New Phytologist

Solanum L. is one of the worlds largest and economically most important plant genera, including 1,245 currently accepted species and several major and minor crops (e.g., tomato, potato, brinjal eggplant, scarlet eggplant, Gboma eggplant, lulo, and pepino). Here we provide an overview of the evolution of 25 key morphological traits for the major and minor clades of this giant genus based on stochastic mapping using a well-sampled recently published phylogeny of Solanum. The most evolutionarily labile traits (showing >150 transitions across the genus) relate to plant structure (growth form and sympodial unit structure), herbivore defence (glandular trichomes), pollination (corolla shape and colour), and dispersal (fruit colour). Ten further traits show evolutionary lability with 50-100 transitions across the genus (e.g., specialised underground organs, trichome structure, leaf type, inflorescence position and branching, stamen heteromorphism). Our results reveal a number of highly convergent traits in Solanum, including tubers, rhizomes, simple leaves, yellow corollas, heteromorphic anthers, dioecy, and dry fruits, and some unexpected pathways of trait evolution that could be explored in future studies. We show that informally named clades of Solanum can be morphologically defined by trait combinations providing a tool for identification and enabling predictive phylogenetic placement of unsampled species.

The genus Silene is an important model system for fields as diverse as sex chromosome evolution, speciation and disease ecology. However, genomic resources remain scarce in the genus. Here, we present a chromosome-scale genome assembly for S. uniflora, a hermaphroditic/gynodioecious species which is an important model for rapid adaptation to anthropogenic disturbance and the role of phenotypic plasticity in adaptive evolution. Using a combination of long-read and Hi-C sequencing technologies, we generated a 1,268 Mb genome assembly with a scaffold N50 of 40.72 Mb and 682 Mb assembled into 12 chromosomes. We annotated the genome using evidence from transcriptome and protein mapping in combination with ab initio gene prediction, resulting in 41,603 protein-coding genes and a BUSCO completeness score of 91%. We also present a linkage map which we used to validate the genome assembly and estimate local recombination rate across the genome. Comparison to the only two other Silene species with chromosome-scale genome assemblies reveals widespread genome rearrangements in the genus, suggesting Silene may be a promising study system for the role of genome rearrangement in evolution, particularly in the evolution of sex chromosomes and adaptation. Significance statementPlant species in the genus Silene (campions) are important study organisms in multiple areas of ecology and evolution. Sea campion (Silene uniflora) is an important model for investigations into rapid adaptation, phenotypic plasticity and parallel evolution. However, only two species have high-quality genome assemblies available, hampering studies of their genetics and evolution. We present a high-quality genome assembly, genetic map and gene annotation for sea campion. These will be important genomic resources for future studies of sea campion, other species in the genus Silene and the family Caryophyllaceae more generally.

The genus Asparagus arose approximately 9-15 million years ago (Ma) and transitions from hermaphroditism to dioecy (separate sexes) occurred [~]3-4 Ma. Roughly 27% of extant Asparagus species are dioecious, while the remaining are bisexual with monoclinous flowers. As such, Asparagus is an ideal model taxon for studying early stages of dioecy and sex chromosome evolution in plants. Until now, however, understanding of diversification and shifts from hermaphroditism to dioecy in Asparagus has been hampered by the lack of robust species tree estimates for the genus. In this study, a genus-wide phylogenomic analysis including 1726 nuclear loci and comprehensive species sampling supports two independent origins of dioecy in Asparagus--first in a widely distributed Eurasian clade, then again in a clade restricted to the Mediterranean Basin. Modeling of ancestral biogeography indicates that both dioecy origins were associated with range expansion out of southern Africa. Our findings also revealed several bursts of diversification across the phylogeny, including an initial radiation in southern Africa that gave rise to 12 major clades in the genus, and more recent radiations that have resulted in paraphyly and polyphyly among closely related species, as expected given active speciation processes. Lastly, we report that the geographic origin of domesticated garden asparagus (Asparagus officinalis L.) was likely in western Asia near the Mediterranean Sea. The presented phylogenomic framework for Asparagus is foundational for ongoing genomic investigations of diversification and functional trait evolution in the genus and contributes to its utility for understanding the origin and early evolution of dioecy and sex chromosomes. Significance StatementAsparagus is an important model system for studying dioecy (separate sexes) evolution in plants. Asparagus taxonomy has been challenging, likely due to rapid species diversifications leading to highly variable species with complicated relationships that are impossible to resolve with limited DNA-sequence data. Using phylogenomics and the largest species sampling to date, we show that all Asparagus lineages originated from an initial radiation in southern Africa and that separate range expansions out of southern Africa set the stage for two distinct origins of dioecy in Asparagus. Our findings provide a deeper understanding of species diversification and the role of long-distance dispersals in the evolution of dioecy. This study also illustrates the utility of phylogenomics for elucidating past and present speciation processes.

