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The special issue 'The evolution of plant metabolism' has brought together original research, reviews and opinions that cover various aspects from the full breath of plant metabolism including its interaction with the environment including other species. Here, we briefly summarize these efforts and attempts to extract a consensus opinion of the best manner in which to tackle this subject both now and in the future. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Sexual reproduction in Charophyceae abounds in complex traits. Their gametangia develop as intricate structures, with oogonia spirally surrounded by envelope cells and richly pigmented antheridia. The red—probably protectant—pigmentation of antheridia is conserved across Charophyceae. Chara tomentosa is, however, unique in exhibiting this pigmentation and also in vegetative tissue. Here, we investigated the two sympatric species, C. tomentosa and Chara baltica, and compared their molecular chassis for pigmentation. Using reversed phase C30 high performance liquid chromatography (RP-C30-HPLC), we uncover that the major pigments are β-carotene, δ-carotene and γ-carotene; using headspace solid-phase microextraction coupled to gas chromatography equipped with a mass spectrometer (HS-SPME-GC-MS), we pinpoint that the unusually large carotenoid pool in C. tomentosa gives rise to diverse volatile apocarotenoids, including abundant 6-methyl-5-hepten-2-one. Based on transcriptome analyses, we uncover signatures of the unique biology of Charophycaee and genes for pigment production, including monocyclized carotenoids. The rich carotenoid pool probably serves as a substrate for diverse carotenoid-derived metabolites, signified not only by (i) the volatile apocarotenoids we detected but (ii) the high expression of a gene coding for a cytochrome P450 enzyme related to land plant proteins involved in the biosynthesis of carotenoid-derived hormones. Overall, our data shed light on a key protection strategy of sexual reproduction in the widespread group of macroalgae. The genetic underpinnings of this are shared across hundreds of millions of years of plant and algal evolution. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

In the course of plant evolution from aquatic to terrestrial environments, land plants (embryophytes) acquired a diverse array of specialized metabolites, including phenylpropanoids, flavonoids and cuticle components, enabling adaptation to various environmental stresses. While embryophytes and their closest algal relatives share candidate enzymes responsible for producing some of these compounds, the complete genetic network for their biosynthesis emerged in embryophytes. In this review, we analysed genomic data from chlorophytes, charophytes and embryophytes to identify genes related to phenylpropanoid, flavonoid and cuticle biosynthesis. By integrating published research, transcriptomic data and metabolite studies, we provide a comprehensive overview on how these specialized metabolic pathways have contributed to plant defence responses to pathogens in non-vascular bryophytes and vascular plants throughout evolution. The evidence suggests that these biosynthetic pathways have provided land plants with a repertoire of conserved and lineage-specific compounds, which have shaped immunity against invading pathogens. The discovery of additional enzymes and metabolites involved in bryophyte responses to pathogen infection will provide evolutionary insights into these versatile pathways and their impact on environmental terrestrial challenges. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

The arbuscular mycorrhizal (AM) symbiosis formed by most extant land plants with symbiotic fungi evolved 450 Ma. AM promotes plant growth by improving mineral nutrient and water uptake, while the symbiotic fungi obtain carbon in return. A number of plant genes regulating the steps leading to an efficient symbiosis have been identified; however, our understanding of the metabolic processes involved in the symbiosis and how they were wired to symbiosis regulation during plant evolution remains limited. Among them, the exchange of chemical signals, the activation of dedicated biosynthesis pathways and the production of secondary metabolites regulating late stages of the AM symbiosis begin to be well described across several land plant clades. Here, we review our current understanding of these processes and propose future directions to fully grasp the phylogenetic distribution and role played by small molecules during this ancient plant symbiosis. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Autophagy is a highly conserved 'self-digesting' mechanism used in eukaryotes to degrade and recycle cellular components by enclosing them in a double membrane compartment and delivering them to lytic organelles (lysosomes or vacuoles). Extensive studies in plants have revealed how autophagy is intricately linked to essential aspects of metabolism and growth, in both normal and stress conditions, including cellular and organelle homeostasis, nutrient recycling, development, responses to biotic and abiotic stresses, senescence and cell death. However, knowledge regarding autophagic processes in other photosynthetic organisms remains limited. In this review, we attempt to summarize the current understanding of autophagy in algae from a metabolic, molecular and evolutionary perspective. We focus on the composition and conservation of the autophagy molecular machinery in eukaryotes and discuss the role of autophagy in metabolic regulation, cellular homeostasis and stress adaptation in algae. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Transcription factors (TFs) provide potentially powerful tools for plant metabolic engineering as they often control multiple genes in a metabolic pathway. However, selecting the best TF for a particular pathway has been challenging, and the selection often relies significantly on phylogenetic relationships. Here, we offer examples where evolutionary relationships have facilitated the selection of the suitable TFs, alongside situations where such relationships are misleading from the perspective of metabolic engineering. We argue that the evolutionary trajectory of a particular TF might be a better indicator than protein sequence homology alone in helping decide the best targets for plant metabolic engineering efforts. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Purine alkaloids are naturally occurring nitrogenous methylated derivatives of purine nucleotide degradation products, having essential roles in medicine, food and various other aspects of our daily lives. They are generated through convergent evolution in different plant species. The pivotal reaction steps within the purine alkaloid metabolic pathways have been largely elucidated, and the convergent evolution of purine alkaloids has been substantiated through bioinformatic, biochemical and other research perspectives within S-adenosyl-ʟ-methionine-dependent N-methyltransferases. Currently, the biological and ecological roles of purine alkaloids, further refinement of the purine alkaloid metabolic pathways and the investigation of purine alkaloid adaptive evolutionary mechanisms continue to attract widespread research interest. The exploration of the purine alkaloid metabolic pathways also enhances our comprehension of the biochemical mechanism, providing insights into inter-species interactions and adaptive evolution and offering potential value in drug development and agricultural applications. Here, we review the progress of research in the distribution, metabolic pathway elucidation and regulation, evolutionary mechanism and ecological roles of purine alkaloids in plants. The opportunities and challenges involved in elucidating the biochemical basis and evolutionary mechanisms of the purine alkaloid metabolic pathways, as well as other research aspects, are also discussed. This article is part of the theme issue 'The evolution of plant meta-bolism'. [ABSTRACT FROM AUTHOR]

