Australia is an excellent setting to explore relationships between climate change and diversification dynamics. Aridification since the Eocene has resulted in spectacular radiations within one or more Australian biomes. Acacia is the largest plant genus on the Australian continent, with around 1000 species, and is present in all biomes. We investigated the macroevolutionary dynamics of Acacia within climate space. We analysed phylogenetic and climatic data for 503 Acacia species to estimate a time‐calibrated phylogeny and central climatic tendencies for BioClim layers from 132 000 herbarium specimens. Diversification rate heterogeneity and rates of climate space exploration were tested. We inferred two diversification rate increases, both associated with significantly higher rates of climate space exploration. Observed spikes in climate disparity within the Pleistocene correspond with onset of Pleistocene glacial–interglacial cycling. Positive time dependency in environmental disparity applies in the basal grade of Acacia, though climate space exploration rates were lower. Incongruence between rates of climate space exploration and disparity suggests different Acacia lineages have experienced different macroevolutionary processes. The second diversification rate increase is associated with a south‐east Australian mesic lineage, suggesting adaptations to progressively aridifying environments and ability to transition into mesic environments contributed to Acacia's dominance across Australia.

Secretory and transmembrane protein synthesis and initial modification are essential processes in protein maturation, and these processes are important for maintaining protein homeostasis in the endoplasmic reticulum (ER). ER homeostasis can be disrupted by the accumulation of misfolded proteins, resulting in ER stress, due to specific intra‐ or extracellular stresses. Processes including the unfolded protein response (UPR), ER‐associated degradation (ERAD) and autophagy are thought to play important roles in restoring ER homeostasis. Here, we focus on summarizing and analysing recent advances in our understanding of the role of ERAD in plant physiological processes, especially in plant adaption to biotic and abiotic stresses, and also identify several issues that still need to be resolved in this field.

Biological invasions offer model systems of contemporary evolution. We examined trait differences and evolution across geographic clines among continents of the intertidal grass Spartina alterniflora within its invasive and native ranges. We sampled vegetative and reproductive traits in the field at 20 sites over 20° latitude in China (invasive range) and 28 sites over 17° in the US (native range). We grew both Chinese and US plants in a glasshouse common garden for 3 yr. Chinese plants were c. 15% taller, c. 10% denser, and set up to four times more seed than US plants in both the field and common garden. The common garden experiments showed a striking genetic cline of seven‐fold greater seed set at higher latitudes in the introduced but not the native range. By contrast, there was a slight genetic cline in some vegetative traits in the native but not the introduced range. Our results are consistent with others showing that introduced plants can evolve rapidly in the new range. S. alterniflora has evolved different trait clines in the native and introduced ranges, showing the importance of phenotypic plasticity and genetic control of change during the invasion process.

Lead (Pb) ranks among the most problematic environmental pollutants. Background contamination of soils is nearly ubiquitous, yet plant Pb accumulation is barely understood. In a survey covering 165 European populations of the metallophyte Arabidopsis halleri, several field samples had indicated Pb hyperaccumulation, offering a chance to dissect plant Pb accumulation. Accumulation of Pb was analysed in A. halleri individuals from contrasting habitats under controlled conditions to rule out aerial deposition as a source of apparent Pb accumulation. Several elemental imaging techniques were employed to study the spatial distribution and ligand environment of Pb. Regardless of genetic background, A. halleri individuals showed higher shoot Pb accumulation than A. thaliana. However, dose–response curves revealed indicator rather than hyperaccumulator behaviour. Xylem sap data and elemental imaging unequivocally demonstrated the in planta mobility of Pb. Highest Pb concentrations were found in epidermal and vascular tissues. Distribution of Pb was distinct from that of the hyperaccumulated metal zinc. Most Pb was bound by oxygen ligands in bidentate coordination. A. halleri accumulates Pb whenever soil conditions render Pb phytoavailable. Considerable Pb accumulation under such circumstances, even in leaves of A. thaliana, strongly suggests that Pb can enter food webs and may pose a food safety risk.

Flowers have been hypothesized to contain either modules of attraction and reproduction, functional modules (pollination‐effecting parts) or developmental modules (organ‐specific). Do pollination specialization and syndromes influence floral modularity? In order to test these hypotheses and answer this question, we focused on the genus Erica: we gathered 3D data from flowers of 19 species with diverse syndromes via computed tomography, and for the first time tested the above‐mentioned hypotheses via 3D geometric morphometrics. To provide an evolutionary framework for our results, we tested the evolutionary mode of floral shape, size and integration under the syndromes regime, and – for the first time – reconstructed the high‐dimensional floral shape of their most recent common ancestor. We demonstrate that the modularity of the 3D shape of generalist flowers depends on development and that of specialists is linked to function: modules of pollen deposition and receipt in bird syndrome, and access‐restriction to the floral reward in long‐proboscid fly syndrome. Only size and shape principal component 1 showed multiple‐optima selection, suggesting that they were co‐opted during evolution to adapt flowers to novel pollinators. Whole floral shape followed an Ornstein–Uhlenbeck (selection‐driven) evolutionary model, and differentiated relatively late. Flower shape modularity thus crucially depends on pollinator specialization and syndrome.

Transposable elements (TEs) are ubiquitous in plants and are the primary genomic component of the majority of taxa. Knowledge of their impact on the structure, function and evolution of plant genomes is therefore a priority in the field of genomics. Rice, as one of the most prevalent crops for food security worldwide, has been subjected to intense research efforts over recent decades. Consequently, a considerable amount of genomic resources has been generated and made freely available to the scientific community. These can be exploited both to improve our understanding of some basic aspects of genome biology of this species and to develop new concepts for crop improvement. In this review, we describe the current knowledge on how TEs have shaped rice chromosomes and propose a new strategy based on a genome‐wide association study (GWAS) to address the important question of their functional impact on this crop.

Vacuolar (H+)‐PPases (VPs), are key regulators of active proton (H+) transport across membranes using the energy generated from PPi hydrolysis. The VPs also play vital roles in plant responses to various abiotic stresses. Their functions in plant responses to pathogen infections are unknown. Here, we show that TaVP, a VP of wheat (Triticum aestivum) is important for wheat resistance to Chinese wheat mosaic virus (CWMV) infection. Furthermore, overexpression of TaVP in plants induces the activity of PPi hydrolysis, leading to plants cell death. A virus‐derived small interfering RNA (vsiRNA‐20) generated from CWMV RNA1 can regulate the mRNA accumulation of TaVP in wheat. The accumulation of vsiRNA‐20 can suppress cell death induced by TaVP in a dosage‐dependent manner. Moreover, we show that the accumulation of vsiRNA‐20 can affect PPi hydrolysis and the concentration of H+ in CWMV‐infected wheat cells to create a more favorable cellular environment for CWMV replication. We propose that vsiRNA‐20 regulates TaVP expression to prevent cell death and to maintain a weak alkaline environment in cytoplasm to enhance CWMV infection in wheat. This finding may be used as a novel strategy to minimize virus pathogenicity and to develop new antiviral stratagems.

As Arctic soils warm, thawed permafrost releases nitrogen (N) that could stimulate plant productivity and thus offset soil carbon losses from tundra ecosystems. Although mycorrhizal fungi could facilitate plant access to permafrost‐derived N, their exploration capacity beyond host plant root systems into deep, cold active layer soils adjacent to the permafrost table is unknown. We characterized root‐associated fungi (RAF) that colonized ericoid (ERM) and ectomycorrhizal (ECM) shrub roots and occurred below the maximum rooting depth in permafrost thaw‐front soil in tussock and shrub tundra communities. We explored the relationships between root and thaw front fungal composition and plant uptake of a 15N tracer applied at the permafrost boundary. We show that ERM and ECM shrubs associate with RAF at the thaw front providing evidence for potential mycelial connectivity between roots and the permafrost boundary. Among shrubs and tundra communities, RAF connectivity to the thaw boundary was ubiquitous. The occurrence of particular RAF in both roots and thaw front soil was positively correlated with 15N recovered in shrub biomass Taxon‐specific RAF associations could be a mechanism for the vertical redistribution of deep, permafrost‐derived nutrients, which may alleviate N limitation and stimulate productivity in warming tundra.