A phylogenetic framework explaining plant secondary metabolite diversity is lacking, but metabolite classes could represent adaptations to habitat resource availability. We test the hypothesis that primary adaptive strategies (competitors, C; stress-tolerators, S; ruderals, R) are associated, respectively, with nitrogenous metabolites synthesized in persistent organs (alkaloids), nitrogen-lacking aromatic terpenes and phenolics, and nitrogenous compounds prevalent in reproductive tissues (cyanogenic glucosides and glucosinolates). A matrix was compiled of 1019 species for which secondary metabolite pathways and CSR strategies are known. Accounting for phylogenetic relatedness and native biomes, we found that most phytochemical pathways did not correlate with strategy axes, but certain key associations were evident. C-selection was positively associated with amino acid-derived phenylpropanoids (low phylogenetic relatedness; {lambda} <0.5) and pyrrolizidine alkaloids and galloyl derivatives (high {lambda}), and negatively with N-lacking linear monoterpenes (low {lambda}). Nitrogenous cyanogenic glucosides positively correlated with R-selection (low {lambda}). Terpenoids were widely distributed, but correlated positively with S- and negatively with R-selection (low {lambda}). Twenty-six correlations between phytochemicals and biomes (low {lambda}) were evident. Most secondary metabolite synthesis pathways are widespread, reflecting common roles and obligate defence, and strong phylogenetic effects are often evident. However, the character of phytochemical/adaptive strategy associations agrees with ecological theory and thus reflects adaptation.

BackgroundMost land plants depend on the ancestral arbuscular mycorrhizal (AM) symbiosis for phosphorus (P) acquisition. However, several plant lineages have independently lost this symbiosis, raising fundamental questions about how these non-mycorrhizal plants meet their nutritional requirements without this crucial partnership. ResultsComparative genomic analyses confirmed that Cyperaceae, Caryophyllaceae, and Brassicaceae lack genes essential for AM symbiosis, indicating that these lineages independently abandoned this association 90-122 million years ago. Field surveys of 42 wild populations across seven sites revealed that while non-mycorrhizal plants generally maintain shoot P levels comparable to those in AM neighbors, lower shoot P levels can be observed in low P soils. To identify fungal taxa potentially associated with P nutrition in non-mycorrhizal plants, we applied a machine-learning approach to predict plant P-accumulation from root microbiome composition. The model explained substantial variance in plant P-accumulation (57-69%), and identified 85 fungal taxa as key predictors of shoot P-accumulation, predominantly belonging to the Helotiales (28%) and Pleosporales (23%) orders. Experimental validation of two phylogenetically distant Helotiales lineages (Tetracladium maxilliforme OTU29 and Helotiales sp. OTU7), using isotopic tracing, demonstrated their capacity to enhance plant growth and transfer P (and N) to their native non-mycorrhizal hosts under P-limiting conditions. ConclusionsOur findings suggest that non-mycorrhizal plants engage in nutritional partnerships with diverse Helotiales lineages that could collectively contribute to their mineral nutrition. However, given the widespread distribution of these Helotiales fungi, including in roots of AM plants, they may play a broader role in plant nutrition, i.e. also in mycorrhizal hosts. This study provides proof of concept for a novel framework integrating machine-learning predictions with experimental validation to identify functionally important microbial partnerships in natural plant communities.