Plant glutathione transferases (GSTs) constitute a large and diverse family of enzymes that are involved in plant stress response, metabolism and defence, yet their physiological functions remain largely elusive. Consistent with the traditional view on GSTs across organisms as detoxification enzymes, in vitro most plant GSTs catalyse glutathionylation, conjugation of the tripeptide glutathione (GSH; γ-Glu-Cys-Gly) onto reactive molecules. However, when it comes to elucidating GST functions, it remains a key challenge that the endogenous plant glutathione conjugates (GS-conjugates) that would result from such glutathionylation reactions are rarely reported. Furthermore, GSTs often display high substrate promiscuity, and their proposed substrates are prone to spontaneous chemical reactions with GSH; hence, single-gene knockouts rarely provide clear chemotypes or phenotypes. In a few cases, GS-conjugates are demonstrated to be biosynthetic intermediates that are rapidly further metabolized towards a pathway end product, explaining their low abundance and rare detection. In this review, we summarize the current knowledge of plant GST functions and how and possibly why evolution has resulted in a broad and extensive expansion of the plant GST family. Finally, we demonstrate that endogenous GS-conjugates are more prevalent in plants than assumed and suggest they are overlooked as clues towards the identification of plant GST functions. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Plants started to colonize land around 500 million years ago. It meant dealing with new challenges like absence of buoyancy, water and nutrients shortage, increased light radiation, reproduction on land, and interaction with new microorganisms. This obviously required the acquisition of novel functions and metabolic capacities. Cytochrome P450 (CYP) monooxygenases form the largest superfamily of enzymes and are present to catalyse critical and rate-limiting steps in most plant-specific pathways. The different families of CYP enzymes are typically associated with specific functions. CYP family emergence and evolution in the green lineage thus offer the opportunity to obtain a glimpse into the timing of the evolution of the critical functions that were required (or became dispensable) for the plant transition to land. Based on the analysis of currently available genomic data, this review provides an evolutionary history of plant CYPs in the context of plant terrestrialization and describes the associated functions in the different lineages. Without surprise it highlights the relevance of the biosynthesis of antioxidants and UV screens, biopolymers, and critical signalling pathways. It also points to important unsolved questions that would deserve to be answered to improve our understanding of plant adaptation to challenging environments and the management of agricultural traits. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Plant specialized metabolism has a complex evolutionary history. Some aspects are conserved across the green lineage, but many metabolites are unique to certain lineages. The network of specialized metabolism continuously diversified, simplified or reshaped during the evolution of streptophytes. Many routes of pan-plant specialized metabolism are involved in plant defence. Biotic interactions are recalled as major drivers of lineage-specific metabolomic diversification. However, the consequences of this diversity of specialized metabolism in the context of plant terrestrialization and land plant diversification into the major lineages of bryophytes, lycophytes, ferns, gymnosperms and angiosperms remain only little explored. Overall, this hampers conclusions on the evolutionary scenarios that shaped specialized metabolism. Recent efforts have brought forth new streptophyte model systems, an increase in genetically accessible species from distinct major plant lineages, and new functional data from a diversity of land plants on specialized metabolic pathways. In this review, we will integrate the recent data on the evolution of the plant immune system with the molecular data of specialized metabolism and its recognition. Based on this we will provide a contextual framework of the pan-plant specialized metabolism, the evolutionary aspects that shape it and the impact on adaptation to the terrestrial environment. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Plants are chemical engineers par excellence. Collectively they make a vast array of structurally diverse specialized metabolites. The raw materials for building new pathways (genes encoding biosynthetic enzymes) are commonly recruited directly or indirectly from primary metabolism. Little is known about how new metabolic pathways and networks evolve in plants, or what key nodes contribute to branches that lead to the biosynthesis of diverse chemicals. Here we review the molecular mechanisms underlying the generation of biosynthetic branchpoints. We also consider examples in which new metabolites are formed through the joining of precursor molecules arising from different biosynthetic routes, a scenario that greatly increases both the diversity and complexity of specialized metabolism. Given the emerging importance of metabolic gene clustering in helping to identify new enzymes and pathways, we further cover the significance of biosynthetic gene clusters in relation to metabolic networks and dedicated biosynthetic pathways. In conclusion, an improved understanding of the branchpoints between metabolic pathways will be key in order to be able to predict and illustrate the complex structure of metabolic networks and to better understand the plasticity of plant metabolism. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Phenolic compounds of land plants are varied: they are chemodiverse, are sourced from different biosynthetic routes and fulfil a broad spectrum of functions that range from signalling phytohormones, to protective shields against stressors, to structural compounds. Their action defines the biology of land plants as we know it. Often, their roles are tied to environmental responses that, however, impacted already the algal progenitors of land plants, streptophyte algae. Indeed, many streptophyte algae successfully dwell in terrestrial habitats and have homologues for enzymatic routes for the production of important phenolic compounds, such as the phenylpropanoid pathway. Here, we synthesize what is known about the production of specialized phenolic compounds across hundreds of millions of years of streptophyte evolution. We propose an evolutionary scenario in which selective pressures borne out of environmental cues shaped the chemodiversity of phenolics in streptophytes. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Recent research on a special type of sexual reproduction and zygospore formation in Zygnematophyceae, the sister group of land plants, is summarized. Within this group, gamete fusion occurs by conjugation. Zygospore development in Mougeotia, Spirogyra and Zygnema is highlighted, which has recently been studied using Raman spectroscopy, allowing chemical imaging and detection of changes in starch and lipid accumulation. Three-dimensional reconstructions after serial block-face scanning electron microscopy (SBF-SEM) or focused ion beam SEM (FIB-SEM) made it possible to visualize and quantify cell wall and organelle changes during zygospore development. The zygospore walls undergo strong modifications starting from uniform thin cell walls to a multilayered structure. The mature cell wall is composed of a cellulosic endospore and exospore and a central mesospore built up by aromatic compounds. In Spirogyra, the exospore and endospore consist of thick layers of helicoidally arranged cellulose fibrils, which are otherwise only known from stone cells of land plants. While starch is degraded during maturation, providing building blocks for cell wall formation, lipid droplets accumulate and fill large parts of the ripe zygospores, similar to spores and seeds of land plants. Overall, data show similarities between streptophyte algae and embryophytes, suggesting that the genetic toolkit for many land plant traits already existed in their shared algal ancestor. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Vitamin B12, also known as cobalamin, is an essential organic cofactor for methionine synthase (METH), and is only synthesized by a subset of bacteria. Plants and fungi have an alternative methionine synthase (METE) that does not need B12 and are typically considered not to utilize it. Some algae facultatively utilize B12 because they encode both METE and METH, while other algae are dependent on B12 as they encode METH only. We performed phylogenomic analyses of METE, METH and 11 further proteins involved in B12 metabolism across more than 1600 plant and algal genomes and transcriptomes (e.g. from OneKp), demonstrating the presence of B12-associated metabolism deep into the streptophytes. METH and five further accessory proteins (MTRR, CblB, CblC, CblD and CblJ) were detected in the hornworts (Anthocerotophyta), and two (CblB and CblJ) were identified in liverworts (Marchantiophyta) in the bryophytes, suggesting a retention of B12-metabolism in the last common land plant ancestor. Our data further show more limited distributions for other B12-related proteins (MCM and RNR-II) and B12 dependency in several algal orders. Finally, considering the collection sites of algae that have lost B12 metabolism, we propose freshwater-to-land transitions and symbiotic associations to have been constraining factors for B12 availability in early plant evolution. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Sesquiterpene lactones (STLs) are a prominent group of plant secondary metabolites predominantly found in the Asteraceae family and have multiple ecological roles and medicinal applications. This review describes the evolutionary and ecological significance of STLs, highlighting their roles in plant defence mechanisms against herbivory and as phytotoxins, alongside their function as environmental signalling molecules. We also cover the substantial role of STLs in medicine and their mode of action in health and disease. We discuss the biosynthetic pathways and the various modifications that make STLs one of the most diverse groups of metabolites. Finally, we discuss methods for identifying and predicting STL biosynthesis pathways. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

