Convergent evolution in plant specialized metabolism

Multiple transitions to high l-DOPA 4,5-dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales

Many specialized metabolic pathways have evolved convergently in plants, but distinguishing multiple origins from alternative evolutionary scenarios can be difficult. Here, we explore the evolution of l-3,4-dihydroxyphenylalanine (l-DOPA) 4,5-dioxygenase (DODA) enzymes to better resolve the convergent evolution of the betalain biosynthetic pathway within the flowering plant order Caryophyllales. We use yeast-based heterologous assays to quantify enzymatic activity of extant proteins and then employ ancestral sequence reconstruction to resurrect and assay ancestral DODA enzymes. We use a combination of ancestral sequence reconstruction, model-based methods, and structural modelling to describe patterns of molecular convergence. We confirm that high l-DOPA 4,5-dioxygenase activity is polyphyletic and show that high activity DODAs evolved at least three times from ancestral proteins with low activity. We show that molecular convergence is concentrated proximally to the binding pockets but also appears distally to active sites. Moreover, our analysis also suggests that many unique and divergent substitutions contribute to the evolution of DODA. Given the key role of DODA in betalain biosynthesis, our analysis further supports the convergent origins of betalains and illustrates how the iterative evolution of betalain biosynthesis has drawn on a complex mixture of convergent, divergent, and unique variation.

Predicting precursors of plant specialized metabolites using DeepMol automated machine learning

Plants produce specialized metabolites, which play critical roles in defending against biotic and abiotic stresses. Due to their chemical diversity and bioactivity, these compounds have significant economic implications, particularly in the pharmaceutical and agrotechnology sectors. Despite their importance, the biosynthetic pathways of these metabolites remain largely unresolved. Automating the prediction of their precursors, derived from primary metabolism, is essential for accelerating pathway discovery. Using DeepMol's automated machine learning engine, we found that regularized linear classifiers offer optimal, accurate, and interpretable models for this task, outperforming state-of-the-art models while providing chemical insights into their predictions. The pipeline and models are available at the repository: https://github.com/jcapels/SMPrecursorPredictor.

Genome assembly of Stewartia sinensis reveals origin and evolution of orphan genes in Theaceae

Orphan genes play crucial roles in diverse biological processes, but the evolutionary trajectories and functional divergence remain largely unexplored. The Theaceae family, including the economically and culturally important tea plant, offers a distinctive model to examine these aspects. Here, we integrated Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods to decode a pseudo-chromosomal genome assembly of Stewartia sinensis, from the earliest-diverging tribe of Theaceae, spanning 2.95 Gb. Comparative genomic analysis revealed the absence of recent whole-genome duplication events in the Theaceae ancestor, highlighting tandem duplications as the predominant mechanism of gene expansion. We identified 31,331 orphan genes, some of which appear to have ancient origins, suggesting early emergence with frequent gains and losses, while others seem more specific and recent. Notably, orphan genes are distinguished by shorter lengths, fewer exons and functional domains compared to genes that originate much earlier, like transcription factors. Moreover, tandem duplication contributes significantly to the adaptive evolution and characteristic diversity of Theaceae, and it is also a major mechanism driving the origination of orphan genes. This study illuminates the evolutionary dynamics of orphan genes, providing a valuable resource for understanding the origin and evolution of tea plant flavor and enhancing genetic breeding efforts.

Lineage-specific patterns in the Moraceae family allow identification of convergent P450 enzymes involved in furanocoumarin biosynthesis

Specialized metabolites are molecules involved in plants' interaction with their environment. Elucidating their biosynthetic pathways is a challenging but rewarding task, leading to societal applications and ecological insights. Furanocoumarins emerged multiple times in Angiosperms, raising the question of how different enzymes evolved into catalyzing identical reactions. To identify enzymes producing lineage-specific metabolites, an evolutionary-based approach was developed and applied to furanocoumarin biosynthesis in Ficus carica (Moraceae). This led to the characterization of CYP71B129-131a, three P450 enzymes whose evolution of the function was investigated using phylogenetics, structural comparisons and site-directed mutagenesis. CYP71B129 and CYP71B130,131a were found to hydroxylate umbelliferone (coumarin) and xanthotoxin (furanocoumarin), respectively. Results suggest that CYP71Bs xanthotoxin hydroxylase activity results from duplications and functional divergence of umbelliferone hydroxylase genes. Structural comparisons highlighted an amino acid affecting CYP71Bs substrate specificity, which may play a key role in allowing xanthotoxin hydroxylation in several P450 subfamilies. CYP71B130-131a characterization validates the proposed enzyme-discovery approach, which can be applied to different pathways and help to avoid the classic bottlenecks of specialized metabolism elucidation. The CYP71Bs also exemplify how furanocoumarin-biosynthetic enzymes can stem from coumarin-biosynthetic ones and provides insights into the molecular mechanisms underlying the multiple emergences of xanthotoxin hydroxylation in distant P450 subfamilies.

The multifaceted roles of gut microbiota in insect physiology, metabolism, and environmental adaptation: implications for pest management strategies

Similar to many other organisms, insects like Drosophila melanogaster, Hypothenemus hampei, and Cockroaches harbor diverse bacterial communities in their gastrointestinal systems. These bacteria, along with other microorganisms like fungi and archaea, are essential to the physiology of their insect hosts, forming intricate symbiotic relationships. These gut-associated microorganisms contribute to various vital functions, including digestion, nutrient absorption, immune regulation, and behavioral modulation. Notably, gut microbiota facilitates the breakdown of complex plant materials, synthesizes essential vitamins and amino acids, and detoxifies harmful substances, including pesticides. Furthermore, these microorganisms are integral to modulating host immune responses and enhancing disease resistance. This review examines the multifaceted roles of gut microbiota in insect physiology, with particular emphasis on their contributions to digestion, detoxification, reproduction, and environmental adaptability. The potential applications of gut microbiota in integrated pest management (IPM) are also explored. Understanding the microbial dynamics within insect pest species opens new avenues for pest control, including developing microbial biocontrol agents, microbial modifications to reduce pesticide resistance, and implementing microbiome-based genetic strategies. In particular, manipulating gut microbiota presents a promising approach to pest management, offering a sustainable and eco-friendly alternative to conventional chemical pesticides.

Adaptive Changes and Genetic Mechanisms in Organisms Under Controlled Conditions: A Review

Adaptive changes encompass physiological, morphological, or behavioral modifications occurring in organisms in response to specific environmental conditions. These modifications may become established within a population through natural selection. While adaptive changes can influence individuals or populations over short timeframes, evolution involves the inheritance and accumulation of these changes over extended periods under environmental pressures through natural selection. At present, addressing climate change, emerging infectious diseases, and food security are the main challenges faced by scientists. A comprehensive and profound understanding of the mechanisms of adaptive evolution is of great significance for solving these problems. The genetic basis of these adaptations can be examined through classical genetics, which includes stochastic gene mutations and chromosomal instability, as well as epigenetics, which involves DNA methylation and histone modifications. These mechanisms not only govern the rate and magnitude of adaptive changes but also affect the transmission of adaptive traits to subsequent generations. In the study of adaptive changes under controlled conditions, short-term controlled experiments are commonly utilized in microbial and animal research to investigate long-term evolutionary trends. However, the application of this approach in plant research remains limited. This review systematically compiles the findings on adaptive changes and their genetic foundations in organisms within controlled environments. It aims to provide valuable insights into fundamental evolutionary processes, offering novel theoretical frameworks and research methodologies for future experimental designs, particularly in the field of plant studies.