Interspecific differences in plant species ranges are shaped by complex mechanistic interactions, which have so far remained largely beyond the reach of comprehensive models and explanations. Previous attempts to find underlying mechanisms by examining physiological tolerances to cold and heat separately have yielded contradictory results. Here we test the hypothesis that, instead of examining single stressors, abiotic stress tolerance syndromes that involve trade-offs between multiple abiotic stressors (namely drought, cold, waterlogging and shade), will provide reliable explanations. We compiled a dataset of actual range size and range filling (the ratio between actual and potential species range) as range metrics for 331 temperate woody plants species from Europe and North America. Tolerance syndromes were expressed as two PCA axes. One axis reflects a drought-cold/waterlogging tolerance trade-off (cold/wet-drought trade-off), the second axis represents a shade tolerance spectrum. Phylogenetic generalized linear mixed models were used to model the range metric-tolerance axes relationships using latitude as an additional main effect, and phylogeny and plant functional type as random effects. Actual range scaled negatively with the cold/wet-drought tolerance trade-off axis, mostly independently of latitude and continent. Thus, cold/wet-tolerant species had the largest ranges and drought tolerant species the smallest. The sign (-) of the relationship was independent of phylogeny and plant functional type. In contrast, range filling depended on latitude. However, deciduous and evergreen species displayed different distributions of range metrics and tolerance syndromes. No significant relationships with the shade tolerance spectrum were found. Our findings demonstrate that the cold/wet-drought trade-off partly explains interspecific range size differences. However, this trade-off did not explain range filling. We also showed that fundamental adaptations of species also significantly influence range sizes - stress avoidance through the deciduous habit also explained interspecific differences in range size.

Understanding how leaf morphology mediates plant responses to environmental variation is essential for predicting species adaptability under climate change. In this study, we investigated natural variation in leaf shape and associated functional- physiological traits (FPTs) across populations of Chenopodium hircinum grown in a common garden. We found that leaf shape strongly correlates with the climatic conditions of population provenance, while functional and physiological traits are independently associated with morphology rather than directly with climate. Landmark-based morphometric analysis revealed that the second principal component, distinguishing deeply lobed from rounded leaves, is significantly linked to key traits such as leaf mass per unit area (LMA) and stomatal conductance. These relationships suggest that morphology mediates a functional continuum between resource-use strategies. Notably, within-population phenotypic variation accounted for much of the observed trait diversity, underscoring the role of individual-level phenotypic plasticity in shaping ecological function. Our results challenge traditional views on the thermoregulatory role of leaf lobation and highlight morphology as a central axis of adaptation. This work advances understanding of trait integration in response to environmental heterogeneity and suggests that plasticity in leaf shape and function may enhance resilience of C. hircinum across its native range.

Leaf intercellular vapor pressure (ei) can be unsaturated, but its effect on leaf water heavy isotope enrichment (LWE) has not yet been quantified. We evaluated the ecological relevance of unsaturated ei for LWE, i.e., for leaf water oxygen-18 and deuterium enrichment, using data from a boreal forest stand and a large-scale dataset. Unsaturated ei can firstly affect LWE by directly decreasing ei in the Craig Gordon model (Mechanism 1), which leads to an increased influence of atmospheric vapor isotopic enrichment above source water ({Delta}v), and a decreased influence of kinetic fractionation by diffusion through the stomata and boundary layer ({varepsilon}k). Unsaturated ei can secondly affect LWE by changing {varepsilon}k (Mechanism 2). To evaluate the effect of Mechanism 1 to LWE, we employed sensitivity tests on LWE model performance using varying measured intercellular relative humidity (RHcellular), or RHcellular fitted to observed LWE. To explore the effects of Mechanism 2 to LWE, we modified the calculation of {varepsilon}k and observed consequences to LWE predictions. Unsaturated ei is relevant to LWE by Mechanism 1, since a lowered RHcellular noticeably changed LWE predictions. It clearly improved deuterium predictions and conditionally improved oxygen-18 predictions. Isotope fractionation by Mechanism 2 is unlikely relevant to oxygen-18 and deuterium enrichment. Unsaturated ei must now be recognized as a variable that introduces error to heavy isotope enrichment models and reconstructions from organic material, via Mechanism 1. We suggest a correction for unsaturated ei for both oxygen-18 and deuterium enrichment using a variable RHcellular calculated from atmospheric relative humidity.

