineering of divergent FLS2 homologues from two distinct plant families, PsFLS2 and TjFLS2. Distinct recipient-specific residue solutions emerged in the two backgrounds, and representative functional variants carrying ten or fewer amino-acid substitutions acquired flg22Xcc recognition. Together, these results show that, for this defined flg22Xcc escape challenge, AF3-guided discovery and iterative local sequence exploration can reconstruct recognition across divergent FLS2 scaffolds through a limited number of receptor substitutions.