Specialized metabolome and transcriptome atlas of developing Arabidopsis thaliana seed under warm temperatures

Seed development, which depends on parent plants genetic background and mother plant environmental conditions, is a major component determining seed composition. Seed quality is a main agricultural concern, impacting both food and non-food applications, while also playing a central role in biodiversity conservation and environment protection. Climate change, in particular the emergence of extremely high temperatures, constitute a critical global threat to agriculture. Specialized metabolites (SMs) play crucial roles in the interactions of plants and seeds with their environments. Several SMs are known to be protective compounds involved in seed stress responses, thus impacting their quality. In this study, we performed untargeted metabolomic (LC-MS/MS) and transcriptomic (RNA-Seq) analyses of Arabidopsis thaliana seeds harvested at six developmental stages (Globular, Transition, Torpedo, Bent cotyledon, Mature green and Dry seed), and developed under control and warm temperature conditions. Those data provide an original and valuable resource that could be used to identify SMs and genes involved in seed heat stress responses and for the study of their regulation and functions during seed development.

Homospermidine synthase evolution and the origin(s) of pyrrolizidine alkaloids in Apocynaceae

PREMISE

Enzymes that are encoded by paralogous genes and produce identical specialized metabolites in distantly related plant lineages are strong evidence of parallel phenotypic evolution. Inference of phenotypic homology for metabolites produced by orthologous genes is less straightforward, since orthologs may be recruited in parallel into novel pathways. In prior research on pyrrolizidine alkaloids (PAs), specialized metabolites of Apocynaceae, the evolution of homospermidine synthase (HSS), an enzyme of PA biosynthesis, was reconstructed and a single origin of PAs inferred because HSS enzymes of all known PA-producing Apocynaceae species are orthologous and descended from an ancestral enzyme with the motif (VXXXD) of an optimized HSS.

METHODS

We increased sampling, tested the effect of amino acid motif on HSS function, revisited motif evolution, and tested for selection to infer evolution of HSS function and its correlation with phenotype.

RESULTS

Some evidence supports a single origin of PAs: an IXXXD HSS-like gene, similar in function to VXXXD HSS, evolved in the shared ancestor of all PA-producing species; loss of HSS function occurred multiple times via pseudogenization and perhaps via evolution of an IXXXN motif. Other evidence indicates multiple origins: the VXXXD motif, highly correlated with the PA phenotype, evolved two or four times independently; the ancestral IXXXD gene was not under positive selection, while some VXXXD genes were; and substitutions at sites experiencing positive selection occurred on multiple branches in the HSS-like gene tree.

CONCLUSIONS

The complexity of the genotype-function-phenotype map confounds the inference of PA homology from HSS-like gene evolution in Apocynaceae.

Acylsugars, Nicotine and a Protease Inhibitor Provide Variable Protection for Nicotiana benthamiana in a Natural Setting

Plants produce an immense diversity of defensive specialized metabolites. However, despite extensive functional characterization, the relative importance of different defensive compounds is rarely examined in natural settings. Here, we compare the efficacy of three Nicotiana benthamiana defensive compounds, nicotine, acylsugars and a serine protease inhibitor, by growing plants with combinations of knockout mutations in a natural setting, quantifying invertebrate interactions and comparing relative plant performance. Among the three tested compounds, acylsugars had the greatest defensive capacity, affecting aphids, leafhoppers, spiders and flies. Nicotine mutants displayed increased leafhopper feeding and aphid colonization. Plants lacking both nicotine and acylsugars were more susceptible to flea beetles and thrips. By contrast, knockout of the serine protease inhibitor did not affect insect herbivory in the field. Complementary experiments under controlled laboratory conditions with caterpillars, grasshoppers and aphids confirmed results obtained in a natural setting. We conclude that the three metabolite groups collectively provide broad-spectrum protection to N. benthamiana. However, there is a gradient in their effects on the interacting invertebrates present in the field. Furthermore, we demonstrate that, even if individual metabolites do not have a measurable defensive benefit on their own, they can have an additive effect when combined with other defensive compounds.

Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

Yerba mate (YM, Ilex paraguariensis) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here, we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large YM genome size is partly due to a whole-genome duplication (Ip-α) during the early evolutionary history of Ilex, in addition to the hexaploidization event (γ) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in YM and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the X-ray diffraction data suggest structural constraints are minimal for the convergent evolution of individual reactions.

Robotic mechanical wounding is sufficient to induce phenylacetaldoxime accumulation in Tococa quadrialata

This study investigated the accumulation of phenlyacetaldoxime (PAOx) and PAOx-Glc in Tococa quadrialata leaves in response to herbivore infestation and mechanical wounding. Results show that PAOx levels peaked at 24 h post-infestation, while PAOx-Glc remained present for several days. The accumulation of PAOx began as early as 3 h after herbivory, with PAOx-Glc significantly increased after 6 h. Mechanical wounding induced similar responses in PAOx and PAOx-Glc accumulation as herbivory, suggesting that continuous tissue damage triggers the production of these compounds. Interestingly, SpitWorm-treated leaves showed the highest levels of both PAOx and PAOx-Glc, indicating that herbivore-derived oral secretions (OS) play a role in the induction of these compounds. Additionally, JA-independent PAOx production was found to be associated with tissue damage rather than specific known signaling compounds. Emission of benzyl cyanide and 2-phenylethanol, PAOx-derived plant volatiles, was observed in response to herbivory and SpitWorm treatment providing plant-derived OS, further highlighting the role of herbivore cues in plant defense responses.

Combination of Probe Electrospray Ionization Mass Spectrometry and Mass Spectrometry Imaging to Analyze Plant Alkaloids in Narcissus tazetta

Plant alkaloids are used in a variety of medicines, such as anti-cancer drugs and analgesics. Among these plant alkaloids, galanthamine is an Amaryllidaceae type alkaloid with acetylcholinesterase inhibition activity used in the treatment of neurological diseases such as Alzheimer's disease. Although the chemical synthesis of galanthamine has been successfully achieved, Narcissus tazetta is the main source of its production. Research shows that the galanthamine content varies not only with the type of daffodil but also with the stage of development and the part of the plant. Pharmaceutical companies seek plant species with higher galanthamine content to increase pharmaceutical availability. In this study, we were able to rapidly confirm the presence of alkaloids, such as galanthamine, lycorine, and tazettine in the N. tazetta sample using the probe electrospray ionization coupled with quadrupole time-of-flight type mass spectrometry. After confirmation of the components, we then visualized the distribution of the alkaloids by mass spectrometry imaging using the atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometer. In our method, we can provide qualitative data and visualized data immediately.

Plant-to-plant defence induction in cotton is mediated by delayed release of volatiles upon herbivory

Caterpillar feeding immediately triggers the release of volatile compounds stored in the leaves of cotton plants. Additionally, after 1 d of herbivory, the leaves release other newly synthesised volatiles. We investigated whether these volatiles affect chemical defences in neighbouring plants and whether such temporal shifts in emissions matter for signalling between plants. Undamaged receiver plants were exposed to volatiles from plants infested with Spodoptera caterpillars. For receiver plants, we measured changes in defence-related traits such as volatile emissions, secondary metabolites, phytohormones, gene expression, and caterpillar feeding preference. Then, we compared the effects of volatiles emitted before and after 24 h of damage on neighbouring plant defences. Genes that were upregulated in receiver plants following exposure to volatiles from damaged plants were the same as those activated directly by herbivory on a plant. Only volatiles emitted after 24 h of damage, including newly produced volatiles, were found to increase phytohormone levels, upregulate defence genes, and enhance resistance to caterpillars. These results indicate that the defence induction by volatiles is a specific response to de novo synthesised volatiles, suggesting that these compounds are honest signals of herbivore attack. These findings point to an adaptive origin of airborne signalling between plants.