Mycorrhizal fungi form essential mutualisms with the majority of land plants, yet their role on plant community composition and diversification remains poorly understood. Orchids provide a model system for studying these interactions because the orchid life cycle obligatorily depends on mycorrhizae. Historically, studies have emphasized the role of niche partitioning and competition avoidance resulting in distinct mycobiome compositions among coexisting orchids. Since closely related orchid species have been found to associate with similar groups of fungi, it has been speculated that different fungal species are needed for coexistence but not for speciation. However, fungi have often been examined at lower resolution levels (i.e., class, order, family, or genus). Using third-generation long-read sequencing (PacBio) of the full ITS region, we characterized fungal communities at fine scale with high accuracy. We evaluated alpha- and beta-diversity of fungal communities in four closely related, narrowly endemic epiphytic orchid species from the rapidly diversifying genus Lepanthes in one of the worlds richest biodiversity hotspots. Our analyses reveal that orchid species have distinct mycobiont assemblages, with differences in composition unevenly distributed across species. These results suggest that shifts in fungal partners may contribute to speciation and rapid diversification in Lepanthes. This study highlights the potential evolutionary role of mycorrhizal fungi in orchid diversification and demonstrates the value of high-resolution sequencing in uncovering cryptic fungal diversity.

Background and AimsHybrid seed failure (HSF) is a common reproductive barrier in flowering plants, but how divergence in so-called effective ploidy translates into genome-wide allelic imbalance in hybrid endosperm remains unresolved. Using wild tomatoes (Solanum sect. Lycopersicon) as our model system, we test whether parent-of-origin expression shifts in hybrids are consistent with simple dosage effects or instead reflect lineage-specific trans regulation. MethodsUsing reciprocal interspecific crosses, we quantified parent-of-origin (allele-specific) expression in developing endosperm and analyzed patterns of differential parent-of-origin expression (DPE) across cross contexts. Guided by strong patterns in parental expression, we further classified DPE genes into four functional classes defined by their relationship to Solanum peruvianum (Per). This exercise captured distinct modes of trans-allelic regulation and guided functional interpretation. Key ResultsParental expression proportions are strongly asymmetric in hybrids, with the most pronounced and repeatable shifts occurring in crosses involving Per. These shifts recur across reciprocal contexts and include elevated maternal proportions even in crosses phenotypically classified as paternal-excess-like, arguing against a dosage-only model. Instead, we observed cross-consistent, coordinated DPE patterns corresponding to trans-acting dominance associated with Per. Functional enrichment of Per-associated DPE highlights chromatin regulation, including DNA methylation/RdDM- and chromatin remodeling-related factors, and Polycomb-linked regulators, implicating disruption of chromatin-based repression in hybrid endosperm. Concurrently, Per-associated activation of auxin- and cell-cycle regulatory pathways in non-Per alleles suggests mis-timed hormone-dependent developmental transitions that can destabilize proliferation-cellularization programs. ConclusionsOur findings support a model of trans-allelic epigenetic dominance in which Per-associated regulatory inputs reshape allelic expression landscapes in hybrid endosperm largely independent of parental origin. This provides a mechanistic link between effective ploidy divergence, genome-wide transcriptional imbalance, and HSF, and motivates reciprocal hybrid studies that integrate expression with chromatin-state and accessibility profiling.