At the colonization site of a foreign entity, plant cells alter their trajectory of growth and development. The resulting structure – a plant gall – accommodates various needs of the foreigner, which are phylogenetically diverse: viruses, bacteria, protozoa, oomycetes, true fungi, parasitic plants, and many types of animals, including rotifers, nematodes, insects, and mites. The plant species that make galls also are diverse. We assume gall production costs the plant. All is well if the foreigner provides a gift that makes up for the cost. Nitrogen‐fixing nodule‐inducing bacteria provide nutritional services. Gall wasps pollinate fig trees. Unfortunately for plants, most galls are made for foes, some of which are deeply studied pathogens and pests: Agrobacterium tumefaciens, Rhodococcus fascians, Xanthomonas citri, Pseudomonas savastanoi, Pantoea agglomerans, ‘Candidatus’ phytoplasma, rust fungi, Ustilago smuts, root knot and cyst nematodes, and gall midges. Galls are an understudied phenomenon in plant developmental biology. We propose gall inception for discovering unifying features of the galls that plants make for friends and foes, talk about molecules that plants and gall‐inducers use to get what they want from each other, raise the question of whether plants colonized by arbuscular mycorrhizal fungi respond in a gall‐like manner, and present a research agenda.

Root water uptake is a key ecohydrological process for which a physically based understanding has been developed in the past decades. However, due to methodological constraints, knowledge gaps remain about the plastic response of whole plant root systems to a rapidly changing environment. We designed a laboratory system for nondestructive monitoring of stable isotopic composition in plant transpiration of a herbaceous species (Centaurea jacea) and of soil water across depths, taking advantage of newly developed in situ methods. Daily root water uptake profiles were obtained using a statistical Bayesian multisource mixing model. Fast shifts in the isotopic composition of both soil and transpiration water could be observed with the setup and translated into dynamic and pronounced shifts of the root water uptake profile, even in well watered conditions. The incorporation of plant physiological and soil physical information into statistical modelling improved the model output. A simple exercise of water balance closure underlined the nonunique relationship between root water uptake profile on the one hand, and water content and root distribution profiles on the other, illustrating the continuous adaption of the plant water uptake as a function of its root hydraulic architecture and soil water availability during the experiment.

Brachypodium distachyon is a weedy grass species that is firmly established as a model for the comparative and functional genomics of temperate cereals and grasses. Its simple, nuclear genome of five chromosomes contrasts it with other relatives of the genus with different, and usually higher, basic chromosome numbers and ploidy levels. This variation in karyotypic structure affords the possibility of reconstructing evolutionary pathways that have shaped the genome structure of extant species. This Tansley insight documents how key refinements in molecular cytogenetic approaches, from simple fluorescence in situ hybridization to comparative chromosome barcoding, have enabled genome structure studies and yielded valuable information about the drivers of karyotypic reorganization and evolution in the model grass genus Brachypodium.

Plants produce and emit terpenes, including sesquiterpenes, during growth and development, which serve different functions in plants. The sesquiterpene nerolidol has health‐promoting properties and adds a floral scent to plants. However, the glycosylation mechanism of nerolidol and its biological roles in plants remained unknown. Sesquiterpene UDP‐glucosyltransferases were selected by using metabolites‐genes correlation analysis, and its roles in response to cold stress were studied. We discovered the first plant UGT (UGT91Q2) in tea plant, whose expression is strongly induced by cold stress and which specifically catalyzes the glucosylation of nerolidol. The accumulation of nerolidol glucoside was consistent with the expression level of UGT91Q2 in response to cold stress, as well as in different tea cultivars. The reactive oxygen species (ROS) scavenging capacity of nerolidol glucoside was significantly higher than that of free nerolidol. Down‐regulation of UGT91Q2 resulted in reduced accumulation of nerolidol glucoside, ROS scavenging capacity and tea plant cold tolerance. Tea plants absorbed airborne nerolidol and converted it to its glucoside, subsequently enhancing tea plant cold stress tolerance. Nerolidol plays a role in response to cold stress as well as in triggering plant–plant communication in response to cold stress. Our findings reveal previously unidentified roles of volatiles in response to abiotic stress in plants.

The 90 kDa heat shock protein (HSP90) is widely involved in various developmental processes and stress responses in plants. However, the molecular chaperone HSP90‐constructed protein complex and its function in cassava remain elusive. In this study, we report that HSP90 is essential for drought stress resistance in cassava by regulating abscisic acid (ABA) and hydrogen peroxide (H2O2) using two specific protein inhibitors of HSP90 (geldanamycin (GDA) and radicicol (RAD)). Among 10 MeHSP90s, the transcript of MeHSP90.9 is largely induced during drought stress. Further investigation identifies MeWRKY20 and MeCatalase1 as MeHSP90.9‐interacting proteins. MeHSP90.9‐, MeWRKY20‐, or MeCatalase1‐silenced plants through virus‐induced gene silencing display drought sensitivity in cassava, indicating that they are important to drought stress response. MeHSP90.9 can promote the direct transcriptional activation of MeWRKY20 on the W‐box element of MeNCED5 promoter, encoding a key enzyme in ABA biosynthesis. Moreover, MeHSP90.9 positively regulates the activity of MeCatalase1, and MeHSP90.9‐silenced cassava leaves accumulate more H2O2 under drought stress. Taken together, we demonstrate that the MeHSP90.9 chaperone complex is a regulator of drought stress resistance in cassava.

Cowpea (Vigna unguiculata) cultivar B301 is resistant to races SG4 and SG3 of the root parasitic weed Striga gesnerioides, developing a hypersensitive response (HR) at the site of parasite attachment. By contrast, race SG4z overcomes B301 resistance and successfully parasitises the plant. Comparative transcriptomics and in silico analysis identified a small secreted effector protein dubbed Suppressor of Host Resistance 4z (SHR4z) in the SG4z haustorium that upon transfer to the host roots causes a loss of host immunity (i.e. decreased HR and increased parasite growth). SHR4z has significant homology to the short leucine‐rich repeat (LRR) domain of SOMATIC EMBRYOGENESIS RECEPTOR‐LIKE KINASE (SERK) family proteins and functions by binding to VuPOB1, a host BTB‐BACK domain‐containing ubiquitin E3 ligase homologue, leading to its rapid turnover. VuPOB1 is shown to be a positive regulator of HR since silencing of VuPOB1 expression in transgenic B301 roots lowers the frequency of HR and increases the levels of successful SG4 parasitism and overexpression decreases parasitism by SG4z. These findings provide new insights into how parasitic weeds overcome host defences and could potentially contribute to the development of novel strategies for controlling Striga and other parasitic weeds thereby enhancing crop productivity and food security globally.

The diversity of cytokinin (CK) metabolites suggests their interconversions are the predominant regulatory mechanism of CK action. Nevertheless, little is known about their directionality and kinetics in planta. CK metabolite levels were measured in 2‐wk‐old Arabidopsis thaliana plants at several time points up to 100 min following exogenous application of selected CKs. The data were then evaluated qualitatively and by mathematical modeling. Apart from elevated levels of trans‐zeatin (tZ) metabolites upon application of N6‐(Δ2‐isopentenyl)adenine (iP), we observed no conversions between the individual CK‐types – iP, tZ, dihydrozeatin (DHZ) and cis‐zeatin (cZ). In particular, there was no sign of isomerization between tZ and cZ families. Also, no increase of DHZ‐type CKs was observed after application of tZ, suggesting low baseline activity of zeatin reductase. Among N‐glucosides, those of iP were not converted back to iP while tZ N‐glucosides were cleaved to tZ bases, thus affecting the whole metabolic spectrum. We present the first large‐scale study of short‐term CK metabolism kinetics and show that tZ N7‐ and N9‐glucosides are metabolized in vivo. We thus refute the generally accepted hypothesis that N‐glucosylation irreversibly inactivates CKs. The subsequently constructed mathematical model provides estimates of the metabolic conversion rates.