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'. [ABSTRACT FROM AUTHOR]

Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'. [ABSTRACT FROM AUTHOR]

Palynotaxonomy is crucial for understanding plant evolution, biodiversity, and ecological history by systematically classifying and identifying species based on pollen morphology. In addition, a regional pollen flora is crucial for precise pollen identification in various applied fields of palynology, including melissopalynology, aeropalynology, forensic palynology, paleopalynology, and copropalynology. In this communication, we explore the pollen morphology of 28 species of Asteraceae, employing both light (LM) and scanning electron microscopy (SEM). The results revealed that the grains were monad, isopolar, radially symmetric, tricolporate, and exhibited oblate-spheroidal to prolate-spheroidal shapes. The infratectum was found to be columellate, caveate, or noncaveate. The supratectum exhibited echinate or microechinate characteristics, with the exine surface showing perforate, microreticulate, or perforate regulate features. Among some species, a lophate pattern was observed, revealing two distinct variations: one characterized by a '15 lacunae type,' while the other exhibited a '21 lacunae type'. Some unusual variations were observed in the aperture character among certain species, like the occurrence of tricolpate grains and pollen dimorphism due to variation in aperture number. Light microscopic examination was preliminary for resolving columellar structure but it clearly showed a double level of columella in some species. A cluster analysis, incorporating qualitative and quantitative features of pollen grains and an artificial pollen key have been set forth to distinguish studied species, supplemented by LM and SEM micrographs. The current findings have enriched the existing pollen database of Asteraceae and could play an important role not only in palynotaxonomy but also in allied fields. [ABSTRACT FROM AUTHOR]

Summary: Local adaptation to contrasting environmental conditions along environmental gradients is a widespread phenomenon in plant populations, yet we lack a mechanistic understanding of how individual agents of selection contribute to this evolutionary process.Here, we developed a novel evolutionary functional–structural plant (E‐FSP) model that recreates local adaptation of virtual plants along an environmental gradient. First, we validate the model by testing if it can reproduce two elevational ecotypes of Dianthus carthusianorum occurring in the Swiss Alps. Second, we use the E‐FSP model to disentangle the relative contribution of abiotic (temperature) and biotic (competition and pollination) selection pressures to elevational adaptation in D. carthusianorum.Our results suggest that elevational adaptation in D. carthusianorum is predominantly driven by the abiotic environment. The model reproduced the qualitative differences between the elevational ecotypes in two phenological (germination and flowering time) and one morphological trait (stalk height), as well as qualitative differences in four performance variables that emerge from G × E interactions (flowering time, number of stalks, rosette area and seed production).Our approach shows how E‐FSP models incorporating physiological, ecological and evolutionary mechanisms can be used in combination with experiments to examine hypotheses about patterns of adaptation observed in the field. [ABSTRACT FROM AUTHOR]

Summary: Accurate divergence times are essential for interpreting and understanding the context in which lineages have evolved. Over the past several decades, debates have surrounded the discrepancies between the inferred molecular ages of crown angiosperms, often estimated from the Late Jurassic into the Permian, and the fossil record, placing angiosperms in the Early Cretaceous. That crown angiosperms could have emerged as early as the Permian or even the Triassic would have major implications for the paleoecological context of the origin of one of the most consequential clades in the tree of life. Here, we argue, and demonstrate through simulations, that the older ages inferred from molecular data and relaxed‐clock models are misled by lineage‐specific rate heterogeneity resulting from life history changes that occurred several times throughout the evolution of vascular plants. To overcome persistent discrepancies in age estimates, more biologically informed and realistic models should be developed, and our results should be considered in the context of their biological implications before we accept inferences that are a major departure from our strongest evidence. [ABSTRACT FROM AUTHOR]

Summary: Hosts and pathogens typically engage in a coevolutionary arms race. This also applies to phytopathogenic powdery mildew fungi, which can rapidly overcome plant resistance and perform host jumps.Using experimental evolution, we show that the powdery mildew pathogen Blumeria hordei is capable of breaking the agriculturally important broad‐spectrum resistance conditioned by barley loss‐of‐function mlo mutants.Partial mlo virulence of evolved B. hordei isolates is correlated with a distinctive pattern of adaptive mutations, including small‐sized (c. 8–40 kb) deletions, of which one is linked to the de novo insertion of a transposable element. Occurrence of the mutations is associated with a transcriptional induction of effector protein‐encoding genes that is absent in mlo‐avirulent isolates on mlo mutant plants. The detected mutational spectrum comprises the same loci in at least two independently isolated mlo‐virulent isolates, indicating convergent multigenic evolution. The mutational events emerged in part early (within the first five asexual generations) during experimental evolution, likely generating a founder population in which incipient mlo virulence was later stabilized by additional events.This work highlights the rapid dynamic genome evolution of an obligate biotrophic plant pathogen with a transposon‐enriched genome. [ABSTRACT FROM AUTHOR]

Summary The ability to accumulate nutrients is a hallmark for living creatures and plants evolved highly effective nutrient transport systems, especially for the uptake of potassium (K+). However, plants also developed mechanisms that enable the rapid extrusion of K+ in combination with anions. The combined release of K+ and anions is probably an ancient extrusion system, as it is found in the Characeae that are closely related to land plants. We postulate that the ion extrusion mechanisms have developed as an emergency valve, which enabled plant cells to rapidly reduce their turgor, and prevent them from bursting. Later in evolution, seed plants adapted this system for various responses, such as the closure of stomata, long‐distance stress waves, dropping of leaves by pulvini, and loading of xylem vessels. We discuss the molecular nature of the transport proteins that are involved in ion extrusion‐based functions of plants and describe the functions that they obtained during evolution. [ABSTRACT FROM AUTHOR]

Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens' genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage an innovative, multi-genome method to construct and annotate the first pangenome graph of an oomycete plant pathogen. We expand on this approach by analysing the graph and creating synteny based single-copy orthogroups for all genes. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, virulence related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens. Author summary: Plant pathogens are known to evolve rapidly and overcome disease resistance of newly introduced crop varieties. This swift adaptation is visible in the genomes of these pathogens, which can be highly variable. Such genomic variation cannot be captured with contemporary comparative genomic methods that rely on a single reference genome or focus solely on protein coding genes. To overcome these limitations and compare multiple genomes in a robust and scalable method, we constructed the first pangenome graph for an oomycete filamentous plant pathogen with six telomere-to-telomere genome assemblies of Peronospora effusa. This high-resolution pangenomic framework enabled detailed comparisons of the genomes at any level, from the nucleotide to the chromosome, and for any subset of protein-coding genes or transposable elements, to discover novel biology and potential mechanisms for the rapid evolution of this devastating pathogen. [ABSTRACT FROM AUTHOR]