Male reproductive investment, in particular pollen production, is a crucial and ecologically relevant component of a plants phenotype and reproductive success. Its evolutionary trajectory, however, remains understudied, partly due to a lack of convenient methods to assess it. We developed a protocol for pollen quantification by flow cytometry and applied it to 107 flowers from 38 Papaveraceae species differing widely in floral traits (e.g., floral symmetry, stamen number), pollination syndromes (e.g., wind and insect pollination) and reproductive systems (e.g., degree of autogamy). We phylogenetically tested whether pollen number evolved in association with ovule, carpel, stamen and flower numbers per inflorescence, and if there were interacting effects between floral symmetry and/or self-compatibility with pollen and ovule production. Compared to manual counts, results using flow cytometry were similar, but much faster to obtain and more precise. Pollen and ovule numbers per flower varied > 39,000x and > 550x, respectively, among species. Pollen production correlated positively with ovule, carpel and stamen numbers. Lineage-specific trajectories to pollen-to-ovule ratio reduction (to values < 300) are observed. One involved increased female investment in ruderal species belonging to the subfamily Papaveroideae, while the other occurs through decreased male investment and is associated with the evolution of floral traits towards greater specialisation. The impact of reproductive systems on male and female investment is limited to ovule production in non-actinomorphic flowers. Taken together, these results revealed that the evolutionary associations between reproductive systems, floral traits, and pollen and ovule production are lineage-specific. Given the profound contrasts at the subfamily level of Papaveraceae, broader surveys across the diversity of flowering plants are clearly needed to better understand factors driving the evolution of reproductive investment. Such studies will certainly be facilitated by our new high-throughput pollen counting method outlined here.

Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last five million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as sexual swindling. However, the rapid and substantial diversification of this genus, combined with its capacity for hybridisation and large genome size, poses significant challenges in addressing its systematics. We used phylotranscriptomics as a genome complexity reduction technique to infer the phylogenetic relationships among Ophrys main lineages. More than seven thousand gene trees enabled us to determine the relative contributions of gene flow and incomplete lineage sorting (ILS) in Ophrys evolution. First, we propose a new phylogenetic hypothesis for the genus with an unprecedented resolution that largely confirms the relationships between the main Ophrys lineages, but also provides new insights within each sub-genera. By combining phylogenetic network inference with introgression analyses based on gene tree topologies and branch lengths, we then show that the numerous phylogenetic incongruences among gene tree topologies result from a pervasive background of ILS, over which stand out several well-supported, ancient and potentially adaptive gene flow events between lineages. These major gene flow events provide a new perspective on the evolution of the Ophrys genus and its pollination, questioning previous hypotheses inferred without considering its reticulate evolution, and providing a better understanding of discrepancies observed among previous phylogenetic studies of the genus.

Flower colour is known to be a classic magic trait, undergoing divergent selection pressures exerted by distinct pollinators and involved in reproductive isolation. However, variation at this trait may also results from other eco-evolutionary factors whose interpretation requires throughout context-specific analyses. Here, we investigated the eco-evolutionary causes of pink- and yellow-flowered morphs in Pedicularis comosa where their parapatric ranges form a contact zone in the East of the Pyrenees Mountains. First, we generated a near-chromosome-scale reference genome assembly for this species. We then used a Genotyping By Sequencing approach to infer patterns of genetic diversity and differentiation between populations and morphs at a total of 158 individuals from 11 localities. We found that neutral genetic structure is primarily consistent with geography rather than with colour. However, admixture analyses and clines suggest the existence of a cryptic hybrid zone between morphs. Outlier detection methods and examination of locus-by-locus cline features, then allowed to pinpoint candidate loci to explain colour variation. To gain insight into the functional aspects of these loci, we finally analysed floral transcriptomes and quantified pigments using Liquid Chromatography coupled with Mass Spectrometry (LC-MS) and confirmed the involvement of key genes in the anthocyanin metabolic pathway (e.g. DFR, FLS) and associated pigments (e.g. cyanidin and delphinidin). Our results show that implementing a highly integrative multi-omic approach can allow unraveling the genetic basis and the eco-evolutionary significance of adaptive traits with even very limited previous knowledge, on species with large and complex genomes.