A frequent hypothesis explaining the high susceptibility of many crops to pests and diseases is that, in the process of domestication, crops have lost defensive genes and traits against pests and diseases. Ecological theory predicts trade‐offs whereby resistance and tolerance go at the cost of each other. We used wild relatives, early domesticated varieties, traditional local landraces and cultivars of tomato (Solanum lycopersicum) to test whether resistance and tolerance trade‐offs were phylogenetically structured or varied according to degree of domestication. We exposed tomato genotypes to the aphid Macrosiphum euphorbiae, the cotton leafworm Spodoptera littoralis, the root knot nematode Meloidogyne incognita and two common insect‐transmitted plant viruses, and reconstructed their phylogenetic relationships using Genotyping‐by‐Sequencing. We found differences in the performance and effect of pest and diseases but such differences were not related with domestication degree nor genetic relatedness, which probably underlie a complex genetic basis for resistance and indicate that resistance traits appeared at different stages and in unrelated genetic lineages. Still, wild and early domesticated accessions showed greater resistance to aphids and tolerance to caterpillars, nematodes and diseases than modern cultivars. Our findings help to understand how domestication affects plant–pest interactions and underline the importance of tolerance in crop breeding.

RIPENING INHIBITOR (RIN)‐deficient fruits generated by CRISPR/Cas9 initiated partial ripening at a similar time to wild‐type (WT) fruits but only 10% WT concentrations of carotenoids and ethylene (ET) were synthesized. RIN‐deficient fruit never ripened completely, even when supplied with exogenous ET. The low amount of endogenous ET that they did produce was sufficient to enable ripening initiation and this could be suppressed by the ET perception inhibitor 1‐MCP. The reduced ET production by RIN‐deficient tomatoes was due to an inability to induce autocatalytic system‐2 ET synthesis, a characteristic feature of climacteric ripening. Production of volatiles and transcripts of key volatile biosynthetic genes also were greatly reduced in the absence of RIN. By contrast, the initial extent and rates of softening in the absence of RIN were similar to WT fruits, although detailed analysis showed that the expression of some cell wall‐modifying enzymes was delayed and others increased in the absence of RIN. These results support a model where RIN and ET, via ERFs, are required for full expression of ripening genes. Ethylene initiates ripening of mature green fruit, upregulates RIN expression and other changes, including system‐2 ET production. RIN, ET and other factors are required for completion of the full fruit‐ripening programme.

Amphibious plants thrive in areas with fluctuating water levels, partly as a result of their capacity to make specialized leaves when submerged or emerged. The tailor‐made leaves improve gas exchange underwater or prevent aerial desiccation. Aquatic leaves are thin with narrow or dissected forms, thin cuticles and fewer stomata. These traits can combine with carbon‐concentrating mechanisms and various inorganic carbon utilization strategies. Signalling networks underlying this plasticity include conserved players like abscisic acid and ethylene, but closer inspection reveals greater variation in regulatory behaviours. Moreover, it seems that amphibious leaf development overrides and reverses conserved signalling pathways of their terrestrial counterparts. The diversity of physiology and signalling makes plant amphibians particularly attractive for gaining insights into the evolution of signalling and crop improvement.

Coordinating stress defense and plant growth is a survival strategy for adaptation to different environments that contains a series of processes, such as, cell growth, division and differentiation. However, little is known about the coordination mechanism for protein conformation change. A cyclophilin OsCYP20‐2 with a variant interacts with SLENDER RICE1 (SLR1) and OsFSD2 in the nucleus and chloroplasts, respectively, to integrate chilling tolerance and cell elongation in rice (Oryza sativa) (FSD2, Fe-superoxide dismutase 2). Mass spectrum assay showed that OsNuCYP20‐2 localized at the nucleus (nuclear located OsCYP20‐2) was a new variant of OsCYP20‐2 that truncated 71 amino‐acid residues in N‐terminal. The loss‐of function OsCYP20‐2 mutant showed sensitivity to chilling stress with accumulation of extra reactive oxygen species (ROS). In chloroplasts, the full‐length OsCYP20‐2 promotes OsFSD2 forming homodimers which enhance its activity, eliminating the accumulation of ROS under chilling stress. However, the mutant had shorter epidermal cells in comparison with wild‐type Hwayoung (HY). In the nucleus, OsCYP20‐2 caused conformation change of SLR1 to promote its degradation for cell elongation. Our data reveal a cyclophilin with a variant with dual‐localization in chloroplasts and the nucleus, which mediate chilling tolerance and cell elongation.

The molecular mechanisms controlling underwater elongation are based extensively on studies on internode elongation in the monocot rice (Oryza sativa) and petiole elongation in Rumex rosette species. Here, we characterize underwater growth in the dicot Nasturtium officinale (watercress), a wild species of the Brassicaceae family, in which submergence enhances stem elongation and suppresses petiole growth. We used a genome‐wide transcriptome analysis to identify the molecular mechanisms underlying the observed antithetical growth responses. Though submergence caused a substantial reconfiguration of the petiole and stem transcriptome, only little qualitative differences were observed between both tissues. A core submergence response included hormonal regulation and metabolic readjustment for energy conservation, whereas tissue‐specific responses were associated with defense, photosynthesis, and cell wall polysaccharides. Transcriptomic and physiological characterization suggested that the established ethylene, abscisic acid (ABA), and GA growth regulatory module for underwater elongation could not fully explain underwater growth in watercress. Petiole growth suppression is likely attributed to a cell cycle arrest. Underwater stem elongation is driven by an early decline in ABA and is not primarily mediated by ethylene or GA. An enhanced stem elongation observed in the night period was not linked to hypoxia and suggests an involvement of circadian regulation.

TaVrn1, encoding a MADS‐box transcription factor (TF), is the central regulator of wheat vernalization‐induced flowering. Considering that the MADS‐box TF usually works by forming hetero‐ or homodimers, we conducted yeast‐two‐hybrid screening and identified an SVP‐like MADS‐box protein TaVrt2 interacting with TaVrn1. However, the specific function of TaVrt2 and the biological implication of its interaction with TaVrn1 remained unknown. We validated the function of TaVrt2 and TaVrn1 by wheat transgenic experiments and their interaction through multiple protein‐binding assays. Population genetic analysis also was used to display their interplay. Transcriptomic sequencing and chromatin immunoprecipitation assays were performed to identify their common targets. TaVrt2 and TaVrn1 are flowering promoters in the vernalization pathway and interact physically in vitro, in planta and in wheat cells. Additionally, TaVrt2 and TaVrn1 were significantly induced in leaves by vernalization, suggesting their spatio‐temporal interaction during vernalization. Genetic analysis indicated that TaVrt2 and TaVrn1 had significant epistatic effects on flowering time. Furthermore, native TaVrn1 was up‐regulated significantly in TaVrn1‐OE (overexpression) and TaVrt2‐OE lines. Moreover, TaVrt2 could bind with TaVrn1 promoter directly. A TaVrt2‐mediated positive feedback loop of TaVrn1 during vernalization was proposed, providing additional understanding on the regulatory mechanism underlying vernalization‐reduced flowering.

Plants produce an array of specialized metabolites with important ecological functions. The mechanisms underpinning the evolution of new biosynthetic pathways are not well‐understood. Here, we exploit available genome sequence resources to investigate triterpene biosynthesis across the Brassicaceae. Oxidosqualene cyclases (OSCs) catalyze the first committed step in triterpene biosynthesis. Systematic analysis of 13 sequenced Brassicaceae genomes was performed to identify all OSC genes. The genome neighbourhoods (GNs) around a total of 163 OSC genes were investigated to identify Pfam domains significantly enriched in these regions. All‐vs‐all comparisons of OSC neighbourhoods and phylogenomic analysis were used to investigate the sequence similarity and evolutionary relationships of the numerous candidate triterpene biosynthetic gene clusters (BGCs) observed. Functional analysis of three representative BGCs was carried out and their triterpene pathway products were elucidated. Our results indicate that plant genomes are remarkably plastic, and that dynamic GNs generate new biosynthetic pathways in different Brassicaceae lineages by shuffling the genes encoding a core palette of triterpene‐diversifying enzymes, presumably in response to strong environmental selection pressure. These results illuminate a genomic basis for diversification of plant‐specialized metabolism through natural combinatorics of enzyme families, which can be mimicked using synthetic biology to engineer diverse bioactive molecules.