Mechanism of action of the toxic proline mimic azetidine 2-carboxylic acid in plants

Plants have an amazing capacity to outcompete neighboring organisms for space and resources. Toxic metabolites are major players in these interactions, which can have a broad range of effectiveness by targeting conserved molecular mechanisms, such as protein biosynthesis. However, lack of knowledge about defensive metabolite pathways, their mechanisms of action, and resistance mechanisms limits our ability to manipulate these pathways for enhanced crop resilience. Nonproteogenic amino acids (NPAAs) are a structurally diverse class of metabolites with a variety of functions but are typically not incorporated during protein biosynthesis. Here, we investigate the mechanism of action of the NPAA azetidine-2-carboxylic acid (Aze), an analog of the amino acid proline (Pro). Using a combination of plate-based assays, metabolite feeding, metabolomics, and proteomics, we show that Aze inhibits the root growth of Arabidopsis and other plants. Aze-induced growth reduction was restored by supplementing L-, but not D-Pro, and nontargeted proteomics confirm that Aze is misincorporated for Pro during protein biosynthesis, specifically on cytosolically translated proteins. Gene expression analysis, free amino acid profiling, and proteomics show that the unfolded protein response is upregulated during Aze treatment implicating that Aze misincorporation results in accumulation of misfolded proteins triggering a global stress response. This study demonstrates the mechanism of action of Aze in plants and provides a foundation for understanding the biological functions of proteotoxic metabolites.

Different metabolite profiles across Penicillium roqueforti populations associated with ecological niche specialisation and domestication

Fungi are known to produce many chemically diversified metabolites, yet their ecological roles are not always fully understood. The blue cheese fungus Penicillium roqueforti thrives in different ecological niches and is known to produce a wide range of metabolites, including mycotoxins. Three P. roqueforti populations have been domesticated for cheese production and two populations thrive in other anthropized environments, i.e., food, lumber and silage. In this study, we looked for differences in targeted and untargeted metabolite production profiles between populations using HPLC-HR-Q-TOF and UHPLC-Q-TOF-HR-MS/MS. The non-cheese populations produced several fatty acids and different terpenoids, lacking in cheese strains. The Termignon cheese population displayed intermediate metabolite profiles between cheese and non-cheese populations, as previously shown for other traits. The non-Roquefort cheese population with the strongest domestication syndrome, produced the lowest quantities of measured metabolites, including mycophenolic acid (MPA), andrastin A and PR toxin. Its inability to produce MPA was due to a deletion in the mpaC gene, while a premature stop codon in ORF 11 of the PR toxin gene cluster explained PR toxin absence and the accumulation of its intermediates, i.e., eremofortins A and B. In the Roquefort population, we detected no PR toxin nor eremofortins A or B, but found no indel or frameshift mutation, suggesting downregulation. The hypotoxigenic trait of domesticated cheese populations can be hypothesized to be linked to the loss of this ability through trait degeneration and/or the selection of low toxin producers. It may also be due to the fact that populations from other anthropized environments maintained high metabolite diversity as the bioactivities of these compounds are likely important in these ecological niches.

Applications of ancestral sequence reconstruction for understanding the evolution of plant specialized metabolism

Studies of enzymes in modern-day plants have documented the diversity of metabolic activities retained by species today but only provide limited insight into how those properties evolved. Ancestral sequence reconstruction (ASR) is an approach that provides statistical estimates of ancient plant enzyme sequences which can then be resurrected to test hypotheses about the evolution of catalytic activities and pathway assembly. Here, I review the insights that have been obtained using ASR to study plant metabolism and highlight important methodological aspects. Overall, studies of resurrected plant enzymes show that (i) exaptation is widespread such that even low or undetectable levels of ancestral activity with a substrate can later become the apparent primary activity of descendant enzymes, (ii) intramolecular epistasis may or may not limit evolutionary paths towards catalytic or substrate preference switches, and (iii) ancient pathway flux often differs from modern-day metabolic networks. These and other insights gained from ASR would not have been possible using only modern-day sequences. Future ASR studies characterizing entire ancestral metabolic networks as well as those that link ancient structures with enzymatic properties should continue to provide novel insights into how the chemical diversity of plants evolved. This article is part of the theme issue 'The evolution of plant metabolism'.

Photoperiodic Effect on Growth, Photosynthesis, Mineral Elements, and Metabolome of Tomato Seedlings in a Plant Factory

The duration of light exposure is a crucial environmental factor that regulates various physiological processes in plants, with optimal timing differing between species and varieties. To assess the effect of photoperiods on the growth and metabolites of a specific truss tomato cultivar, three photoperiods (12 h, 16 h, and 20 h) were tested in a plant factory. Growth parameters, including plant height, stem diameter, fresh and dry weights of shoots and roots, photosynthetic characteristics, mineral content, and metabolome profiles, were analyzed under these conditions. The results indicated that prolonged light exposure enhanced plant growth, with the highest photosynthesis and chlorophyll content observed under a 20 h photoperiod. However, no significant correlation was observed between the photoperiod and the mineral element content, particularly for macro minerals. Metabolome analysis revealed that different photoperiods influenced the accumulation of metabolites, particularly in the lipid metabolism, amino acid metabolism, and membrane transport pathways. Long periods of light would enhance photosynthesis and metabolism, improving the rapid growth of tomato seedlings. Overall, this study provides a theoretical basis for understanding the responses of truss tomato cultivars to varying photoperiods in plant factories and proposes an optimizable method for accelerating the progress of tomato seedling cultivation.

Transcriptome analysis of the genes and regulators involving in vitamin E biosynthesis in Elaeagnus mollis diels

Elaeagnus mollis is an important newly developing woody oil plant species and the vitamin E (VitE) content in its kernel oil is relatively high. In the present study, the VitE component content and functional genes involving in VitE biosynthesis in E. mollis kernel at different developmental stage were investigated. The VitE content increased with kernel development, reaching up to ~ 7.96 mg/g oil in kernel mature stage. The content of tocopherol was much higher than that of tocotrienol and γ-tocopherol became the dominant component. E. mollis kernel extracts had relatively strong antioxidant capacity. We identified 17 genes (16 VTEs and 1 homogentisic acid geranylgeranyl transferase (HGGT)) directly involving in VitE biosynthesis in RNA-Seq data. Phylogenetic and qRT-PCR results indicated that the annotation and reliability of the RNA-Seq were accurate. Transient overexpression of EmVTE3 and EmWRKY13 in tobacoo leaves increased and decreased the VitE content to 192.18 and 118.29 µg/g, respectively. Weighted gene co-expression analysis elucidated that the blue module showed significant correlation with tocopherol content. Co-expression network analysis revealed that 2-methyl-6-phytobenzoquinone methyltransferase (MPBQ-MT/VTE3) played a vital role and EmWRKY13 may be a key negative regulator in E. mollis VitE biosynthesis. This study not only revealed the traditional VitE biosynthesis pathway in E. mollis, but also set a solid foundation for future genetic breeding of this species.