Reconstructing the biogeographical history and timing of the diversification of temperate forests is essential for understanding their history and resolving uncertainties about how flowering plants emerged from their deep tropical origins to dominate in todays freezing terrestrial environments. The angiosperm order Fagales, comprising iconic components of temperate forests worldwide with an extensive fossil record, are an excellent plant system in which to apply a fossil-aware paradigm, such as the fossilized birth-death (FBD) process, for investigating the macroevolution of temperate forest biomes. Here, we improve upon previous efforts to resolve phylogeny and incorporate fossils in Fagales using low-copy nuclear loci and an expanded morphological matrix to reevaluate the Fagales fossil record and: (1) infer the phylogenetic relationships and the time of origin of the clade using the FBD model as implemented in RevBayes, (2) provide a framework for evaluating the climatic and biogeographic history of Fagales, and (3) investigate how the inclusion of fossils via the FBD method influences ancestral reconstruction and diversification estimation. The phylogenetic relationships we recovered are conventional except for the position of Nothofagaceae, while our inferred ages support older timelines than previously proposed, with a mid-Cretaceous date for the most recent common ancestor (MRCA) of the order. Biogeographical analysis shows an origin of Fagales consistent with an ancestral circumboreal temperate distribution corroborated by ancestral niche reconstructions. While distributions today largely reflect the general conservatism of temperate forests, we identified two episodes of high diversification, one at the mid-Cretaceous origin of the clade and the other continuing from the Miocene to the present. Removing fossil taxa from the tree reveals a different story, shifting the origin of extant families from North America to East Asia, reflecting refugial distributions in this biodiversity "museum" and implying a general bias towards low extinction areas in biogeographic reconstruction. Likewise, without fossil data, diversification estimates were higher and unable to detect an early diversification burst. Based on our analyses, we close with recommendations regarding the interpretation of estimates of diversification and ancestral state reconstruction using phylogenetic trees with only extant species as tips.

Dioecy, the condition in which male and female individuals exist as separate plants, represents a fascinating and relatively rare reproductive strategy, offering unique opportunities to study the genetic and epigenetic regulation of sexual dimorphism. While sex determining genes underlying dioecy have already been described for several plant species, the role of epigenetic modifications in meristematic cell populations remains poorly understood. In this study we describe the spatio-temporal deposition of three epigenetic markers during early stages of floral development in model dioecious species Silene latifolia. We selected H3K4me1, H3K9me2 and active Ser2 phosphorylated form of RNA Polymerase II (Pol-IIS2ph), to assess levels of chromatin condensation and transcriptional activity of meristematic cells during key developmental stages. Utilizing the novel approach of an AI-assisted nuclei segmentation and high-content imaging we created a single-cell resolution atlas for male and female floral meristems. Our results show a relationship between transcription activity and sex determination during early meristem development. Moreover, our results suggest that H3K9me2 deposition in the developing meristem is linked to sex-specific chromatin reprogramming events, such as pollen mother cell formation during anther maturation. Overall, these results offer new insights into the role of chromatin regulation during floral meristem development and improves our understanding of sexual dimorphism in dioecious species.

Despite the global importance of species with C4 photosynthesis, there is a lack of consensus regarding C4 performance under fluctuating light. Contrasting hypotheses and experimental evidence suggest that C4 photosynthesis is either less, or more efficient in fixing carbon under fluctuating light than the ancestral C3 form. Two main issues were identified that may underly the lack of consensus: neglect of evolutionary distance between selected C3 and C4 species and use of contrasting fluctuating light treatments. To circumvent these issues, we compared photosynthetic responses to fluctuating light across three independent phylogenetically controlled comparisons between C3 and C4 species from Alloteropsis, Flaveria, and Cleome genera under 21% and 2% O2. Leaves were subjected to repetitive stepwise changes in light intensity (800 and 100 {micro}mol m-2 s-1 PFD) with three contrasting durations: 6, 30 and 300 seconds. These experiments reconcile the opposing results found across previous studies showing that 1) stimulation of CO2 assimilation in C4 species during the low light phase was both stronger and more sustained than in C3 species; 2) CO2 assimilation patterns during the high light phase were genus-specific rather than impacted by photosynthetic pathway; and 3) the duration of each light step in the fluctuation regime can strongly influence experimental outcomes. One sentence significance statementComparing photosynthesis in three pairs of closely related C3 and C4 species across three fluctuating light regimes showed that C4 photosynthesis has a systematic advantage under the low light phase not related to suppression of photorespiration, while the comparative efficiency under the high light phase was not determined by photosynthetic pathway.