In the processes controlling ecosystem fertility, fungi are increasingly acknowledged as key drivers. However, our understanding of the rules behind fungal community assembly regarding the effect of soil fertility level remains limited. Using soil samples from typical tea plantations spanning c. 2167 km north‐east to south‐west across China, we investigated the assemblage complexity and assembly processes of 140 fungal communities along a soil fertility gradient. The community dissimilarities of total fungi and fungal functional guilds increased with increasing soil fertility index dissimilarity. The symbiotrophs were more sensitive to variations in soil fertility compared with pathotrophs and saprotrophs. Fungal networks were larger and showed higher connectivity as well as greater potential for inter‐module connection in more fertile soils. Environmental factors had a slightly greater influence on fungal community composition than spatial factors. Species abundance fitted the Zipf–Mandelbrot distribution (niche‐based mechanisms), which provided evidence for deterministic‐based processes. Overall, the soil fungal communities in tea plantations responded in a deterministic manner to soil fertility, with high fertility correlated with complex fungal community assemblages. This study provides new insights that might contribute to predictions of fungal community complexity.

Vegetation nutrient limitation is essential for understanding ecosystem responses to global change. In particular, leaf nitrogen (N) is known to be plastic under changed nutrient limitation. However, models can often not capture these observed changes, leading to erroneous predictions of whole‐ecosystem stocks and fluxes. We hypothesise that an optimality approach can improve representation of leaf N content compared to existing empirical approaches. Unlike previous optimality‐based approaches, which adjust foliar N concentrations based on canopy carbon export, we use a maximisation criterion based on whole‐plant growth, and allow for a lagged response of foliar N to this maximisation criterion to account for the limited plasticity of this plant trait. We test these model variants at a range of Free‐Air CO2 Enrichment and N fertilisation experimental sites. We show that a model based solely on canopy carbon export fails to reproduce observed patterns and predicts decreasing leaf N content with increased N availability. However, an optimal model which maximises total plant growth can correctly reproduce the observed patterns. The optimality model we present here is a whole‐plant approach which reproduces biologically realistic changes in leaf N and can thereby improve ecosystem‐level predictions under transient conditions.

The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)‐RELATED (CLE) peptide ligands in connection with their receptors are important players in cell‐to‐cell communications in plants. Here, we investigated the function of the Populus CLV3/ESR‐RELATED 47 (PttCLE47) gene during secondary growth and wood formation in hybrid aspen (Populus tremula × tremuloides) using an RNA interference (RNAi) approach. Expression of PttCLE47 peaks in the vascular cambium. Silencing of the PttCLE47 gene expression affected lateral expansion of stems and decreased apical height growth and leaf size. In particular, PttCLE47 RNAi trees exhibited a narrower secondary xylem zone with less xylem cells/cell file. The reduced radial growth phenotype also correlated with a reduced number of cambial cell layers. In agreement with these results, expression of several cambial regulator genes was downregulated in the stems of the transgenic trees in comparison with controls. Altogether, these results suggest that the PttCLE47 gene is a major positive regulator of cambial activity in hybrid aspen, mainly promoting the production of secondary xylem. Furthermore, in contrast to previously characterized CLE genes expressed in the wood‐forming zone, PttCLE47 appears to be active at its site of expression.

We studied the maize leaf to understand how long‐distance signals, auxin and cytokinin, control leaf growth dynamics. We constructed a mathematical model describing the transport of these hormones along the leaf growth zone and their interaction with the local gibberellin (GA) metabolism in the control of cell division. Assuming gradually declining auxin and cytokinin supply at the leaf base, the model generated spatiotemporal hormone distribution and growth patterns that matched experimental data. At the cellular level, the model predicted a basal leaf growth as a result of cell division driven by auxin and cytokinin. Superimposed on this, GA synthesis regulated growth through the control of the size of the region of active cell division. The predicted hormone and cell length distributions closely matched experimental data. To correctly predict the leaf growth profiles and final organ size of lines with reduced or elevated GA production, the model required a signal proportional to the size of the emerged part of the leaf that inhibited the basal leaf growth driven by auxin and cytokinin. Excision and shading of the emerged part of the growing leaf allowed us to demonstrate that this signal exists and depends on the perception of light intensity.

Despite numerous attempts to elucidate the developmental mechanisms responsible for the observed diversity of pollen and spore walls, the processes involved remained obscure until the structures observed during exine development were recognized as a sequence of self‐assembling micellar mesophases. To confirm this, a series of in vitro experiments was undertaken in which exine‐like patterns were generated in colloidal mixtures by self‐assembly, without any genomic participation. The intention was to test whether all the main types of exine structure could be simulated experimentally. Mixtures of substances, analogous to those involved in microspore development, were left undisturbed while water evaporated and self‐assembly occurred. We varied the substances, their combinations and concentrations, and the physical constraints to make the experiments closer to the situation in nature. The resulting dry films were then examined using transmission electron microscopy. A variety of microstructures, simulating the full range of exine types, was obtained by micellar self‐assembly. Moreover, the signs of related physicochemical process (i.e. phase separation) were also observed. Simple, energy‐efficient, physical–chemical interactions, phase separation and self‐assembly, are capable of generating exine‐like patterns, providing evidence that these processes share control of exine formation with the well‐documented program of gene expression.

Arabidopsis plants overexpressing glycolate oxidase in chloroplasts (GO5) and loss‐of‐function mutants of the major peroxisomal catalase isoform, cat2‐2, produce increased hydrogen peroxide (H2O2) amounts from the respective organelles when subjected to photorespiratory conditions like increased light intensity. Here, we have investigated if and how the signaling processes triggered by H2O2 production in response to shifts in environmental conditions and the concomitant induction of indole phytoalexin biosynthesis in GO5 affect susceptibility towards the hemibiotrophic fungus Colletotrichum higginsianum. Combining histological, biochemical, and molecular assays, we found that the accumulation of the phytoalexin camalexin was comparable between GO genotypes and cat2‐2 in the absence of pathogen. Compared with wild‐type, GO5 showed improved resistance after light‐shift‐mediated production of H2O2, whereas cat2‐2 became more susceptible and allowed significantly more pathogen entry. Unlike GO5, cat2‐2 suffered from severe oxidative stress after light shifts, as indicated by glutathione pool size and oxidation state. We discuss a connection between elevated oxidative stress and dampened induction of salicylic acid mediated defense in cat2‐2. Genetic analyses demonstrated that induced resistance of GO5 is dependent on WRKY33, but not on camalexin production. We propose that indole carbonyl nitriles might play a role in defense against C. higginsianum.

Exotic pathogens cause severe damage in natural populations in the absence of coevolutionary dynamics with their hosts. However, some resistance to such pathogens may occur in naive populations. The objective of this study was to investigate the genetics of this so‐called ‘exapted’ resistance to two pathogens of Asian origin (Erysiphe alphitoides and Phytophthora cinnamomi) in European oak. Host–pathogen compatibility was assessed by recording infection success and pathogen growth in a full‐sib family of Quercus robur under controlled and natural conditions. Two high‐resolution genetic maps anchored on the reference genome were used to study the genetic architecture of resistance and to identify positional candidate genes. Two genomic regions, each containing six strong and stable quantitative trait loci (QTLs) accounting for 12–19% of the phenotypic variation, were mainly associated with E. alphitoides infection. Candidate genes, especially genes encoding receptor‐like‐kinases and galactinol synthases, were identified in these regions. The three QTLs associated with P. cinnamomi infection did not colocate with QTLs found for E. alphitoides. These findings provide evidence that exapted resistance to E. alphitoides and P. cinnamomi is present in Q. robur and suggest that the underlying molecular mechanisms involve genes encoding proteins with extracellular signaling functions.

It is hypothesised that tree distributions in Europe are largely limited by their ability to cope with the summer drought imposed by the Mediterranean climate in the southern areas and by their competitive potential in central regions with more mesic conditions. We investigated the extent to which leaf and plant morphology, gas exchange, leaf and stem hydraulics and growth rates have evolved in a coordinated way in oaks (Quercus) as a result of adaptation to contrasting environmental conditions in this region. We implemented an experiment in which seedlings of 12 European/North African oaks were grown under two watering treatments, a well‐watered treatment and a drought treatment in which plants were subjected to three cycles of drought. Consistent with our hypothesis, species from drier summers had traits conferring more tolerance to drought such as small sclerophyllous leaves and lower percent loss of hydraulic conductivity. However, these species did not have lower growth rates as expected by a trade‐off with drought tolerance. Overall, our results revealed that climate is an important driver of functional strategies in oaks and that traits have evolved along two coordinated functional axes to adapt to different precipitation and temperature regimes.