Gene duplications have contributed to the innovation of morphological traits during plant evolution. An outstanding example is the role of CYCLOIDEA2 (CYC2) gene duplications in the formation of the complex structure of Asteraceae capitula. Previous studies have shown that Chrysanthemum lavandulifolium (Fischer ex Trautv.) Makino and a few other species of the Asteraceae harbor two copies of CYC2e. Here, we identified a lineage‐specific CYC2e duplication event at the root of the phylogeny of the tribe Anthemideae by analyzing the evolutionary history of CYC2 genes across the Asteraceae. Although the gene expression patterns of CYC2e1 and CYC2e2 were similar in most of floral organs, CYC2e1 promoted ligule elongation by promoting cell expansion, whereas CYC2e2 showed a weak inhibiting effect on the ray‐floret development, and overexpression of CYC2e2 resulted in the maldevelopment of stamens in disc florets. These results indicated differentiated functions of CYC2e1 and CYC2e2 in the capitulum development of the Anthemideae. Given the previous data that identified CYC2g and CYC2d as main regulators in ligule morphogenesis, we comparatively analyzed 10 Asteraceae genomic data, and identified tandem arrays of CYC2g, CYC2d, and CYC2e. We further investigated the regulatory relationships between CYC2g/CYC2d and CYC2e genes, and found that CYC2g can activate the expression of CYC2e1. The findings of this study elucidate the synergistic roles of CYC2 genes in regulating the formation of the Asteraceae capitula and enhance understanding of the mechanism of duplicated gene retention during plant evolution. [ABSTRACT FROM AUTHOR]

Symbiotic associations play a role in plant ecology and evolution, but the outcome of the interaction depends on the life‐history traits of the partners and the environmental context. Although symbiosis with vertically transmitted microorganisms should result in mutualism, it is not clear how the transmission process aligns with the outcome of the context‐dependent symbiosis. For 3 years, we sampled individuals of an annual plant species that forms symbiosis with a vertically transmitted fungal endophyte, in paired stands of two contrasting vegetation communities (humid mesophytic meadows [HMM]: productive/low stress, and humid prairies [HP]: less productive/high stress). We estimated the prevalence of symbiosis at the population level, and the fitness of the plant, the symbiotic status and vertical transmission efficiency at the individual level. Over 3 years, the prevalence of symbiosis was ≈100% in HMM and ≈75% in HP. Plant fitness was very low and high in years with precipitation below and above the yearly mean, respectively. The higher fitness of endophyte‐symbiotic plants was evident in the HMM and high precipitation years. Vertical transmission of endophytes was higher in HMM (≈96%) compared to HP (≈93%) and was not related to plant fitness. Despite transmission inefficiencies in HP, changes in prevalence within the growing season (from seeds to the final plant stand) suggest a fitness advantage for symbiotic plants. Vertical transmission is expected to promote mutualism as it aligns partners' fitness. Although symbiotic plants showed higher fitness and the probability of transmission failures was higher among low‐fitness plants, the variation in transmission efficiency between plants and vegetation communities was not related to the fitness of the individual host. Our study provides evidence that context‐dependent vertical transmission efficiency and endophyte‐mediated fitness advantages interact complexly to determine the prevalence of symbiosis in populations that occur in contrasting vegetation communities. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Introduction: Zicaitai (Brassica rapa var. purpuraria) is a Brassica variety renowned for its distinctive taste and rich nutritional profile. In recent years, the mitochondrial genomes of several Brassica species have been documented, but the mitogenome of Zicaitai remains unreported. Methods: In this study, we characterized the Zicaitai mitogenome achieved through the assembly of sequencing reads derived from both the Oxford Nanopore and Illumina platforms. A detailed comparative analysis was carried out with other Brassica species to draw comparisons and contrasts. In-depth analyses of codon usage patterns, instances of RNA editing, and the prevalence of sequence repeats within the mitogenome were also conducted to gain a more nuanced understanding of its genetic architecture. A phylogenetic analysis was performed, utilizing the coding sequences (CDS) from the mitochondrial genome of Zicaitai and that of 20 closely related species/varieties to trace evolutionary connections. Results: The Zicaitai mitogenome is characterized by a circular structure spanning 219,779 base pairs, and it encompasses a total of 59 genes. This gene set includes 33 protein-coding genes, 23 tRNA genes, and 3 rRNA genes, providing a rich foundation for further genomic study. An analysis of the Ka/Ks ratios for 30 protein-coding genes shared by the mitogenomes of Zicaitai and seven other Brassica species revealed that most of these genes had undergone purifying selection. Additionally, the study explored the migration of genes between the chloroplast and nuclear genomes and the mitogenome, offering insights into the dynamics of genetic exchange within the Brassica genus. Discussion: The collective results in this study will serve as a foundational resource, aiding future evolutionary studies focused on B. rapa, and contributing to a broader understanding of the complexities of plant evolution. [ABSTRACT FROM AUTHOR]

Summary The evolution of adjustable stomatal pores, enabling CO2 acquisition, was one of the most significant events in the development of life on land. Here, we investigate how the guard cell signalling pathways that regulate stomatal movements evolved. We compare fern and angiosperm guard cell transcriptomes and physiological responses, and examine the functionality of ion channels from diverse plant species. We find that, despite conserved expression in guard cells, fern anion channels from the SLAC/SLAH family are not activated by the same abscisic acid (ABA) pathways that provoke stomatal closure in angiosperms. Accordingly, we find an insensitivity of fern stomata to ABA. Moreover, our analysis points to a complex evolutionary history, featuring multiple gains and/or losses of SLAC activation mechanisms, as these channels were recruited to a role in stomatal closure. Our results show that the guard cells of flowering and nonflowering plants share similar core features, with lineage‐specific and ecological niche‐related adaptations, likely underlying differences in behaviour. [ABSTRACT FROM AUTHOR]

The conserved microRNA (miRNA) miR408 enhances photosynthesis and compromises stress tolerance in multiple plants, but the cellular mechanism underlying its function remains largely unclear. Here, we show that in Arabidopsis (Arabidopsis thaliana), the transcript encoding the blue copper protein PLANTACYANIN (PCY) is the primary target for miR408 in vegetative tissues. PCY is preferentially expressed in the guard cells, and PCY is associated with the endomembrane surrounding individual chloroplasts. We found that the MIR408 promoter is suppressed by multiple abscisic acid (ABA)-responsive transcription factors, thus allowing PCY to accumulate under stress conditions. Genetic analysis revealed that PCY elevates reactive oxygen species (ROS) levels in the guard cells, promotes stomatal closure, reduces photosynthetic gas exchange, and enhances drought resistance. Moreover, the miR408–PCY module is sufficient to rescue the growth and drought tolerance phenotypes caused by gain- and loss-of-function of MYB44, an established positive regulator of ABA responses, indicating that the miR408–PCY module relays ABA signaling for regulating ROS homeostasis and drought resistance. These results demonstrate that miR408 regulates stomatal movement to balance growth and drought resistance, providing a mechanistic understanding of why miR408 is selected during land plant evolution and insights into the long-pursued quest of breeding drought-tolerant and high-yielding crops. The microRNA miR408 is repressed by ABA signaling and regulates PCY abundance in the guard cells thus modulating ROS homeostasis and stomatal movement. MicroRNA408 regulates PCY abundance in guard cells to modulate ROS homeostasis and stomatal movement, thereby balancing growth and drought resistance in Arabidopsis. [ABSTRACT FROM AUTHOR]