Quantifying the variation in plant traits reveals the trade-offs involved in plant ecological strategies and is fundamental to understanding underlying plant fitness mechanisms. Thus, the ecological success of plant species in a certain habitat may depend on the coordinated performance of both leaves and roots. However, despite the growing interest in trait variation, it is still uncertain i) to what extent the leaf economics spectrum (LES) and root economics space (RES) hold across locally coexisting tree species and ii) whether leaf and fine-root traits are correlated. In a research arboretum, we simultaneously measured eight key traits in leaves and fine-roots on 270 individuals belonging to 90 tree species, encompassing both angiosperm and gymnosperm species. We find varied plant resource strategies associated with leaves and fine-roots for angiosperms and gymnosperms. We observe a clear LES for gymnosperms and a clear RES for angiosperms. Our results support the existence of a correlation between analogous leaf and fine-root traits across all species. However, varying trait coordination across clades indicates varying resource acquisition strategies above- and belowground, highlighting the need to consider large-scale phylogenetic relatedness to better understand plant fitness.

Euphorbia peplus (petty spurge) is a small, fast-growing plant that is native to Eurasia and has become a naturalized weed in North America and Australia. E. peplus is not only medicinally valuable, serving as a source for the skin cancer drug ingenol mebutate, but also has great potential as a model for latex production owing to its small size, ease of manipulation in the laboratory, and rapid reproductive cycle. To help establish E. peplus as a new model, we generated a 267.2 Mb HiC-anchored PacBio HiFi nuclear genome assembly with an embryophyta BUSCO score of 98.5%, a genome annotation based on RNA-seq data from six tissues, and publicly accessible tools including a genome browser and an interactive organ-specific expression atlas. Chromosome number is highly variable across Euphorbia species. Using a comparative analysis of our newly sequenced E. peplus genome with other Euphorbiaceae genomes, we show that variation in Euphorbia chromosome number is likely due to fragmentation and rearrangement rather than aneuploidy. Moreover, we found that the E. peplus genome is relatively compact compared to related members of the genus in part due to restricted expansion of the Ty3 transposon family. Finally, we identify a large gene cluster that contains many previously identified enzymes in the putative ingenol mebutate biosynthesis pathway, along with additional gene candidates for this biosynthetic pathway. The genomic resources we have created for E. peplus will help advance research on latex production and ingenol mebutate biosynthesis in the commercially important Euphorbiaceae family. Significance statementEuphorbia is one of the five largest genera in the plant kingdom. Despite an impressive phenotypic and metabolic diversity in this genus, only one Euphorbia genome has been sequenced so far, restricting insights into Euphorbia biology. Euphorbia peplus has excellent potential as a model species due to its latex production, fast growth rate and production of the anticancer drug ingenol mebutate. Here, we present a chromosome-level E. peplus genome assembly and publicly accessible resources to support molecular research for this unique species and the broader genus. We also provide an explanation of one reason the genome is so small, and identify more candidate genes for the anticancer drug and related compounds.