The evolution of tropane alkaloids: Coca does it differently

It is undeniable that tropane alkaloids (TAs) have been both beneficial and detrimental to human health in the modern era. Understanding their biosynthesis is vital for using synthetic biology to engineer organisms for pharmaceutical production. The most parsimonious approaches to pathway elucidation are traditionally homology-based methods. However, this approach has largely failed for TA biosynthesis in angiosperms. In the recent decade, significant progress has been made in elucidating the TA synthesis pathway in Erythroxylum coca, highlighting the parallel development of TAs in both the Solanaceae and Erythroxylaceae families. This separate evolutionary path has uncovered substantial divergence in the TAs formed by E. coca and distinct enzymatic reactions that differ from the traditional TA biosynthetic pathway found in TA-producing nightshade plants.

Trading acyls and swapping sugars: metabolic innovations in Solanum trichomes

Solanaceae (nightshade family) species synthesize a remarkable array of clade- and tissue-specific specialized metabolites. Protective acylsugars, one such class of structurally diverse metabolites, are produced by ACYLSUGAR ACYLTRANSFERASE (ASAT) enzymes from sugars and acyl-coenzyme A esters. Published research has revealed trichome acylsugars composed of glucose and sucrose cores in species across the family. In addition, acylsugars have been analyzed across a small fraction of the >1,200 species in the phenotypically megadiverse Solanum genus, with a handful containing inositol and glycosylated inositol cores. The current study sampled several dozen species across subclades of Solanum to get a more detailed view of acylsugar chemodiversity. In depth characterization of acylsugars from the clade II species brinjal eggplant (Solanum melongena) led to the identification of eight unusual structures with inositol or inositol glycoside cores and hydroxyacyl chains. Liquid chromatography-mass spectrometry analysis of 31 additional species in the Solanum genus revealed striking acylsugar diversity, with some traits restricted to specific clades and species. Acylinositols and inositol-based acyldisaccharides were detected throughout much of the genus. In contrast, acylglucoses and acylsucroses were more restricted in distribution. Analysis of tissue-specific transcriptomes and interspecific acylsugar acetylation differences led to the identification of the brinjal eggplant ASAT 3-LIKE 1 (SmASAT3-L1; SMEL4.1_12g015780) enzyme. This enzyme is distinct from previously characterized acylsugar acetyltransferases, which are in the ASAT4 clade, and appears to be a functionally divergent ASAT3. This study provides a foundation for investigating the evolution and function of diverse Solanum acylsugar structures and harnessing this diversity in breeding and synthetic biology.

How did plants evolve the prenylation of specialized phenolic metabolites by means of UbiA prenyltransferases?

Prenylated phenolics occur in over 4000 species in the plant kingdom, most of which are known as specialized metabolites with high chemical diversity. Many of them have been identified as pharmacologically active compounds from various medicinal plants, in which prenyl residues play a key role in these activities. Prenyltransferases (PTs) responsible for their biosynthesis have been intensively studied in the last two decades. These enzymes are membrane-bound proteins belonging to the UbiA superfamily that occurs from bacteria to humans, and in particular those involved in plant specialized metabolism show strict specificities for both substrates and products. This article reviews the enzymatic features of plant UbiA PTs, including C- and O-prenylation, molecular evolution, and application of UbiA PTs in synthetic biology.

Impact of External Sources of Indole Acetic Acid and 2,3,5-Triiodobenzoic Acid on Alkaloid Production and Their Relationships with Primary Metabolism and Antioxidant Activity in Annona emarginata (Schltdl.) H. Rainer

Annona emarginata is a native Brazilian species capable of producing at least ten alkaloids of ecological, agronomic, and pharmacological importance. Some studies have explored the effect of external phytoregulators on the production of alkaloids, including the effect of auxins, which, like alkaloids, derive from the shikimic acid pathway. Thus, this study aimed to evaluate how indole acetic acid (IAA) and its inhibitor 2,3,5-triiodobenzoic acid (TIBA) impact the production of alkaloids and the primary metabolism of A. emarginata, which brings advances in the understanding of the mechanisms of alkaloid synthesis and can aid in the bioprospection of molecules of interest in Annonaceae. The design was completely randomized, with three treatments (control, IAA [10-6 M] and TIBA [10-6 M]) and five collection times (12, 36, 84, 156, and 324 h). The following variables were analyzed: total alkaloids, alkaloid profile, nitrate reductase activity, gas exchange in photosynthesis, chlorophyll a fluorescence, sugars, starch, and antioxidant activity. Of the twelve alkaloids analyzed, discretine and xylopine were not detected in the control plants; however, both were detected when IAA was applied (in roots and leaves) and xylopine (in roots) when the inhibitor was applied. The alkaloid asimilobine was not detected with the use of TIBA. Variations in alkaloid concentrations occurred in a punctual manner, without significant variations in photosynthesis and nitrate reductase activity, but with variations in the antioxidant system and sugar concentrations, mainly at 156 h, when the highest alkaloid concentrations were observed with the use of TIBA. It could be concluded that IAA is capable of selectively modulating the production of alkaloids in A. emarginata, either due to an external source or by the application of its inhibitor (TIBA).

Dynamic Metabolic Responses of Resistant and Susceptible Poplar Clones Induced by Hyphantria cunea Feeding

Poplar trees are significant for both economic and ecological purposes, and the fall webworm (Hyphantria cunea Drury) poses a major threat to their plantation in China. The preliminary resistance assessment in the previous research indicated that there were differences in resistance to the insect among these varieties, with '2KEN8' being more resistant and 'Nankang' being more susceptible. The present study analyzed the dynamic changes in the defensive enzymes and metabolic profiles of '2KEN8' and 'Nankang' at 24 hours post-infestation (hpi), 48 hpi, and 96 hpi. The results demonstrated that at the same time points, compared to susceptible 'Nankang', the leaf consumption by H. cunea in '2KEN8' was smaller, and the larval weight gain was slower, exhibiting clear resistance to the insect. Biochemical analysis revealed that the increased activity of the defensive enzymes in '2KEN8' triggered by the feeding of H. cunea was significantly higher than that of 'Nankang'. Metabolomics analysis indicated that '2KEN8' initiated an earlier and more intense reprogramming of the metabolic profile post-infestation. In the early stages of infestation, the differential metabolites induced in '2KEN8' primarily included phenolic compounds, flavonoids, and unsaturated fatty acids, which are related to the biosynthesis pathways of phenylpropanoids, flavonoids, unsaturated fatty acids, and jasmonates. The present study is helpful for identifying the metabolic biomarkers for inductive resistance to H. cunea and lays a foundation for the further elucidation of the chemical resistance mechanism of poplar trees against this insect.

Integrated transcriptomic, metabolomic, and functional analyses unravel the mechanism of bagging delaying fruit cracking of pomegranate (Punica granatum L.)