Abiotic and biotic stress factors seriously affect plant growth and development. The process of plant response to abiotic stress involves the synergistic action of multiple resistance genes. The ASR (Abscisic acid stress-ripening) gene is a plant-specific transcription factor that plays a central role in regulating plant senescence, fruit ripening, and response to abiotic stress. ASR family members are highly conserved in plant evolution and contain ABA/WBS domains. ASR was first identified and characterized in tomatoes (Solanum lycopersicum L.). Subsequently, the ASR gene has been reported in many plant species, extending from gymnosperms to monocots and dicots, but lacks orthologues in Arabidopsis (Arabidopsis thaliana). The promoter regions of ASR genes in most species contain light-responsive elements, phytohormone-responsive elements, and abiotic stress-responsive elements. In addition, ASR genes can respond to biotic stresses via regulating the expression of defense genes in various plants. This review comprehensively summarizes the evolutionary history, gene and protein structures, and functions of the ASR gene family members in plant responses to salt stress, low temperature stress, pathogen stress, drought stress, and metal ions, which will provide valuable references for breeding high-yielding and stress-resistant plant varieties. [ABSTRACT FROM AUTHOR]

In this article, we propose a data‐driven networked control architecture for unknown and constrained cyber‐physical systems capable of detecting networked false‐data‐injection attacks and ensuring plant's safety. In particular, on the controller's side, we design a novel robust anomaly detector that can discover the presence of network attacks using a data‐driven outer approximation of the expected robust one‐step reachable set. On the other hand, on the plant's side, we design a data‐driven safety verification module, which resorts to worst‐case arguments to determine if the received control input is safe for the plant's evolution. Whenever necessary, the same module is in charge of replacing the networked controller with a local data‐driven set‐theoretic model predictive controller, whose objective is to keep the plant's trajectory in a pre‐established safe configuration until an attack‐free condition is recovered. Numerical simulations involving a two‐tank water system illustrate the features and capabilities of the proposed control architecture. [ABSTRACT FROM AUTHOR]

In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is expected. However, no study has explored these long‐term dimensions of plant–pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population genetic and epigenetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, given the higher sensitivity of small, isolated population to gene flow, we expect a stronger association of pollinators with population genetic and epigenetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). We characterized the pollinators in up to three populations per species to estimate their diversity and visitation rates. Additionally, we calculated the genetic and epigenetic diversity and distinctiveness of each population using AFLP markers and methylation‐sensitive AFLP markers (MSAP), respectively. We assessed the relationship between pollinator diversity and visitation rates. The diversity of pollinators did not vary according to the plant´s distribution range, but visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the importance of investigating the relationship between pollinator diversity and population genetics and epigenetics to better understand the evolution of plant rarity. [ABSTRACT FROM AUTHOR]

SUMMARY: Plants synthesize natural products via lineage‐specific offshoots of their core metabolic pathways, including fatty acid synthesis. Recent studies have shed light on new fatty acid‐derived natural products and their biosynthetic pathways in disparate plant species. Inspired by this progress, we set out to develop tools for exploring the evolution of fatty‐acid derived products. We sampled multiple species from all major clades of euphyllophytes, including ferns, gymnosperms, and angiosperms (monocots and eudicots), and we show that the compositional profiles (though not necessarily the total amounts) of fatty‐acid derived surface waxes from preserved plant specimens are consistent with those obtained from freshly collected tissue in a semi‐quantitative and sometimes quantitative manner. We then sampled herbarium specimens representing 57 monocot species to assess the phylogenetic distribution and evolution, of two fatty acid‐derived natural products found in that clade: beta‐diketones and alkylresorcinols. These chemical data, combined with analyses of 26 monocot genomes, revealed a co‐occurrence (though not necessarily a causal relationship) between whole genome duplication and the evolution of diketone synthases from an ancestral alkylresorcinol synthase‐like polyketide synthase. Limitations of using herbarium specimen wax profiles as proxies for those of fresh tissue seem likely to include effects from loss of epicuticular wax crystals, effects from preservation techniques, and variation in wax chemical profiles due to genotype or environment. Nevertheless, this work reinforces the widespread utility of herbarium specimens for studying leaf surface waxes (and possibly other chemical classes) and reveals some of the evolutionary history of fatty acid‐derived natural products within monocots. Significance Statement: Plant chemicals are key components in our food and medicine, and advances in genomic technologies are accelerating plant chemical research. However, access to tissue from specific plant species can still be rate limiting, especially for species that are difficult to cultivate, endangered, or inaccessible. Here, we demonstrate that herbarium specimens provide a semiquantitative proxy for the cuticular wax composition of their fresh counterparts, thus reducing the need to collect fresh tissue for studies of wax chemicals and suggesting the same may also be true of other plant chemical classes. We also demonstrate the utility of combining herbarium‐based plant chemical profiling with genomic analyses to understand the evolution of plant natural products. [ABSTRACT FROM AUTHOR]

Plant–hummingbird interactions are considered a classic example of coevolution, a process in which mutually dependent species influence each other's evolution. Plants depend on hummingbirds for pollination, whereas hummingbirds rely on nectar for food. As a step towards understanding coevolution, this review focuses on the macroevolutionary consequences of plant–hummingbird interactions, a relatively underexplored area in the current literature. We synthesize prior studies, illustrating the origins and dynamics of hummingbird pollination across different angiosperm clades previously pollinated by insects (mostly bees), bats, and passerine birds. In some cases, the crown age of hummingbirds pre‐dates the plants they pollinate. In other cases, plant groups transitioned to hummingbird pollination early in the establishment of this bird group in the Americas, with the build‐up of both diversities coinciding temporally, and hence suggesting co‐diversification. Determining what triggers shifts to and away from hummingbird pollination remains a major open challenge. The impact of hummingbirds on plant diversification is complex, with many tropical plant lineages experiencing increased diversification after acquiring flowers that attract hummingbirds, and others experiencing no change or even a decrease in diversification rates. This mixed evidence suggests that other extrinsic or intrinsic factors, such as local climate and isolation, are important covariables driving the diversification of plants adapted to hummingbird pollination. To guide future studies, we discuss the mechanisms and contexts under which hummingbirds, as a clade and as individual species (e.g. traits, foraging behaviour, degree of specialization), could influence plant evolution. We conclude by commenting on how macroevolutionary signals of the mutualism could relate to coevolution, highlighting the unbalanced focus on the plant side of the interaction, and advocating for the use of species‐level interaction data in macroevolutionary studies. [ABSTRACT FROM AUTHOR]

Understanding the evolution and the effect of plasticity in plant responses to environmental changes is crucial to combat global climate change. It is particularly interesting in species that survive in distinct environments, such as Eugenia uniflora, which thrives in contrasting ecosystems within the Atlantic Forest (AF). In this study, we combined transcriptome analyses of plants growing in nature (Restinga and Riparian Forest) with greenhouse experiments to unveil the DEGs within and among adaptively divergent populations of E. uniflora. We compared global gene expression among plants from two distinct ecological niches. We found many differentially expressed genes between the two populations in natural and greenhouse-cultivated environments. The changes in how genes are expressed may be related to the species' ability to adapt to specific environmental conditions. The main difference in gene expression was observed when plants from Restinga were compared with their offspring cultivated in greenhouses, suggesting that there are distinct selection pressures underlying the local environmental and ecological factors of each Restinga and Riparian Forest ecosystem. Many of these genes engage in the stress response, such as water and nutrient transport, temperature, light intensity, and gene regulation. The stress-responsive genes we found are potential genes for selection in these populations. These findings revealed the adaptive potential of E. uniflora and contributed to our understanding of the role of gene expression reprogramming in plant evolution and niche adaptation. [ABSTRACT FROM AUTHOR]