The mechanisms underlying cellular coordination within tissues remain enigmatic. Most models focus on interactions between just two levels of organization - cell and tissue - and do not leverage data across deeper hierarchies that best represent living processes, with many spatial and temporal scales interacting. Integrating many scales, from molecular to cellular to tissular to organismal to populational, may be necessary to fully elucidate tissue function, especially in cases of sparse data at each level. Here, we investigate multiscale, robust regulation of tissue-level decision-making, using experimental studies of cold induced dormancy release in terminal buds of hybrid aspen trees as our case study. We develop a network model of terminal bud meristematic tissue, incorporating expression data from a key cold induced regulator gene, FLOWERING LOCUS T (FT1), which controls bud dormancy release, combined with data on variability in cell-to-cell communication controlled by FT1 mediated regulation of plasmodesmata. The model can explain dormancy breaking under constant temperature, but not variable temperature. We introduce constraints from organismal-level data and show how the presence of coordinated cellular interactions within individual plant tissues is necessary to reproduce data of population-level statistics. Our findings demonstrate how mechanisms of tissue function may be better constrained when data are used across more scales. They also hint at potential tantalizing new insights such as how tissue function might not be solely dictated bottom-up from molecular interactions, but also top-down from constraints imposed by the organismal and population context. Both implications illustrate the critical importance of incorporating cross-scale information processing in modeling biological decision-making. Significance StatementBiological hierarchies involve decision-making mediated via nested feedback loops. Data-informed modeling of this hierarchal complexity remains challenging. Here, we leverage unique features of plant biology - stationary growth, prolonged decision-making, and physical structure - to study multiscale dynamics determining cellular mechanisms of bud dormancy breaking in aspen trees. We examine how tissue function can be driven bottom-up from gene regulatory networks and top-down from organismal population-level statistics. Modeling experimental data collected at genetic, cellular, and organismal levels, reveals how population-level data allow constraining mechanisms of cellular coordination within individual plants when cellular data are sparse. Our findings demonstrate how multiscale methods can combat data sparsity and suggest new ways to study cellular coordination within organisms could be dictated by organismal population-level constraints.

The seed coat that encases the embryo is constituted from multiple specialized-cell layers and their permeability significantly influences seed quality traits that have major agronomic impact. The regulatory mechanisms that modulate seed coat permeability are, however, not well understood. Here, we identified a novel regulatory gene for seed permeability through a genome wide association study (GWAS) in Arabidopsis based on image analysis of tetrazolium staining. Type-A ARABIDOPSIS RESPONSE REGULATOR 16 (ARR16) is a component of the signal transduction pathway for the plant hormone cytokinins (CKs), and in addition to less permeable seed coats, arr16 mutant seeds were larger, had a longer lifespan, and more suberin phenolics, the hydrophobic lipid biopolyester components of cell walls that act as a water-repellant. Moreover, double mutants in CK receptor ARABIDOPSIS HISTIDINE KINASE genes, notably ahk2 ahk4 and ahk3 ahk4, showed similar seed phenotypes to those of arr16. Based on naturally-occurring variation in the ARR16 gene, eight haplotypes were detected and associated with permeable or impermeable phenotypes. Permeable haplotypes had significantly lower suberin autofluorescence compared to impermeable haplotypes. RT-qPCR analysis demonstrated that ARR16 transcripts were highly abundant in developing seeds of representative accessions having permeable haplotypes but not in those of having impermeable haplotypes, indicating that these haplotypes were causal for ARR16 transcript abundance and thereby regulate seed coat permeability in natural accessions. Our findings demonstrate a new role for CKs signaling in seed coat differentiation and that this underlies natural variation for seed permeability through the modulation of suberin accumulation. Significance StatementSeed coat permeability affects key traits that impact seed quality, such as dormancy, longevity, and germination tolerance to abiotic stress. Little is currently known about how seed coat permeability is modulated. Here, we developed an original method for quantification of seed coat permeability through imaging and used this in a genome-wide association study with Arabidopsis accessions. The CKs response regulator ARR16 was identified as a causal gene thereby establishing a novel function for this phytohormone in seed coat differentiation. Moreover, this was linked to the modulation of suberin accumulation by ARR16 and for the first time implicates CKs signal transduction in the control of suberin deposition in seeds.