The economic impact of fruit cracking in pomegranate products is substantial. In this study, we present the inaugural comprehensive analysis of transcriptome and metabolome in the outermost pericarp of pomegranate fruit in bagging conditions. Our investigation revealed a notable upregulation of differentially expressed genes (DEGs) associated with the calcium signaling pathway (76.92%) and xyloglucan endotransglucosylase/hydrolase (XTH) genes (87.50%) in the fruit peel of non-cracking fruit under bagging. Metabolomic analysis revealed that multiple phenolics, flavonoids, and tannins were identified in pomegranate. Among these, calmodulin-like 23 (PgCML23) exhibited a significant correlation with triterpenoids and demonstrated a marked upregulation under bagging treatment. The transgenic tomatoes overexpressing PgCML23 exhibited significantly higher cellulose content and xyloglucan endotransglucosylase (XET) enzyme activity in the pericarp at the red ripening stage compared to the wild type. Conversely, water-soluble pectin content, polygalacturonase (PG), and β-galactosidase (β-GAL) enzyme activities were significantly lower in the transgenic tomatoes. Importantly, the heterologous expression of PgCML23 led to a substantial reduction in the fruit cracking rate in tomatoes. Our findings highlight the reduction of fruit cracking in bagging conditions through the manipulation of PgCML23 expression.

Structural insights into catalytic promiscuity of chalcone synthase from Glycine max (L.) Merr.: Coenzyme A-induced alteration of product specificity

Catalytic promiscuity of enzymes plays a pivotal role in driving the evolution of plant specialized metabolism. Chalcone synthase (CHS) catalyzes the production of 2',4,4',6'-tetrahydroxychalcone (THC), a common precursor of plant flavonoids, from p-coumaroyl-coenzyme A (-CoA) and three malonyl-CoA molecules. CHS has promiscuous product specificity, producing a significant amount of p-coumaroyltriacetic lactone (CTAL) in vitro. However, mechanistic aspects of this CHS promiscuity remain to be clarified. Here, we show that the product specificity of soybean CHS (GmCHS1) is altered by CoA, a reaction product, which selectively inhibits THC production (IC50, 67 μM) and enhances CTAL production. We determined the structure of a ternary GmCHS1/CoA/naringenin complex, in which CoA is bound to the CoA-binding tunnel via interactions with Lys55, Arg58, and Lys268. Replacement of these residues by alanine resulted in an enhanced THC/CTAL production ratio, suggesting the role of these residues in the CoA-mediated alteration of product specificity. In the ternary complex, a mobile loop ("the K-loop"), which contains Lys268, was in a "closed conformation" placing over the CoA-binding tunnel, whereas in the apo and binary complex structures, the K-loop was in an "open conformation" and remote from the tunnel. We propose that the production of THC involves a transition of the K-loop conformation between the open and closed states, whereas synthesis of CTAL is independent of it. In the presence of CoA, an enzyme conformer with the closed K-loop conformation becomes increasingly dominant, hampering the transition of K-loop conformations to result in decreased THC production and increased CTAL production.

SCPL acyltransferases catalyze the metabolism of chlorogenic acid during purple coneflower seed germination

The metabolism of massively accumulated chlorogenic acid is crucial for the successful germination of purple coneflower (Echinacea purpurea (L.) Menoch). A serine carboxypeptidase-like (SCPL) acyltransferase (chicoric acid synthase, CAS) utilizes chlorogenic acid to produce chicoric acid during germination. However, it seems that the generation of chicoric acid lags behind the decrease in chlorogenic acid, suggesting an earlier route of chlorogenic acid metabolism. We discovered another chlorogenic acid metabolic product, 3,5-dicaffeoylquinic acid, which is produced before chicoric acid, filling the lag phase. Then, we identified two additional typical clade IA SCPL acyltransferases, named chlorogenic acid condensing enzymes (CCEs), that catalyze the biosynthesis of 3,5-dicaffeoylquinic acid from chlorogenic acid with different kinetic characteristics. Chlorogenic acid inhibits radicle elongation in a dose-dependent manner, explaining the potential biological role of SCPL acyltransferases-mediated continuous chlorogenic acid metabolism during germination. Both CCE1 and CCE2 are highly conserved among Echinacea species, supporting the observed metabolism of chlorogenic acid to 3,5-dicaffeoylquinic acid in two Echinacea species without chicoric acid accumulation. The discovery of SCPL acyltransferase involved in the biosynthesis of 3,5-dicaffeoylquinic acid suggests convergent evolution. Our research clarifies the metabolism strategy of chlorogenic acid in Echinacea species and provides more insight into plant metabolism.

Arogenate dehydratase isoforms strategically deregulate phenylalanine biosynthesis in Akebia trifoliata

Arogenate dehydratase (ADT) is key for phenylalanine (Phe) biosynthesis in plants. To examine ADT components and function in Akebia trifoliata, a representative of Ranunculaceae, we first identified eight ADTs (AktADT1-8, encoding sequences varying from 1032 to 1962 bp) in the A. trifoliata reference genome and five proteins (AktADT1, AktADT4, AktADT7, AktADT8 and AktADT8s) with moonlighting prephenate dehydratase (PDT) activity and Km values varying from 0.43 to 2.17 mM. Structurally, two basic residue combinations (Val314/Ala317 and Ala314/Val317) in the PAC domain are essential for the moonlighting PDT activity of ADTs. Functionally, AktADT4 and AktADT8 successfully restored the wild-type phenotype of pha2, a knockout mutant of Saccharomyces cerevisiae. In addition, AktADTs are ubiquitously expressed, but their expression levels are tissue specific, and the half maximal inhibitory concentration (IC50) of Phe for AktADTs ranged from 49.81 to 331.17 μM. Both AktADT4 and AktADT8 and AktADT8s localized to chloroplast stromules and the cytosol, respectively, while the remaining AktADTs localized to the chloroplast stroma. These findings suggest that various strategies exist for regulating Phe biosynthesis in A. trifoliata. This provides a reasonable explanation for the high Phe content and insights for further genetic improvement of the edible fruits of A. trifoliata.

Metabolite-based genome-wide association studies enable the dissection of the genetic bases of flavonoids, betaine and spermidine in wolfberry (Lycium)

Wolfberry is a plant with medicinal and food values. However, its bioactive ingredients and the corresponding genetic bases have not been determined. Here, we de novo generated a chromosome-level genome assembly for wolfberry, yielding a genome sequence of ~1.77 Gb with contig N50 of 50.55 Mb and 39 224 predicted gene models. A variation map, using 307 re-sequenced accessions, was called based on this genome assembly. Furthermore, the fruit metabolome of these accessions was profiled using 563 annotated metabolites, which separated Lycium barbarum L. and non-L. barbarum L. The flavonoids, coumarins, alkaloids and nicotinic acid contents were higher in the former than in the latter. A metabolite-based genome-wide association study mapped 156 164 significant single nucleotide polymorphisms corresponding to 340 metabolites. This included 19 219 unique lead single nucleotide polymorphisms in 1517 significant association loci, of which three metabolites, flavonoids, betaine and spermidine, were highlighted. Two candidate genes, LbUGT (evm.TU.chr07.2692) and LbCHS (evm.TU.chr07.2738), with non-synonymous mutations, were associated with the flavonoids content. LbCHS is a structural gene that interacts with a nearby MYB transcription factor (evm.TU.chr07.2726) both in L. barbarum and L. ruthenicum. Thus, these three genes might be involved in the biosynthesis/metabolism of flavonoids. LbSSADH (evm.TU.chr09.627) was identified as possibly participating in betaine biosynthesis/metabolism. Four lycibarbarspermidines (E-G and O) were identified, and only the lycibarbarspermidines O content was higher in L. barbarum varieties than in non-L. barbarum varieties. The evm.TU.chr07.2680 gene associated with lycibarbarspermidines O was annotated as an acetyl-CoA-benzylalcohol acetyltransferase, suggesting that it is a candidate gene for spermidine biosynthesis. These results provide novel insights into the specific metabolite profile of non-L. barbarum L. and the genetic bases of flavonoids, betaine and spermidine biosynthesis/metabolism.