Sphingolipids act as regulators of programmed cell death (PCD) and the plant defence response. The homeostasis between long‐chain base (LCB) and ceramide (Cer) seems to play an important role in executions of PCD. Therefore, deciphering the role of neutral ceramidases (NCER) is crucial to identify the sphingolipid compounds that trigger and execute PCD. We performed comprehensive sphingolipid and phytohormone analyses of Arabidopsis ncer mutants, combined with gene expression profiling and microscopic analyses. While ncer1 exhibited early leaf senescence (developmentally controlled PCD – dPCD) and an increase in hydroxyceramides, ncer2 showed spontaneous cell death (pathogen‐triggered PCD‐like – pPCD) accompanied by an increase in LCB t18:0 at 35 d, respectively. Loss of NCER1 function resulted in accumulation of jasmonoyl‐isoleucine (JA‐Ile) in the leaves, whereas disruption of NCER2 was accompanied by higher levels of salicylic acid (SA) and increased sensitivity to Fumonisin B1 (FB1). All mutants were also found to activate plant defence pathways. These data strongly suggest that NCER1 hydrolyses ceramides whereas NCER2 functions as a ceramide synthase. Our results reveal an important role of NCER in the regulation of both dPCD and pPCD via a tight connection between the phytohormone and sphingolipid levels in these two processes.

Diatom cell walls, called frustules, are main sources of biogenic silica in the ocean and their intricate morphology is an inspiration for nanoengineering. Here we show dynamic aspects of frustule biosynthesis involving acidification of the silica deposition vesicle (SDV) by V‐type H+ ATPase (VHA). Transgenic Thalassiosira pseudonana expressing the VHA B subunit tagged with enhanced green fluorescent protein (VHAB‐eGFP) enabled subcellular protein localization in live cells. In exponentially growing cultures, VHAB‐eGFP was present in various subcellular localizations including the cytoplasm, SDVs and vacuoles. We studied the role of VHA during frustule biosynthesis in synchronized cell cultures of T. pseudonana. During the making of new biosilica components, VHAB‐eGFP first localized in the girdle band SDVs, and subsequently in valve SDVs. In single cell time‐lapse imaging experiments, VHAB‐eGFP localization in SDVs precluded accumulation of the acidotropic silica biomineralization marker PDMPO. Furthermore, pharmacological VHA inhibition prevented PDMPO accumulation in the SDV, frustule biosynthesis and cell division, as well as insertion of the silicalemma‐associated protein SAP1 into the SDVs. Finally, partial inhibition of VHA activity affected the nanoscale morphology of the valve. Altogether, these results indicate that VHA is essential for frustule biosynthesis by acidifying the SDVs and regulating the insertion of other structural proteins into the SDV.

Climate change will increase frequency of drought and flooding, which threaten global crop productivity and food security. Rice (Oryza sativa) is unique in that it is able to grow in both flooded and upland conditions, which have large differences in the concentrations and chemical forms of mineral elements available to plants. To comprehensively understand the mechanisms of rice for coping with different water status, we performed ionomics and transcriptomics analysis of the roots, nodes and leaves of rice grown in flooded and upland conditions. Focusing the analysis on genes encoding proteins involved in transport functions for mineral elements, it was found that, although rice plants maintained similar levels of each element in the shoots for optimal growth, different transporters for mineral elements were utilised for nitrogen, iron, copper and zinc to deal with different soil water conditions. For example, under flooded conditions, rice roots take up nitrogen using transporters for both ammonium (OsAMT1/2) and nitrate (OsNPF2.4, OsNRT1.1A and OsNRT2.3), whereas under upland conditions, nitrogen uptake is mediated by different nitrate transporters (OsNRT1.1B and OsNRT1.5A). This study shows that rice possesses plastic transport systems for mineral elements in response to different water conditions (upland and flooding).

During the evolution of land plants from aquatic to terrestrial environments, their aerial surfaces were surrounded by cuticle composed of cutin and cuticular waxes to protect them from environmental stresses. Glycerol‐3‐phosphate acyltransferase (GPAT) harboring bifunctional sn‐2 acyltransferase/phosphatase activity produces 2‐monoacylglycerol, a precursor for cutin synthesis. Here, we report that bifunctional sn‐2 GPATs play roles in cuticle biosynthesis and gametophore development of Physcomitrella patens. Land plant‐type cuticle was observed in gametophores but not in protonema. The expression of endoplasmic reticulum‐localized PpGPATs was significantly upregulated in gametophores compared with protonema. Floral organ fusion and permeable cuticle phenotypes of Arabidopsis gpat6‐2 petals were rescued to the wild type (WT) by the expression of PpGPAT2 or PpGPAT4. Disruption of PpGPAT2 and PpGPAT4 caused a significant reduction of total cutin loads, and a prominent decrease in the levels of palmitic and 10,16‐dihydroxydecanoic acids, which are major cutin monomers in gametophores. Δppgpat2 mutants displayed growth retardation, delayed gametophore development, increased cuticular permeability, and reduced tolerance to drought, osmotic and salt stresses compared to the WT. Genome‐wide analysis of genes encoding acyltransferase or phosphatase domains suggested that the occurrence of sn‐2 GPATs with both domains may be a key event in cuticle biogenesis of land plants.

Root hair development is crucial for phosphate absorption, but how phosphorus deficiency affects root hair initiation and elongation remains unclear. We demonstrated the roles of auxin efflux carrier PIN‐FORMED2 (PIN2) and phospholipase D (PLD)‐derived phosphatidic acid (PA), a key signaling molecule, in promoting root hair development in Arabidopsis thaliana under a low phosphate (LP) condition. Root hair elongation under LP conditions was greatly suppressed in pin2 mutant or under treatment with a PLDζ2‐specific inhibitor, revealing that PIN2 and polar auxin transport and PLDζ2‐PA are crucial in LP responses. PIN2 was accumulated and degraded in the vacuole under a normal phosphate (NP) condition, whereas its vacuolar accumulation was suppressed under the LP or NP plus PA conditions. Vacuolar accumulation of PIN2 was increased in pldζ2 mutants under LP conditions. Increased or decreased PIN2 vacuolar accumulation is not observed in sorting nexin1 (snx1) mutant, indicating that vacuolar accumulation of PIN2 is mediated by SNX1 and the relevant trafficking process. PA binds to SNX1 and promotes its accumulation at the plasma membrane, especially under LP conditions, and hence promotes root hair development by suppressing the vacuolar degradation of PIN2. We uncovered a link between PLD‐derived PA and SNX1‐dependent vacuolar degradation of PIN2 in regulating root hair development under phosphorus deficiency.

Forest trees are able to thrive in nutrient‐poor soils in part because they obtain growth‐limiting nutrients, especially nitrogen (N), through mutualistic symbiosis with ectomycorrhizal (ECM) fungi. Addition of inorganic N into these soils is known to disrupt this mutualism and reduce the diversity of ECM fungi. Despite its ecological impact, the mechanisms governing the observed effects of elevated inorganic N on mycorrhizal communities remain unknown. We address this by using a compartmentalized in vitro system to independently alter nutrients to each symbiont. Using stable isotopes, we traced the nutrient flux under different nutrient regimes between Eucalyptus grandis and its ectomycorrhizal symbiont, Pisolithus albus. We demonstrate that giving E. grandis independent access to N causes a significant reduction in root colonization by P. albus. Transcriptional analysis suggests that the observed reduction in colonization may be caused, in part, by altered transcription of microbe perception genes and defence genes. We show that delivery of N to host leaves is not increased by host nutrient deficiency but by fungal nutrient availability instead. Overall, this advances our understanding of the effects of N fertilization on ECM fungi and the factors governing nutrient transfer in the E. grandis–P. microcarpus interaction.