Inbreeding depression is a key factor regulating the evolution of self-fertilization in plants. Despite predictions that inbreeding depression should evolve with selfing rates as deleterious alleles are increasingly exposed and removed by selection, evidence of purging the genetic load in wild populations is equivocal at best. This discordance could be explained, in part, if the load underlying inbreeding depression is subject to soft selection, i.e., the fitness of selfed individuals depends on the frequency and density of selfed vs. outcrossed individuals in the population. Somewhat counterintuitively, this means that populations with contrasting mutation load can have similar fitness. Soft selection against selfed individuals may be expected when there is inbreeding depression for competitive ability in density-regulated populations. We tested population-level predictions of inbreeding depression in competitive ability by creating a density series of potted plants consisting of either purely outcrossed, purely selfed, or mixed (50% outcrossed, 50% selfed) seed of the mixed-mating biennial Sabatia angularis (Gentianaceae) representing ecological neighborhoods. Focusing on the growth and survival of juveniles, we show that mean plant size is independent of neighborhood composition when resources are limiting, but greatest in outcrossed neighborhoods at low densities. Across a range of densities, this manifests as stronger densitydependence in outcrossed populations compared to selfed or mixed ones. We also found significantly greater size inequalities among individuals in mixed neighborhoods, even at high densities where mean juvenile size converged, a key signature of asymmetric competition between outcrossed and selfed individuals. Our work illustrates how soft selection could shelter the genetic load underlying inbreeding depression and its demographic consequences. [ABSTRACT FROM AUTHOR]

Rapeseed (Brassica napus) is an important oilseed crop worldwide. Plant vascular tissues are responsible for long-distance transport of water and nutrients and for providing mechanical support. The lateral roots absorb water and nutrients. The genetic basis of vascular tissue and lateral root development in rapeseed remains unknown. This study characterized an ethyl methanesulfonate-mutagenized rapeseed mutant, T16 , which showed dwarf stature, reduced lateral roots, and leaf wilting. SEM observations showed that the internode cells were shortened. Observations of tissue sections revealed defects in vascular bundle development in the stems and petioles. Genetic analysis revealed that the phenotypes of T16 were controlled by a single semi-dominant nuclear gene. Map-based cloning and genetic complementarity identified BnaA03.IAA13 as the functional gene; a G-to-A mutation in the second exon changed glycine at position 79 to glutamic acid, disrupting the conserved degron motif VGWPP. Transcriptome analysis in roots and stems showed that auxin and cytokinin signaling pathways were disordered in T16. Evolutionary analysis showed that AUXIN/INDOLE-3-ACETIC ACID is conserved during plant evolution. The heterozygote of T16 showed significantly reduced plant height while maintaining other agronomic traits. Our findings provide novel insights into the regulatory mechanisms of vascular tissue and lateral root development, and offer a new germplasm resource for rapeseed breeding. [ABSTRACT FROM AUTHOR]

This study investigates the relationship between seed morphological traits and dimensions to adapt to arid environments, focusing on microlevel seed structures. Utilizing advanced imaging techniques, we visualized complex seed features and explored their role in enhancing plant adaptability to dry climates, shedding light on crucial mechanisms underlying seed germination and survival strategies in water‐limited ecosystems. Seed morphotypes refer to the physical attributes of seeds, such as size, shape, color, texture, and structure. Fifteen species belonging to ten plant families were examined to investigate seed micromorphological features. Each species exhibits unique seed traits adapted for survival in harsh conditions. Features such as seed size, shape, texture, and surface ornamentation varied significantly among species, reflecting adaptations to optimize seed dispersal, germination, and resilience to arid climates. Seed shape, color, and texture were observed under scanning electron and stereomicroscopes. Micromorphological ultrastructural information has proven useful in determining plant evolution, classification, and ecology. Seed shape varied from elliptic, oblong, ovate, pyramidal to spherical. Surface stratification varied from rugulate, striate reticulate, foveolate, granular to rugose. The seed size varied among species, from very small in Cleome arabica (L = 1.4 mm and W = 0.7 mm) to very large in Aerva (L = 5.1 mm and W = 2.6 mm). Seed color varied from brown, dark brown to black. The microstructural seed traits in arid environments provide valuable insights into plant adaptations to dry climates and have significant implications for crop breeding programs and ecological restoration efforts. [ABSTRACT FROM AUTHOR]

The interest in and significance of herbarium collections for the study of plant biodiversity and evolution has significantly expanded in recent decades due to the introduction of new technologies for large‐scale, automated digitization and the availability of new techniques for DNA sequencing. These innovative methods gave rise to new initiatives with the goal of compiling a sizable molecular and phenological data set. In light of the various national projects that are currently underway and driving the study of herbarium specimens for the purpose of understanding biodiversity loss and habitat shifts as a result of climate change and habitat destruction due to human activity. Here, we showcased a number of cutting‐edge research, mini‐reviews, and technical comments that demonstrate the ever‐growing range of applications for herbarium specimens. It examines the variety of applications for which herbarium specimens are employed, the primary users' profiles of herbarium collections, patterns and systematics of biodiversity, and the evolution of lineages and traits. [ABSTRACT FROM AUTHOR]

The phenylpropanoid pathway is one of the plant metabolic pathways most prominently linked to the transition to terrestrial life, but its evolution and early functions remain elusive. Here, we show that activity of the t -cinnamic acid 4-hydroxylase (C4H), the first plant-specific step in the pathway, emerged concomitantly with the CYP73 gene family in a common ancestor of embryophytes. Through structural studies, we identify conserved CYP73 residues, including a crucial arginine, that have supported C4H activity since the early stages of its evolution. We further demonstrate that impairing C4H function via CYP73 gene inactivation or inhibitor treatment in three bryophyte species—the moss Physcomitrium patens, the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis —consistently resulted in a shortage of phenylpropanoids and abnormal plant development. The latter could be rescued in the moss by exogenous supply of p -coumaric acid, the product of C4H. Our findings establish the emergence of the CYP73 gene family as a foundational event in the development of the plant phenylpropanoid pathway, and underscore the deep-rooted function of the C4H enzyme in embryophyte biology. Synopsis: The phenylpropanoid pathway is assumed to represent a key plant metabolic adaptation associated with terrestrial life, and processes about 30% of all photosynthetic carbon on Earth. This study highlights the importance of the evolutionary co-emergence of the CYP73 gene family, which encodes t -cinnamic acid 4-hydroxylase (C4H) enzymes, in establishing this pathway in a land plant's ancestor. The CYP73 gene family emerged in an ancestor of land plants and has subsequently been conserved. The CYP73 gene family encodes C4H, the first plant-specific enzyme in the phenylpropanoid pathway, from the earliest stages of its evolution. Alteration of C4H function via CYP73 gene inactivation or inhibitor treatment consistently disrupts phenylpropanoid synthesis and development in land plants. This paper shows that the t -cinnamic acid 4-hydroxylase activity emerged with the CYP73 gene family in a common ancestor of all land plants. [ABSTRACT FROM AUTHOR]