A terpenoids database with the chemical content as a novel agronomic trait

Natural products play a pivotal role in drug discovery, and the richness of natural products, albeit significantly influenced by various environmental factors, is predominantly determined by intrinsic genetics of a series of enzymatic reactions and produced as secondary metabolites of organisms. Heretofore, few natural product-related databases take the chemical content into consideration as a prominent property. To gain unique insights into the quantitative diversity of natural products, we have developed the first TerPenoids database embedded with Content information (TPCN) with features such as compound browsing, structural search, scaffold analysis, similarity analysis and data download. This database can be accessed through a web-based computational toolkit available at http://www.tpcn.pro/. By conducting meticulous manual searches and analyzing over 10 000 reference papers, the TPCN database has successfully integrated 6383 terpenoids obtained from 1254 distinct plant species. The database encompasses exhaustive details including isolation parts, comprehensive molecule structures, chemical abstracts service registry number (CAS number) and 7508 content descriptions. The TPCN database accentuates both the qualitative and quantitative dimensions as invaluable phenotypic characteristics of natural products that have undergone genetic evolution. By acting as an indispensable criterion, the TPCN database facilitates the discovery of drug alternatives with high content and the selection of high-yield medicinal plant species or phylogenetic alternatives, thereby fostering sustainable, cost-effective and environmentally friendly drug discovery in pharmaceutical farming. Database URL: http://www.tpcn.pro/.

Specialized metabolite modifications in Brassicaceae seeds and plants: diversity, functions and related enzymes

Covering: up to 2023Specialized metabolite (SM) modifications and/or decorations, corresponding to the addition or removal of functional groups (e.g. hydroxyl, methyl, glycosyl or acyl group) to SM structures, contribute to the huge diversity of structures, activities and functions of seed and plant SMs. This review summarizes available knowledge (up to 2023) on SM modifications in Brassicaceae and their contribution to SM plasticity. We give a comprehensive overview on enzymes involved in the addition or removal of these functional groups. Brassicaceae, including model (Arabidopsis thaliana) and crop (Brassica napus, Camelina sativa) plant species, present a large diversity of plant and seed SMs, which makes them valuable models to study SM modifications. In this review, particular attention is given to the environmental plasticity of SM and relative modification and/or decoration enzymes. Furthermore, a spotlight is given to SMs and related modification enzymes in seeds of Brassicaceae species. Seeds constitute a large reservoir of beneficial SMs and are one of the most important dietary sources, providing more than half of the world's intake of dietary proteins, oil and starch. The seed tissue- and stage-specific expressions of A. thaliana genes involved in SM modification are presented and discussed in the context of available literature. Given the major role in plant phytochemistry, biology and ecology, SM modifications constitute a subject of study contributing to the research and development in agroecology, pharmaceutical, cosmetics and food industrial sectors.

Hordeum vulgare CYP76M57 catalyzes C2 shortening of tryptophan side chain by C-N bond rearrangement in gramine biosynthesis

The indole alkaloid gramine, 3-(dimethylaminomethyl)indole, is a defensive specialized metabolite found in some barley cultivars. In its biosynthetic process, the tryptophan (Trp) side chain is shortened by two carbon atoms to produce 3-(aminomethyl)indole (AMI), which is then methylated by N-methyltransferase (HvNMT) to produce gramine. Although side chain shortening is one of the crucial scaffold formation steps of alkaloids originating from aromatic amino acids, the gene and enzyme involved in the Trp-AMI conversion reactions are unknown. In this study, through RNA-seq analysis, 35 transcripts were shown to correlate with gramine production; among them, an uncharacterized cytochrome P450 (CYP) gene, CYP76M57, and HvNMT were identified as candidate genes for gramine production. Transgenic Arabidopsis thaliana and rice overexpressing CYP and HvNMT accumulate AMI, N-methyl-AMI, and gramine. CYP76M57, heterologously expressed in Pichia pastoris, was able to act on Trp to produce AMI. Furthermore, the amino group nitrogen of Trp was retained during the CYP76M57-catalyzed reaction, indicating that the C2 shortening of Trp proceeds with an unprecedented biosynthetic process, the removal of the carboxyl group and Cα and the rearrangement of the nitrogen atom to Cβ. In some gramine-non-accumulating barley cultivars, arginine 104 in CYP76M57 is replaced by threonine, which abolished the catalytic activity of CYP76M57 to convert Trp into AMI. These results uncovered the missing committed enzyme of gramine biosynthesis in barley and contribute to the elucidation of the potential functions of CYPs in plants and undiscovered specialized pathways.

Unraveling the mechanism of potato (Solanum tuberosum L.) tuber sprouting using transcriptome and metabolome analyses

Sprouting is an irreversible deterioration of potato quality, which leads to the production of harmful toxins and loss of the commercial value of potatoes. However, there is no report on the changes in different stages of potato sprouting through transcriptome and metabonomics. In this study, 1471 differentially expressed genes (DEGs) were found between DP and BP. In comparison with SP, a total of 6309 DEGs were detected in BP. Additionally, 6624 DEGs were identified between DP and SP. Moreover, 96 and 117 differentially accumulated metabolites (DAMs) were detected between DP and BP and between BP and SP, respectively. Furthermore, 130 DAMs were identified in total between DP and SP. In each group, a correlation analysis of DAMs and DEGs was performed to examine the regulatory network. The results indicated that the sprouting of tubers is mainly regulated by plant hormone signals, and during the sprouting of tubers, significant changes in metabolic products occur in the body. According to the combined analysis of transcriptomics and metabolomics, multiple metabolites were both positive and negative regulated by genes.

Gut bacteria mediated adaptation of diamondback moth, Plutella xylostella, to secondary metabolites of host plants

IMPORTANCE

In this study, we identify an important role of gut bacteria in mediating the adaptation of diamondback moth (DBM) to plant secondary metabolites. We demonstrate that kaempferol's presence in radish seedlings greatly reduces the fitness of DBM with depleted gut biota. Reinstatement of gut biota, particularly Enterobacter sp. EbPXG5, improved insect performance by degrading kaempferol. This bacterium was common in the larval gut of DBM, lining the epithelium as a protective film. Our work highlights the role of symbiotic bacteria in insect herbivore adaptation to plant defenses and provides a practical and mechanistic framework for developing a more comprehensive understanding of insect-gut microbe-host plant co-evolution.

Genome-wide identification of the OMT gene family in Cucumis melo L. and expression analysis under abiotic and biotic stress

Background

O-methyltransferase (OMT)-mediated O-methylation is a frequent modification that occurs during natural product biosynthesis, and it increases the diversity and stability of secondary metabolites. However, detailed genome-wide identification and expression analyses of OMT gene family members have not been performed in melons. In this study, we aimed to perform the genome-wide identification of OMT gene family members in melon to identify and clarify their actions during stress.

Methods

Genome-wide identification of OMT gene family members was performed using data from the melon genome database. The Cucumis melo OMT genes (CmOMTs) were then compared with the genes from two representative monocotyledons and three representative dicotyledons. The basic information, cis-regulatory elements in the promoter, predicted 3-D-structures, and GO enrichment results of the 21 CmOMTs were analyzed.