Herbaceous perennial wetland monocots in Northern Ontario, Canada, show dichotomous root overwintering patterns, either with full senescence in autumn or survival over the winter, comparable to deciduous and evergreen leaf habits in trees. To test if these root strategies differ in their associations with growing season length, soil temperatures were recorded in autumn, winter and spring on 38 wetland sites with their dominant species being either of these two root overwintering strategies, altogether 19 monocot species. Traits associated with these strategies were assessed in garden experiments for a subset of these species. Sites with species with autumn‐senescing roots were, on average, warmer than sites with species with overwintering roots. The 13 coldest sites were all sites of species with overwintering roots. Spring shoot growth in the field was delayed in species with autumn‐senescing roots, despite their higher shoot relative growth rates in the garden, possibly due to the necessity to produce roots first. We conclude that species with autumn‐senescing roots are more constrained by temperature than species with overwintering roots, limiting their occurrence in cool climates to locally warm soils and constraining their distribution towards the north. This is comparable to constraints on distribution of deciduous and evergreen trees.

The major consequence of hypoxia is a dramatic reduction in energy production. At the onset of hypoxia, both oxygen and ATP availability decrease. Oxygen and energy sensing therefore converge to induce an adaptive response at both the transcriptional and translational levels. Oxygen sensing results in stabilization of the transcription factors that activate hypoxia‐response genes, including enzymes required for efficient sugar metabolism, allowing plants to produce enough energy to ensure survival. The translation of the resulting mRNAs is mediated by SnRK1, acting as an energy sensor. However, as soon as the sugar availability decreases, a homeostatic mechanism, detecting sugar starvation, dampens the hypoxia‐dependent transcription to reduce energy consumption and preserves carbon reserves for regrowth when oxygen availability is restored.

The papaya diminutive mutant exhibits miniature stature, retarded growth and reduced fertility. This undesirable mutation appeared in the variety ‘Sunset’, the progenitor of the transgenic line ‘SunUp’, and was accidentally carried forward into breeding populations. The diminutive mutation was mapped to chromosome 2 and fine mapped to scaffold 25. Sequencing of a bacterial artificial chromosome in the fine mapped region led to the identification of the target gene responsible for the diminutive mutant, a gene orthologous to MMS19 with a 36.8 kb deletion co‐segregating with the diminutive mutant. The genomic sequence of CpMMS19 is 62 kb, consisting of 20 exons and 19 introns. It encodes a protein of 1143 amino acids while the diminutive allele encodes a truncated protein of 287 amino acids. Expression of the full‐length CpMMS19 was able to complement the thermosensitive growth of the yeast mms19 deletion mutant while expression of the diminutive allele resulted in increased thermosensitivity. Over‐expression of the diminutive allele in Arabidopsis met18 mutant results in a high frequency of seed abortion. The papaya diminutive phenotype is caused by an alteration in gene function rather than a loss‐of‐function mutation. SCAR (sequence characterized amplified region) markers were developed for rapid detection of the diminutive allele in breeding populations.

Powdery mildew disease, elicited by the obligate fungal pathogen Blumeria graminis f.sp. tritici (Bgt), causes widespread yield losses in global wheat crop. However, the molecular mechanisms governing wheat defense to Bgt are still not well understood. Here we found that TuACO3, encoding the 1‐aminocyclopropane‐1‐carboxylic acid (ACC) oxidase functioning in ethylene (ET) biosynthesis, was induced by Bgt infection of the einkorn wheat Triticum urartu, which was accompanied by increased ET content. Silencing TuACO3 decreased ET production and compromised wheat defense to Bgt, whereas both processes were enhanced in the transgenic wheat overexpressing TuACO3. TuMYB46L, phylogenetically related to Arabidopsis MYB transcription factor AtMYB46, was found to bind to the TuACO3 promoter region in yeast‐one‐hybrid and EMSA experiments. TuMYB46L expression decreased rapidly following Bgt infection. Silencing TuMYB46L promoted ET content and Bgt defense, but the reverse was observed when TuMYB46L was overexpressed. Hence, decreased expression of TuMYB46L permits elevated function of TuACO3 in ET biosynthesis in Bgt‐infected wheat. The TuMYB46L‐TuACO3 module regulates ET biosynthesis to promote einkorn wheat defense against Bgt. Furthermore, we found four chitinase genes acting downstream of the TuMYB46L‐TuACO3 module. Collectively, our data shed a new light on the molecular mechanisms underlying wheat defense to Bgt.

Serendipitous findings and studies on Tuber species suggest that some ectomycorrhizal fungi, beyond their complex interaction with ectomycorrhizal hosts, also colonise roots of nonectomycorrhizal plants in a loose way called endophytism. Here, we investigate endophytism of T. melanosporum and T. aestivum. We visualised endophytic T. melanosporum hyphae by fluorescent in situ hybridisation on nonectomycorrhizal plants. For the two Tuber species, microsatellite genotyping investigated the endophytic presence of the individuals whose mating produced nearby ascocarps. We quantified the expression of four T. aestivum genes in roots of endophyted, non‐ectomycorrhizal plants. Tuber melanosporum hyphae colonised the apoplast of healthy roots, confirming endophytism. Endophytic Tuber melanosporum and T. aestivum contributed to nearby ascocarps, but only as maternal parents (forming the flesh). Paternal individuals (giving only genes found in meiotic spores of ascocarps) were not detected. Gene expression of T. aestivum in non‐ectomycorrhizal plants confirmed a living status. Tuber species, and likely other ectomycorrhizal fungi found in nonectomycorrhizal plant roots in this study, can be root endophytes. This is relevant for the ecology (brûlé formation) and commercial production of truffles. Evolutionarily speaking, endophytism may be an ancestral trait in some ectomycorrhizal fungi that evolved from root endophytes.

Environment‐sensitive genic male sterility (EGMS) lines are used widely in two‐line hybrid breeding in rice (Oryza sativa). At present, photoperiod‐sensitive genic male sterility (PGMS) lines and thermo‐sensitive genic male sterility (TGMS) lines are predominantly used in two‐line hybrid rice, with humidity‐sensitive genic male sterility (HGMS) lines rarely being reported. Here, it is shown that HUMIDITY‐SENSITIVE GENIC MALE STERILITY 1 (HMS1), encoding a β‐ketoacyl‐CoA synthase, plays key roles in the biosynthesis of very‐long‐chain fatty acids (VLCFAs) and HGMS in rice. The hms1 mutant displayed decreased seed setting under low humidity, but normal seed setting under high humidity. HMS1 catalyzed the biosynthesis of the C26 and C28 VLCFAs, contributing to the formation of bacula and tryphine in the pollen wall, which protect the pollen from dehydration. Under low‐humidity conditions, hms1 pollen showed poor adhesion and reduced germination on the stigmas, which could be rescued by increasing humidity. HMS1‐INTERACTING PROTEIN (HMS1I) interacted with HMS1 to coregulate HGMS. Furthermore, both japonica and indica rice varieties with defective HMS1 exhibited HGMS, suggesting that hms1 potentially could be used in hybrid breeding. The results herein reveal the novel mechanism of VLCFA‐mediated pollen wall formation, which protects pollen from low‐humidity stress in rice, and has a potential use in hybrid crop breeding.

Hornworts are crucial to understand the phylogeny of early land plants. The emergence of ‘reverse’ U‐to‐C RNA editing accompanying the widespread C‐to‐U RNA editing in plant chloroplasts and mitochondria may be a molecular synapomorphy of a hornwort–tracheophyte clade. C‐to‐U RNA editing is well understood after identification of many editing factors in models like Arabidopsis thaliana and Physcomitrella patens, but there is no plant model yet to investigate U‐to‐C RNA editing. The hornwort Anthoceros agrestis is now emerging as such a model system. We report on the assembly and analyses of the A. agrestis chloroplast and mitochondrial genomes, their transcriptomes and editomes, and a large nuclear gene family encoding pentatricopeptide repeat (PPR) proteins likely acting as RNA editing factors. Both organelles in A. agrestis feature high amounts of RNA editing, with altogether > 1100 sites of C‐to‐U and 1300 sites of U‐to‐C editing. The nuclear genome reveals > 1400 genes for PPR proteins with variable carboxyterminal DYW domains. We observe significant variants of the ‘classic’ DYW domain, in the meantime confirmed as the cytidine deaminase for C‐to‐U editing, and discuss the first attractive candidates for reverse editing factors given their excellent matches to U‐to‐C editing targets according to the PPR‐RNA binding code.