Germline fate determination is a critical event in sexual reproduction. Unlike animals, plants specify the germline by reprogramming somatic cells at the late stages of their development. However, the genetic basis of germline fate determination and how it evolved during the land plant evolution are still poorly understood. Here, we report that the plant homeodomain finger protein GERMLINE IDENTITY DETERMINANT (GLID) is a key regulator of the germline specification in liverwort, Marchantia polymorpha. Loss of the MpGLID function causes failure of germline initiation, leading to the absence of sperm and egg cells. Remarkably, the overexpression of MpGLID in M. polymorpha induces the ectopic formation of cells with male germline cell features exclusively in male thalli. We further show that MpBONOBO (BNB), with an evolutionarily conserved function, can induce the formation of male germ cell-like cells through the activation of MpGLID by directly binding to its promoter. The Arabidopsis (Arabidopsis thaliana) MpGLID ortholog, MALE STERILITY1 (AtMS1), fails to replace the germline specification function of MpGLID in M. polymorpha, demonstrating that a derived function of MpGLID orthologs has been restricted to tapetum development in flowering plants. Collectively, our findings suggest the presence of the BNB–GLID module in complex ancestral land plants that has been retained in bryophytes, but rewired in flowering plants for male germline fate determination. The genetic module underlying germline fate determination has been rewired during the land plant evolution. [ABSTRACT FROM AUTHOR]

SUMO modification is part of the spectrum of Ubiquitin-like (UBL) systems that give rise to proteoform complexity through post-translational modifications (PTMs). Proteoforms are essential modifiers of cell signaling for plant adaptation to changing environments. Exploration of the evolutionary emergence of Ubiquitin-like (UBL) systems unveils their origin from prokaryotes, where it is linked to the mechanisms that enable sulfur uptake into biomolecules. We explore the emergence of the SUMO machinery across the plant lineage from single-cell to land plants. We reveal the evolutionary point at which plants acquired the ability to form SUMO chains through the emergence of SUMO E4 ligases, hinting at its role in facilitating multicellularity. Additionally, we explore the possible mechanism for the neofunctionalization of SUMO proteases through the fusion of conserved catalytic domains with divergent sequences. We highlight the pivotal role of SUMO proteases in plant development and adaptation, offering new insights into target specificity mechanisms of SUMO modification during plant evolution. Correlating the emergence of adaptive traits in the plant lineage with established experimental evidence for SUMO in developmental processes, we propose that SUMO modification has evolved to link developmental processes to adaptive functions in land plants. The post-translational modification SUMO has evolved to link developmental processes to adaptive functions in land plants. [ABSTRACT FROM AUTHOR]

Polyploidy, a prevalent event in plant evolution, drives phenotypic diversification and speciation. While transcriptional changes and regulation in polyploids have been extensively studied, the translational level impact remains largely unexplored. To address this gap, we conducted a comparative transcriptomic and translatomic analysis of cotton leaves from allopolyploid species G. hirsutum (AD1) and G. barbadense (AD2) relative to their model A-genome and D-genome diploid progenitors. Our data revealed that while allopolyploidization significantly affects the transcriptional landscape, its impact on translation was relatively modest, evidenced by a narrower expression range and fewer expression changes in ribosome-protected fragments than in mRNA levels. Allopolyploid-specific changes commonly identified in both AD1 and AD2 were observed in 7393 genes at either transcriptional or translational levels. Interestingly, the majority of translational changes exhibited concordant down-regulation in both ribosome-protected fragments and mRNA, particularly associated with terpenoid synthesis and metabolism (352 genes). Regarding translational efficiency (TE), at least one-fifth of cotton genes exhibit translational level regulation, with a general trend of more down-regulation (13.9–15.1%) than up-regulation (7.3–11.2%) of TE. The magnitude of translational regulation was slightly reduced in allopolyploids compared with diploids, and allopolyploidy tends to have a more profound impact on genes and functional associations with ultra-low TE. Moreover, we demonstrated a reduced extent of homeolog expression biases during translation compared with transcription. Our study provides insights into the regulatory consequences of allopolyploidy post-transcription, contributing to a comprehensive understanding of regulatory mechanisms of duplicated gene expression evolution. [ABSTRACT FROM AUTHOR]

Cleomella serrulata is a native flowering plant found in North America. Even though this plant is of ecological and native medicinal importance, very little is known about the genomic makeup of Cleomella and the Cleomaceae family at large. Here, we report the complete chloroplast genome of Cleomella serrulata and provide an evolutionary comparison to other chloroplast genomes from Cleomaceae and closely related families. This study not only confirms the taxonomic placement of Cleomella as a distinct genus, but also provides phylogenetic insights that imply potential adaptive strategies and evolutionary mechanisms driving the genomic diversity of the Cleomella genus. Whole-genome-based and ANI comparisons indicate that the Cleomella species form a distinct clade that is about equidistant from the other Cleomaceae genera as it is from the genera from the nearby Capparaceae and Brassicaceae. This is the first complete chloroplast-based phylogenetic comparison of Cleomella species to other related genera and helps refine the complex taxonomic distinctions of Cleomaceae. [ABSTRACT FROM AUTHOR]

Land plants are astounding processors of information; due to their sessile nature, they adjust the molecular programs that define their development and physiology in accordance with the environment in which they dwell. Transduction of the external input to the respective internal programs hinges to a large degree on molecular signaling cascades, many of which have deep evolutionary origins in the ancestors of land plants and its closest relatives, streptophyte algae. In this Review, we discuss the evolutionary history of the defining factors of streptophyte signaling cascades, circuitries that not only operate in extant land plants and streptophyte algae, but that also likely operated in their extinct algal ancestors hundreds of millions of years ago. We hope this Review offers a starting point for future studies on the evolutionary mechanisms contributing to the current diversity and complexity of plant signaling pathways, with an emphasis on recognizing potential biases. [ABSTRACT FROM AUTHOR]

Aim: Reproductive systems strongly influence plants' evolution and adaption, and the biogeographic pattern of its variation has intrigued biologists and ecologists. Here, to test the impacts of paleoglaciation on plants' reproductive system variation, we compared the geographical pattern and environmental drivers in the proportions of different reproductive systems in Primula in regions affected and unaffected by paleoglaciation. Location: Global. Time Period: Since the Last Glacial Maximum (LGM). Major Taxa Studied: Primula. Methods: Using data on reproductive systems and distributions of 604 Primula taxa around the world and 221 along the elevational gradient of the Himalayas, we demonstrated the global pattern and the elevational pattern in the proportions of homostylous taxa. We employed general linear models to establish the relationship between the proportion of homostylous taxa and environmental variables and hierarchical partitioning to assess the relative contributions of these variables in both regions affected and unaffected by paleoglaciation, respectively. Results: We found a higher proportion of homostylous taxa in regions glaciated during the LGM than those unglaciated, with different latitudinal patterns and climate drivers. The proportion of homostylous taxa showed varying trends across different regions: increasing with latitude and temperature anomaly in glaciated regions while concentrating at lower latitudes with higher winter temperatures in unglaciated regions. Additionally, homostylous taxa were more prevalent at lower elevations in the Himalayas. Main Conclusions: Our study provides the first quantitative evidence for the hypothesis that selfers are more prevailing in regions affected by paleoglaciation facilitated by recolonization via comparing the geographic pattern and drivers in regions affected and unaffected by paleoglaciation. Our findings also reveal the concentrated distribution of homostylous taxa in Primula at low latitudes, which may be the result of population shrinkage caused by heat stress, facing a more severe survival crisis under the circumstances of global warming and increasing human activities. [ABSTRACT FROM AUTHOR]