Results

In our study, 21 CmOMTs (named CmOMT1-21) were obtained by analyzing the melon genome. These genes were located on six chromosomes and divided into three groups composed of nine, six, and six CmOMTs based on phylogenetic analysis. Gene structure and motif descriptions were similar within the same classes. Each CmOMT gene contains at least one cis-acting element associated with hormone transport regulation. Analysis of cis-acting elements illustrated the potential role of CmOMTs in developmental regulation and adaptations to various abiotic and biotic stresses. The RNA-seq and quantitative real-time PCR (qRT-PCR) results indicated that NaCl stress significantly induced CmOMT6/9/14/18 and chilling and high temperature and humidity (HTH) stresses significantly upregulated CmOMT14/18. Furthermore, the expression pattern of CmOMT18 may be associated with Fusarium oxysporum f. sp. melonis race 1.2 (FOM1.2) and powdery mildew resistance. Our study tentatively explored the biological functions of CmOMT genes in various stress regulation pathways and provided a conceptual basis for further detailed studies of the molecular mechanisms.

Chemistry, biosynthesis and biology of floral volatiles: roles in pollination and other functions

Covering: 2010 to 2023Floral volatiles are a chemically diverse group of plant metabolites that serve multiple functions. Their composition is shaped by environmental, ecological and evolutionary factors. This review will summarize recent advances in floral scent research from chemical, molecular and ecological perspectives. It will focus on the major chemical classes of floral volatiles, on notable new structures, and on recent discoveries regarding the biosynthesis and the regulation of volatile emission. Special attention will be devoted to the various functions of floral volatiles, not only as attractants for different types of pollinators, but also as defenses of flowers against enemies. We will also summarize recent findings on how floral volatiles are affected by abiotic stressors, such as increased temperatures and drought, and by other organisms, such as herbivores and flower-dwelling microbes. Finally, this review will indicate current research gaps, such as the very limited knowledge of the isomeric pattern of chiral compounds and its importance in interspecific interactions.

The contribution of plant life and growth forms to global gradients of vascular plant diversity

Plant life and growth forms (shortened to 'plant forms') represent key functional strategies of plants in relation to their environment and provide important insights into the ecological constraints acting on the distribution of biodiversity. Despite their functional importance, how the spectra of plant forms contribute to global gradients of plant diversity is unresolved. Using a novel dataset comprising > 295 000 species, we quantify the contribution of different plant forms to global gradients of vascular plant diversity. Furthermore, we establish how plant form distributions in different biogeographical regions are associated with contemporary and paleoclimate conditions, environmental heterogeneity and phylogeny. We find a major shift in representation of woody perennials in tropical latitudes to herb-dominated floras in temperate and boreal regions, following a sharp latitudinal gradient in plant form diversity from the tropics to the poles. We also find significant functional differences between regions, mirroring life and growth form responses to environmental conditions, which is mostly explained by contemporary climate (18-87%), and phylogeny (6-62%), with paleoclimate and heterogeneity playing a lesser role (< 23%). This research highlights variation in the importance of different plant forms to diversity gradients world-wide, shedding light on the ecological and evolutionary pressures constraining plant-trait distributions.

Characterization of the horse chestnut genome reveals the evolution of aescin and aesculin biosynthesis

Horse chestnut (Aesculus chinensis) is an important medicinal tree that contains various bioactive compounds, such as aescin, barrigenol-type triterpenoid saponins (BAT), and aesculin, a glycosylated coumarin. Herein, we report a 470.02 Mb genome assembly and characterize an Aesculus-specific whole-genome duplication event, which leads to the formation and duplication of two triterpenoid biosynthesis-related gene clusters (BGCs). We also show that AcOCS6, AcCYP716A278, AcCYP716A275, and AcCSL1 genes within these two BGCs along with a seed-specific expressed AcBAHD6 are responsible for the formation of aescin. Furthermore, we identify seven Aesculus-originated coumarin glycoside biosynthetic genes and achieve the de novo synthesis of aesculin in E. coli. Collinearity analysis shows that the collinear BGC segments can be traced back to early-diverging angiosperms, and the essential gene-encoding enzymes necessary for BAT biosynthesis are recruited before the splitting of Aesculus, Acer, and Xanthoceras. These findings provide insight on the evolution of gene clusters associated with medicinal tree metabolites.

Comparative Analysis of the Wood Metabolites of Three Poplar Clones Using UPLC-Triple-TOF-MS

Poplar, a woody tree species, is widely used for industrial production and as a protective forest belt. Different clones of poplar exhibit clear variation in terms of morphological and physiological features, however, the impact of the genetic variation on the composition and abundance of wood metabolite have not been fully determined. In this study, ultra-high pressure liquid chromatography-triple time of flight-mass spectrometer (UPLC-Triple-TOF-MS) was used to explore the metabolite changes in poplar wood from three clones, including Populus deltoides CL. '55/65', P. deltoides CL. 'Danhong', and P. nigra CL. 'N179'. A total of 699 metabolites were identified. Clustering analysis and principal component analysis display that the metabolic differences of wood have allowed distinguishing different species of poplar. Meanwhile, eight significantly different metabolites were screened between P. deltoides and P. nigra, which may be considered as valuable markers for chemotaxonomy. In addition, the highly discriminant 352 metabolites were obtained among the three clones, and those may be closely related to the distinction in unique properties (e.g., growth, rigidity and tolerance) of the poplar wood cultivars. This study provides a foundation for further studies on wood metabolomics in poplar, and offers chemotaxonomic markers that will stimulate the early screening of potentially superior trees.

Regional variation in the antibacterial activity of a wild plant, wild garlic (Allium ursinum L.)

Antibacterial activity is a common and highly studied property of plant secondary metabolites. Despite the extensive literature focusing on identifying novel antibacterial metabolites, little work has been undertaken to examine variation in levels of antibacterial activity in any plant species. Here, we used large-scale sampling of leaves of the antibacterial plant, wild garlic (Allium ursinum L.), assembling a set of tissue extracts from 168 plants, with 504 leaves collected and analysed. We assayed extracts for antibacterial activity against Bacillus subtilis and used LC-MS to carry out a chemometric analysis examining variation in individual metabolites, comparing them with several ecological parameters. We found that allicin was the only metabolite which was positively related to antibacterial activity. Soil temperature was a key determinant of variability in the concentrations of many foliar metabolites, however, neither allicin concentrations nor antibacterial activity was related to any of our measured ecological parameters, other than roadside proximity. We suggest that the synthesis of allicin precursors may be largely independent of growing conditions. This may be to ensure that allicin is synthesised rapidly and in sufficiently high concentrations to effectively prevent herbivory and pest damage. This finding contrasts with flavonoids which were found to vary greatly between plants and across sites. Our findings suggest that key biologically active metabolites are constrained in their concentration range compared to other compounds in the metabolome. This has important implications for the development of wild garlic as a health supplement or animal feed additive.

Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.

Primary and Secondary Metabolites in Lotus japonicus

Lotus japonicus is a leguminous model plant used to gain insight into plant physiology, stress response, and especially symbiotic plant-microbe interactions, such as root nodule symbiosis or arbuscular mycorrhiza. Responses to changing environmental conditions, stress, microbes, or insect pests are generally accompanied by changes in primary and secondary metabolism to account for physiological needs or to produce defensive or signaling compounds. Here we provide an overview of the primary and secondary metabolites identified in L. japonicus to date. Identification of the metabolites is mainly based on mass spectral tags (MSTs) obtained by gas chromatography linked with tandem mass spectrometry (GC-MS/MS) or liquid chromatography-MS/MS (LC-MS/MS). These MSTs contain retention index and mass spectral information, which are compared to databases with MSTs of authentic standards. More than 600 metabolites are grouped into compound classes such as polyphenols, carbohydrates, organic acids and phosphates, lipids, amino acids, nitrogenous compounds, phytohormones, and additional defense compounds. Their physiological effects are briefly discussed, and the detection methods are explained. This review of the exisiting literature on L. japonicus metabolites provides a valuable basis for future metabolomics studies.