Brassica napus (oilseed rape) is an important oil crop in temperate regions, which originated from hybridization of Brassica oleracea and Brassica rapa. Owing to its polyploidy, the functional study of single genes is cumbersome. Phytic acid is considered as an antinutritive compound, and we aimed to knock out the underlying synthesis and transporter genes to identify low phytic acid mutants. We implemented a high‐throughput next‐generation sequencing screening protocol for an ethylmethane sulfonate population of 7680 plants in six gene families (BnMIPS, BnMIK, Bn2‐PGK, BnIPK1, BnIPK2, and BnMRP5) with two paralogues for each gene. A total of 1487 mutations were revealed, and the vast majority (96%) were confirmed by Sanger sequencing. Furthermore, the characterization of double mutants of Bn.2‐PGK2 showed a significant reduction of phytic acid contents. We propose to use three‐dimensional pooling combined with amplicon stacking and next‐generation sequencing to identify mutations in polyploid oilseed rape in a fast and cost‐effective manner for complex metabolic pathways. Furthermore, the mutants identified in Bn2‐PGK2 might be a very valuable resource for industrial production of oilseed rape protein for human consumption.

Limitation to root growth results from forces required to overcome soil resistance to deformation. The variations in individual particle forces affects root development and often deflects the growth trajectory. We have developed transparent soil and optical projection tomography microscopy systems where measurements of growth trajectory and particle forces can be acquired in a granular medium at a range of confining pressures. We developed image‐processing pipelines to analyse patterns in root trajectories and a stochastic‐mechanical theory to establish how root deflections relate to particle forces and thickening of the root. Root thickening compensates for the increase in mean particle forces but does not prevent deflections from 5% of most extreme individual particle forces causing root deflection. The magnitude of deflections increases with pressure but they assemble into helices of conserved wavelength in response linked to gravitropism. The study reveals mechanisms for the understanding of root growth in mechanically impeding soil conditions and provides insights relevant to breeding of drought‐resistant crops.

Soil organic carbon (SOC) sequestration under elevated CO2 concentration (eCO2) is a function of carbon (C) input and C retention. Nitrogen (N) limitation in natural ecosystems can constrain plant responses to eCO2 and their subsequent effects on SOC, but the effect of eCO2 on SOC in N‐enriched agroecosystems with cultivars highly responsive to eCO2 is largely unknown. We reported results of SOC dynamics from a field free‐air CO2 enrichment experiment with two rice cultivars having distinct photosynthetic capacities under eCO2. A reciprocal incubation experiment was further conducted to disentangle the effect of changes in litter quality and soil microbial community on litter‐derived C dynamics. eCO2 significantly increased total SOC content, dissolved organic C and particulate organic C under the strongly responsive cultivar, likely due to enhanced organic C inputs originated from CO2 stimulation of shoot and root biomass. Increases in the residue C : N ratio and fungal abundance induced by eCO2 under the strongly responsive cultivar reduced C losses from decomposition, possibly through increasing microbial C use efficiency. Our findings suggest that applications of high‐yielding cultivars may substantially enhance soil C sequestration in rice paddies under future CO2 scenarios.

Betanin has been widely used as an additive for many centuries, and its use has increased because of its market application as an additive, high free radical scavenging activity, and safety, health‐promoting properties. The main source of betanin is red beet, but many factors notably affect the yield of betanin from red beets. Betanin is not produced in cereal grains. Thus, developing biofortified crops with betanin is another alternative to health‐promoting food additives. Here, rice endosperm was bioengineered for betanin biosynthesis by introducing three synthetic genes (meloS, BvDODA1S, and BvCYP76AD1S). The overexpression of these genes driven by rice endosperm‐specific promoter established the betanin biosynthetic pathways in the endosperm, resulting in new types of germplasm – ‘Betanin Rice’ (BR). The BR grains were enriched with betanin and had relatively high antioxidant activity. Our results proved that betanin can be biosynthesized de novo in rice endosperm by introducing three genes in the committed betanin biosynthetic pathway. The betanin‐fortified rice in this study can be used as a functional grain to promote health and as a raw material to process dietary supplements.

Glandular trichomes are epidermal outgrowths that are the site of biosynthesis and storage of large quantities of specialized metabolites. Besides their role in the protection of plants against biotic and abiotic stresses, they have attracted interest owing to the importance of the compounds they produce for human use; for example, as pharmaceuticals, flavor and fragrance ingredients, or pesticides. Here, we review what novel concepts investigations on glandular trichomes have brought to the field of specialized metabolism, particularly with respect to chemical and enzymatic diversity. Furthermore, the next challenges in the field are understanding the metabolic network underlying the high productivity of glandular trichomes and the transport and storage of metabolites. Another emerging area is the development of glandular trichomes. Studies in some model species, essentially tomato, tobacco, and Artemisia, are now providing the first molecular clues, but many open questions remain: How is the distribution and density of different trichome types on the leaf surface controlled? When is the decision for an epidermal cell to differentiate into one type of trichome or another taken? Recent advances in gene editing make it now possible to address these questions and promise exciting discoveries in the near future.

The ratio of leaf internal (ci) to ambient (ca) partial pressure of CO2, defined here as χ, is an index of adjustments in both leaf stomatal conductance and photosynthetic rate to environmental conditions. Measurements and proxies of this ratio can be used to constrain vegetation model uncertainties for predicting terrestrial carbon uptake and water use. We test a theory based on the least‐cost optimality hypothesis for modelling historical changes in χ over the 1951–2014 period, across different tree species and environmental conditions, as reconstructed from stable carbon isotopic measurements across a global network of 103 absolutely dated tree‐ring chronologies. The theory predicts optimal χ as a function of air temperature, vapour pressure deficit, ca and atmospheric pressure. The theoretical model predicts 39% of the variance in χ values across sites and years, but underestimates the intersite variability in the reconstructed χ trends, resulting in only 8% of the variance in χ trends across years explained by the model. Overall, our results support theoretical predictions that variations in χ are tightly regulated by the four environmental drivers. They also suggest that explicitly accounting for the effects of plant‐available soil water and other site‐specific characteristics might improve the predictions.

Investigations of plant cell division would greatly benefit from a fast, inducible system. Therefore, we aimed to establish a mitotic model by transiently expressing D‐type cyclins in tobacco leaf cells. Two different D‐type cyclins, CYCD3;1 and CYCD4;2 from Arabidopsis thaliana, were expressed by agrobacterial infiltration in the cells of expanded leaves in tobacco (Nicotiana benthamiana). Leaf pavement cells were examined after cyclin expression while target and reference (histone or tubulin) proteins were marked by fluorescent protein‐tagging. Ectopic expression of the D‐type cyclin induced pavement cells to re‐enter cell division by establishing mitotic microtubule arrays. The induced leaf cells expressed M phase‐specific genes of Arabidopsis encoding the mitotic kinase AtAurora 1, the microtubule‐associated proteins AtEDE1 and AtMAP65‐4, and the vesicle fusion protein AtKNOLLE by recognizing their genomic elements. Their distinct localizations at spindle poles (AtAurora1), spindle microtubules (AtEDE1), phragmoplast microtubules (AtMAP65‐4) and the cell plate (AtKNOLLE) were indistinguishable from those in their native Arabidopsis cells. The dividing cells also revealed two rice (Oryza sativa) microtubule‐associated proteins in the phragmoplast and uncovered a novel spindle‐associated microtubule motor protein. Hence, this cell division‐enabled leaf system predicts hypothesized cell cycle‐dependent functions of heterologous genes by reporting the dynamics of encoded proteins.

Transposable elements (TEs) are the main reason for the high plasticity of plant genomes, where they occur as communities of diverse evolutionary lineages. Because research has typically focused on single abundant families or summarized TEs at a coarse taxonomic level, our knowledge about how these lineages differ in their effects on genome evolution is still rudimentary. Here we investigate the community composition and dynamics of 32 long terminal repeat retrotransposon (LTR‐RT) families in the 272‐Mb genome of the Mediterranean grass Brachypodium distachyon. We find that much of the recent transpositional activity in the B. distachyon genome is due to centromeric Gypsy families and Copia elements belonging to the Angela lineage. With a half‐life as low as 66 kyr, the latter are the most dynamic part of the genome and an important source of within‐species polymorphisms. Second, GC‐rich Gypsy elements of the Retand lineage are the most abundant TEs in the genome. Their presence explains > 20% of the genome‐wide variation in GC content and is associated with higher methylation levels. Our study shows how individual TE lineages change the genetic and epigenetic constitution of the host beyond simple changes in genome size.