Equisetaleans are a frequent floral element in the upper Palaeozoic of Gondwana and traditionally have been assigned to a few species of Phyllotheca based mainly on vegetative features. However, studies have suggested that the reproductive organs of Gondwanan equisetaleans may be more complex than previously thought, and new Gondwanan taxa have been reported during recent decades. The evolution of these plants is believed to have been driven by changes in their reproductive organs, including the emergence of simple sporangia or cruciate sporangiophores at the internodes as well as the development of strobilar structures. Here, we describe new records of Cruciatheca Cúneo et Escapa and Conustheca gen. nov. from Gzhelian-earliest Cisuralian deposits in the southeastern boundary of the Paganzo Basin, Argentina. The new species with whorls of strobilus-like structures provides further evidence of a diverse equisetalean flora across the southern continents. These records also suggest that the evolution of these equisetaleans was complex, with multiple lineages and distinct morphologies. [ABSTRACT FROM AUTHOR]

Global climate change is affecting plant photosynthesis and transpiration processes, as well as increasing weather extremes impacting socio‐political and environmental events and decisions for decades to come. One major research challenge in plant biology and ecology is the interaction of photosynthesis with the environment. Stomata control plant gas exchange and their evolution was a crucial innovation that facilitated the earliest land plants to colonize terrestrial environments. Stomata couple homoiohydry, together with cuticles, intercellular gas space, with the endohydric water‐conducting system, enabling plants to adapt and diversify across the planet. Plants control stomatal movement in response to environmental change through regulating guard cell turgor mediated by membrane transporters and signaling transduction. However, the origin, evolution, and active control of stomata remain controversial topics. We first review stomatal evolution and diversity, providing fossil and phylogenetic evidence of their origins. We summarize functional evolution of guard cell membrane transporters in the context of climate changes and environmental stresses. Our analyses show that the core signaling elements of stomatal movement are more ancient than stomata, while genes involved in stomatal development co‐evolved de novo with the earliest stomata. These results suggest that novel stomatal development‐specific genes were acquired during plant evolution, whereas genes regulating stomatal movement, especially cell signaling pathways, were inherited ancestrally and co‐opted by dynamic functional differentiation. These two processes reflect the different adaptation strategies during land plant evolution. Summary statement: We review stomatal diversity and functional evolution in the context of environmental stresses. Our analyses suggest that novel stomatal development‐specific genes were acquired during plant evolution, whereas genes regulating stomatal movement were co‐opted by dynamic functional differentiation. [ABSTRACT FROM AUTHOR]

Evolution is the integrative framework of the life sciences. Even though the topic is often not formally introduced before high school, young children already have various ideas about evolutionary principles (variation, inheritance, and selection) and their underlying key concepts (e.g., differential fitness, reproduction, and speciation). Describing and refining those ideas has increasingly received attention over the last two decades. However, we see two scopes of improvement in the field: (1) There is a need to examine children's ideas about evolutionary concepts holistically rather than focusing at specific aspects. (2) Although research has shown that older students have different ideas about animal and plant evolution, there is little data on children's ideas about plant evolution to compare with their ideas about animal evolution. All of this results in an incomplete record of children's pre‐existing ideas that would help to design assessments or interventions. Consequently, we developed a set of questions, about the evolutionary principles and interviewed 24 kindergarten children. Most children had basic ideas about individual variation in animals and plants but experienced a lack of knowledge about the origin of variation. Most children seemed to acknowledge plants as living beings and reasoned equally about animals and plants for most concepts. However, many children failed to reason about reproduction and inheritance in plants because they believed plants would not reproduce sexually. Confronted with a selection scenario, most children struggled applying concepts previously shown on an individual level to a population level. Considering our findings, we propose ideas about how to measure and foster children's pre‐existing ideas about evolution. [ABSTRACT FROM AUTHOR]

SUMMARY: Nucleotide‐binding leucine‐rich repeat (NLR) proteins are crucial intracellular immune receptors in plants, responsible for detecting invading pathogens and initiating defense responses. While previous studies on the evolution and function of NLR genes were mainly limited to land plants, the evolutionary trajectory and immune‐activating character of NLR genes in algae remain less explored. In this study, genome‐wide NLR gene analysis was conducted on 44 chlorophyte species across seven classes and seven charophyte species across five classes. A few but variable number of NLR genes, ranging from one to 20, were identified in five chlorophytes and three charophytes, whereas no NLR gene was identified from the remaining algal genomes. Compared with land plants, algal genomes possess fewer or usually no NLR genes, implying that the expansion of NLR genes in land plants can be attributed to their adaptation to the more complex terrestrial pathogen environments. Through phylogenetic analysis, domain composition analysis, and conserved motifs profiling of the NBS domain, we detected shared and lineage‐specific features between NLR genes in algae and land plants, supporting the common origin and continuous evolution of green plant NLR genes. Immune‐activation assays revealed that both TNL and RNL proteins from green algae can elicit hypersensitive responses in Nicotiana benthamiana, indicating the molecular basis for immune activation has emerged in the early evolutionary stage of different types of NLR proteins. In summary, the results from this study suggest that NLR proteins may have taken a role as intracellular immune receptors in the common ancestor of green plants. Significance Statement: By surveying 44 chlorophyte species across seven classes and seven charophyte species across five classes, this study reports a few but variable number of NLR genes in five chlorophytes and three charophytes. Immune‐activation assays reveal that NLR proteins from green algae can elicit immune response in Nicotiana benthamiana, indicating the molecular basis for immune activation of NLR proteins has emerged in the early evolutionary stage of green plants. [ABSTRACT FROM AUTHOR]

Abstract Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance, and stress tolerance. As the number of sequenced genomes grows and the accuracy and contiguity of genome assemblies improve, structural annotation of plant genomes continues to be a significant challenge due to their large size, polyploidy, and rich repeat content. In this paper, we present an overview of the current landscape in crop genomics research, highlighting the diversity of genomic characteristics across various crop species. We also assessed the accuracy of popular gene prediction tools in identifying genes within crop genomes and examined the factors that impact their performance. Our findings highlight the strengths and limitations of BRAKER2 and Helixer as leading structural genome annotation tools and underscore the impact of genome complexity, fragmentation, and repeat content on their performance. Furthermore, we evaluated the suitability of the predicted proteins as a reliable search space in proteomics studies using mass spectrometry data. Our results provide valuable insights for future efforts to refine and advance the field of structural genome annotation.