Integrated Transcriptomic and Metabolomic Analyses Reveal the Effects of Grafting on Special Metabolites of Acanthopanax senticosus Leaves

Acanthopanax senticosus (A. senticosus) is a member of Acanthopanax Miq. and is used in traditional Chinese medicine, and it has been found that grafting technology can be used to alter plant metabolite composition and transcriptome characteristics. In this study, shoots of A. senticosus were grafted onto the rootstocks of the vigorous Acanthopanax sessiliflorus (A. sessiliflorus) to improve its varietal characteristics. In order to investigate the changes in metabolites and transcriptional patterns in grafted A. senticosus leaves (GSCL), fresh leaves were collected from 2-year-old grafted A. senticosus scions, while self-rooted seedling A. senticosus leaves (SCL) were used as controls to analyse the transcriptome and metabolome. Metabolic profiles and gene expression patterns were further identified and correlated in special metabolite target pathways. The content of chlorogenic acid and triterpenoids in the GSCL was higher than in the control, while the quercetin content was lower. All these metabolic changes were associated with changes in the expression pattern of transcripts. Our results revealed the transcriptome and metabolome characteristics of GSCL. This may help to improve leaf quality in A. senticosus cultivation, suggesting that it is feasible to improve the medicinal quality of GSCL through asexual propagation, but the long-term effects need further investigation. In conclusion, this dataset provides a useful resource for future studies on the effects of grafting on medicinal plants.

Metabolic consequences of various fruit-based diets in a generalist insect species

Most phytophagous insect species exhibit a limited diet breadth and specialize on a few or a single host plant. In contrast, some species display a remarkably large diet breadth, with host plants spanning several families and many species. It is unclear, however, whether this phylogenetic generalism is supported by a generic metabolic use of common host chemical compounds ('metabolic generalism') or alternatively by distinct uses of diet-specific compounds ('multi-host metabolic specialism')? Here, we simultaneously investigated the metabolomes of fruit diets and of individuals of a generalist phytophagous species, Drosophila suzukii, that developed on them. The direct comparison of metabolomes of diets and consumers enabled us to disentangle the metabolic fate of common and rarer dietary compounds. We showed that the consumption of biochemically dissimilar diets resulted in a canalized, generic response from generalist individuals, consistent with the metabolic generalism hypothesis. We also showed that many diet-specific metabolites, such as those related to the particular color, odor, or taste of diets, were not metabolized, and rather accumulated in consumer individuals, even when probably detrimental to fitness. As a result, while individuals were mostly similar across diets, the detection of their particular diet was straightforward. Our study thus supports the view that dietary generalism may emerge from a passive, opportunistic use of various resources, contrary to more widespread views of an active role of adaptation in this process. Such a passive stance towards dietary chemicals, probably costly in the short term, might favor the later evolution of new diet specializations.

Many different flowers make a bouquet: Lessons from specialized metabolite diversity in plant-pollinator interactions

Flowering plants have evolved extraordinarily diverse metabolites that underpin the floral visual and olfactory signals enabling plant-pollinator interactions. In some cases, these metabolites also provide unusual rewards that specific pollinators depend on. While some metabolites are shared by most flowering plants, many have evolved in restricted lineages in response to the specific selection pressures encountered within different niches. The latter are designated as specialized metabolites. Recent investigations continue to uncover a growing repertoire of unusual specialized metabolites. Increased accessibility to cutting-edge multi-omics technologies (e.g. genome, transcriptome, proteome, metabolome) is now opening new doors to simultaneously uncover the molecular basis of their synthesis and their evolution across diverse plant lineages. Drawing upon the recent literature, this perspective discusses these aspects and, where known, their ecological and evolutionary relevance. A primer on omics-guided approaches to discover the genetic and biochemical basis of functional specialized metabolites is also provided.

Evolutionary repeatability of emergent properties of ecological communities

Most species belong to ecological communities where their interactions give rise to emergent community-level properties, such as diversity and productivity. Understanding and predicting how these properties change over time has been a major goal in ecology, with important practical implications for sustainability and human health. Less attention has been paid to the fact that community-level properties can also change because member species evolve. Yet, our ability to predict long-term eco-evolutionary dynamics hinges on how repeatably community-level properties change as a result of species evolution. Here, we review studies of evolution of both natural and experimental communities and make the case that community-level properties at least sometimes evolve repeatably. We discuss challenges faced in investigations of evolutionary repeatability. In particular, only a handful of studies enable us to quantify repeatability. We argue that quantifying repeatability at the community level is critical for approaching what we see as three major open questions in the field: (i) Is the observed degree of repeatability surprising? (ii) How is evolutionary repeatability at the community level related to repeatability at the level of traits of member species? (iii) What factors affect repeatability? We outline some theoretical and empirical approaches to addressing these questions. Advances in these directions will not only enrich our basic understanding of evolution and ecology but will also help us predict eco-evolutionary dynamics. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.

Insights into the convergent evolution of fructan biosynthesis in angiosperms from the highly characteristic chicory genome

Fructans in angiosperms play essential roles in physiological functions and environmental adaptations. As a major source of industrial fructans (especially inulin-type), chicory (Cichorium intybus L.) is a model species for studying fructan biosynthesis. However, the genes underlying this process and their evolutionary history in angiosperms remain elusive. We combined multiple sequencing technologies to assemble and annotate the chicory genome and scan its (epi)genomic features, such as genomic components, DNA methylation, and three-dimensional (3D) structure. We also performed a comparative genomics analysis to uncover the associations between key traits and gene families. We achieved a nearly complete chicory genome assembly and found that continuous bursts of a few highly active retrotransposon families largely shaped the (epi)genomic characteristics. The highly methylated genome with its unique 3D structure potentially influences critical biological processes. Our comprehensive comparative genomics analysis deciphered the genetic basis for the rich sesquiterpene content in chicory and indicated that the fructan-accumulating trait resulted from convergent evolution in angiosperms due to shifts in critical sites of fructan-active enzymes. The highly characterized chicory genome provides insight into Asteraceae evolution and fructan biosynthesis in angiosperms.

Mining for a New Class of Fungal Natural Products: The Evolution, Diversity, and Distribution of Isocyanide Synthase Biosynthetic Gene Clusters

The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) have notable bioactivities that mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We developed the first genome-mining pipeline to identify ICS BGCs, locating 3,800 ICS BGCs in 3,300 genomes. Genes in these clusters share promoter motifs and are maintained in contiguous groupings by natural selection. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1 / 2 gene cluster family (GCF), which was thought to only exist in yeast, is present in ∼30% of all Ascomycetes, including many filamentous fungi. The evolutionary history of the dit GCF is marked by deep divergences and phylogenetic incompatibilities that raise questions about convergent evolution and suggest selection or horizontal gene transfers have shaped the evolution of this cluster in some yeast and dimorphic fungi. Our results create a roadmap for future research into ICS BGCs. We developed a website ( www.isocyanides.fungi.wisc.edu ) that facilitates the exploration, filtering, and downloading of all identified fungal ICS BGCs and GCFs.