Vacuolar processing enzyme (VPE) is a cysteine‐type endopeptidase that has a substrate‐specificity for asparagine or aspartic acid residues and cleaves peptide bonds at their carboxyl‐terminal side. Various vacuolar proteins are synthesized as larger proprotein precursors, and VPE is an important initiator of maturation and activation of these proteins. It mediates programmed cell death (PCD) by provoking vacuolar rupture and initiating the proteolytic cascade leading to PCD. Vacuolar processing enzyme also possesses a peptide ligation activity, which is responsible for producing cyclic peptides in several plant species. These unique functions of VPE support developmental and environmental responses in plants. The number of VPE homologues is higher in angiosperm species, indicating that there has been differentiation and specialization of VPE function over the course of evolution. Angiosperm VPEs are separated into two major types: the γ‐type VPEs, which are expressed mainly in vegetative organs, and the β‐type VPEs, whose expression occurs mainly in storage organs; in eudicots, the δ‐type VPEs are further separated within γ‐type VPEs. This review also considers the importance of processing and peptide ligation by VPE in vacuolar protein maturation.

Light is one of the most essential environmental factors affecting many aspects of growth and developmental processes in plants. Plants undergo skotomorphogenic or photomorphogenic development dependent on the absence or presence of light. These two developmental programs enable a germinated seed to become a healthy seedling at the early stage of the plant life cycle. CULLIN 4‐DNA DAMAGE‐BINDING PROTEIN 1 (DDB1)‐based CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1)‐SUPPRESSOR OF PHYA and COP10‐DEETIOLATED 1‐DDB1 E3 ubiquitin ligase complexes promote the skotomorphogenesis by ubiquitinating and degrading a number of photomorphogenic‐promoting factors in darkness. Photoreceptors sense and transduce light information to downstream signaling, thereby initiating a set of molecular events and subsequent photomorphogenesis. These processes are precisely modulated by a group of components including various photoreceptors, E3 ubiquitin ligase, and transcription factors at the molecular level. This review provides an overview of the current understanding of the COP1, ELONGATED HYPOCOTYL 5, and B‐BOX CONTAINING PROTEINs‐mediated light signal transduction pathway and highlights still open questions in the field.

The fact that angiosperms are so species‐rich and ecologically diverse – Darwin's second abominable mystery – could be explained by their ability to ‘reinvent' themselves by evolving functional traits repeatedly over time, space and taxonomic clades. These trait innovations may facilitate adaptation and increase diversification rates. In this article, I quantify this ‘trait flexibility' by reviewing the literature on trait transition rates and trait‐dependent diversification rates in angiosperms and their extant sister clade, acrogymnosperms. I show that angiosperms indeed evolved elevated trait transition and trait‐dependent diversification rates compared to gymnosperms, and rates are highest within species‐rich angiosperm orders (e.g. Fabales, Lamiales). The (genetic) ability of certain angiosperm lineages to repeatedly evolve adaptive traits may have facilitated sustained high net diversification resulting from numerous episodic radiations.

Phylogenomics is increasingly used to infer deep‐branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep‐branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome‐scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear‐encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as ‘basal’ or ‘early‐diverging’ with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.

Vascular stem cell maintenance is regulated by a peptide signaling involving Tracheary Element Differentiation Inhibitory Factor (TDIF) and Receptor TDR/PXY (Phloem intercalated with Xylem) and co‐receptor BAK1 (BRI1‐associated receptor kinase1). The regulatory mechanism of this signaling pathway is largely unknown despite its importance in stem cell maintenance in the vascular meristem. We report that activation of a NAC domain transcription factor XVP leads to precocious Xylem differentiation, disruption of Vascular Patterning, and reduced cell numbers in vascular bundles. We combined molecular and genetic studies to elucidate the biological functions of XVP. XVP is expressed in the cambium, localized on the plasma membrane and forms a complex with TDIF co‐receptors PXY‐BAK1. Simultaneous mutation of XVP and its close homologous NAC048 enhances TDIF signaling. In addition, genetics analysis indicated that XVP promotes xylem differentiation through a known master regulator VASCULAR‐RELATED NAC‐DOMAIN6 (VND6). Expression analyses indicate that XVP activates CLAVATA3/ESR (CLE)‐related protein 44 (CLE44), the coding gene of TDIF, whereas TDIF represses XVP expression, suggesting a feedback mechanism. Therefore, XVP functions as a negative regulator of the TDIF‐PXY module and fine‐tunes TDIF signaling in vascular development. These results shed new light on the mechanism of vascular stem cell maintenance.

During land colonization, plants acquired a range of body plan adaptations, of which the innovation of three‐dimensional (3D) tissues increased organismal complexity and reproductivity. In the moss, Physcomitrella patens, a 3D leafy gametophore originates from filamentous cells that grow in a two‐dimensional (2D) plane through a series of asymmetric cell divisions. Asymmetric cell divisions that coincide with different cell division planes and growth directions enable the developmental switch from 2D to 3D, but insights into the underlying mechanisms coordinating this switch are still incomplete. Using 2D and 3D imaging and image segmentation, we characterized two geometric cues, the width of the initial cell and the angle of the transition division plane, which sufficiently distinguished a gametophore initial cell from a branch initial cell. These identified cues were further confirmed in gametophore formation mutants. The identification of a fluorescent marker allowed us to successfully predict the gametophore initial cell with > 90% accuracy before morphological changes, supporting our hypothesis that, before the transition division, parental cells of the gametophore initials possess different properties from those of the branch initials. Our results suggest that the cell fate decision of the initial cell is determined in the parental cell, before the transition division.

The genus Quercus is among the most widespread and species‐rich tree genera in the northern hemisphere. The extraordinary species diversity in America and Asia together with the continuous continental distribution of a limited number of European species raise questions about how macro‐ and microevolutionary processes made the genus Quercus an evolutionary success. Synthesizing conclusions reached during the past three decades by complementary approaches in phylogenetics, phylogeography, genomics, ecology, paleobotany, population biology and quantitative genetics, this review aims to illuminate evolutionary processes leading to the radiation and expansion of oaks. From opposing scales of time and geography, we converge on four overarching explanations of evolutionary success in oaks: accumulation of large reservoirs of diversity within populations and species; ability for rapid migration contributing to ecological priority effects on lineage diversification; high rates of evolutionary divergence within clades combined with convergent solutions to ecological problems across clades; and propensity for hybridization, contributing to adaptive introgression and facilitating migration. Finally, we explore potential future research avenues, emphasizing the integration of microevolutionary and macroevolutionary perspectives.

From the cellular perspective, organ growth is determined by production and growth of cells. Uncovering how these two processes are coordinated is essential for understanding organogenesis and regulation of organ growth. We utilized phenotypic and genetic variation of 252 natural accessions of Arabidopsis thaliana to conduct genome‐wide association studies (GWAS) for identifying genes underlying root growth variation; using a T‐DNA line candidate approach, we identified one gene involved in root growth control and characterized its function using microscopy, root growth kinematics, G2/M phase cell count, ploidy levels and ribosome polysome profiles. We identified a factor contributing to root growth control: Arabidopsis Adenylate Kinase 6 (AAK6). AAK6 is required for normal cell production and normal cell elongation, and its natural genetic variation is involved in determining root growth differences between Arabidopsis accessions. A lack of AAK6 reduces cell production in the aak6 root apex, but this is partially compensated for by longer mature root cells. Thereby, aak6 mutants exhibit compensatory cell enlargement, a phenomenon unexpected in roots. Moreover, aak6 plants accumulate 80S ribosomes while the polysome profile remains unchanged, consistent with a phenotype of perturbed ribosome biogenesis. In conclusion, AAK6 impacts ribosome abundance, cell production and thereby root growth.

Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioritization. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth. Regions containing nonrandom concentrations of young (neo‐) and old (paleo‐) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time‐calibrated mega‐phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs). At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo‐ and paleo‐endemism. By contrast, the Guineo‐Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%). We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large‐scale taxonomically verified distribution datasets and mega‐phylogenies lead to an improved understanding of tropical plant biodiversity evolution.