Introduction The Apocynaceae family is renowned for its exceptional diversity of monoterpenoid indole alkaloids (MIAs), a class of structurally complex and pharmaceutically significant natural products. Clinically important drugs, such as the anticancer drugs vinblastine and vincristine, exemplify the therapeutic value of MIAs (De Luca et al., 2012). These compounds are categorized based on their carbon

Biophysical CO2 concentrating mechanisms (CCMs) operating at the single-cell level have evolved independently in eukaryotic algae and a single land plant lineage, hornworts. An important component for an efficient eukaryotic CCM is a pyrenoid whose biology is well-characterized in the unicellular green alga, Chlamydomonas reinhardtii. By contrast, pyrenoids and CCM are little understood in hornworts

Introduction Maize (Zea mays L. subsp. mays) was domesticated from teosinte (Zea mays L. subsp. parviglumis Iltis & Doebley and Zea mays L. subsp. mexicana (Schrad.) Iltis) in central Mexico c. 9000 yr before present (yrBP) (Matsuoka et al., 2002; Yang et al., 2023). While the importance of roots for environmental adaptation is well established (Lynch et al., 2022; McLaughlin et al., 2024), their specific

Summary Plant host cell‐cycle hyperactivation is essential for nematode feeding site (NFS) ontogenesis, but the balanced mitotic and endoreplication cycles must occur for homeostasis. Alterations in core cell cycle gene expression are well known to disturb root‐knot and cyst‐NFS development. Herein, our investigation focused on the activity of E2FA and E2FB transcription factors in root‐knot nematode‐induced

Carnivorous plants, which capture animal prey to thrive in nutrient-poor environments, have independently originated 12 times in angiosperms (Fleischmann et al., 2018; Lin et al., 2021). These plants have evolved various types of traps, with sticky traps being the most common strategy (Freund et al., 2022). The sticky trap has independently evolved in at least six lineages, including the Caryophyllales

Summary Foraging in soil nutrient‐rich patches is a key nutrient acquisition strategy for plants. However, how arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) trees integrate root and mycorrhizal fungal responses in exploring different nutrient patches is poorly understood, especially in generally phosphorus‐limited subtropical forests. We established five nutrient patch treatments (control; nitrogen

Summary Podocarpus pollen morphology is shaped by both phylogenetic history and the environment. We analyzed the relationship between pollen traits quantified using deep learning and environmental factors within a comparative phylogenetic framework. We investigated the influence of mean annual temperature, annual precipitation, altitude, and solar radiation in driving morphological change. We used

SummaryTransfer RNA (tRNA) modifications refer to the chemical alterations that occur on tRNA molecules, which are essential for their structure, stability, and function. These modifications have been shown to play crucial roles in diverse biological processes across different organisms. Recent studies have highlighted that specific tRNA modifications are directly linked to virulence traits and infection

SummaryLong noncoding RNAs (lncRNAs) have been gradually verified as functional regulators in plants, yet their functions remain underexplored, especially in the Solanaceae family. While substantial progress has been made in identifying lncRNAs in different Solanaceae species, systematic functional annotations are lacking. In this study, we uniformly identified and systematically characterized lncRNAs

SummarySphagnum is emerging as a useful system for advancing knowledge at the interface between ecology and evolutionary biology. Here, we explore: the importance of the Sphagnum microbiome to ecosystem structure and function; the value of naturally occurring genetic variation within Sphagnum populations; and the ongoing process of speciation and ecological divergence in the genus. Recent advances

SummaryPhotosynthetic induction is the leaf‐level process by which a plant assimilates CO2 from the atmosphere once exposed to a change in light intensity after a period of darkness or shade. In the field, photosynthetic induction can take place hundreds of times in a single day in response to rapid fluctuations in the light environment due to cloud cover, wind, solar angle, and neighbourly shading

Summary The mobility of transposable elements (TEs) partly drives genome evolution, potentially leading to either adaptive or deleterious effects. However, it remains far from clear whether and how TEs contribute to adaptation to changing environments, especially in plants. We analyzed whole‐genome sequencing data from 29 ecologically diverse Tetrastigma hemsleyanum populations to infer the species'

Summary Flavones, a key group of flavonoids, play a significant role in plant adaptation to ecological niches and are valuable medicinal resources. However, the genetic basis underlying their contribution to ecological adaptation remains largely unknown. Here, using metabolite‐based genome‐wide association study, we report that the natural variation of flavone contents in Chrysanthemum indicum, a wild

Summary Plant–soil feedback (PSF) is a standing concept helping to explain plant species coexistence. Accumulating evidence suggests that PSF depends on the environmental context. One particularly impactful disruption of the environmental context is the invasion of alien species into a community. While PSF between native and non‐native species has been linked to invasion success, the effect of an invader

SummaryPlant specialized metabolites (PSMs) are compounds that are not involved in primary metabolism but instead confer other roles for the plant host, often related to ecological interactions. In the field of plant–microbe interactions, many PSMs have traditionally been considered for their roles in shaping interactions with pathogens. However, it is increasingly clear that ‘defensive’ PSMs have

Summary Maple trees repair cold‐induced embolism by generating positive stem pressure during their leafless state, altering sap transport in ways that remain poorly understood. This xylem pressure also drives sap exudation, enabling maple sap harvest for syrup production. This study investigates water source dynamics in leafless maples in early spring and its impact on sap yields. We used heavy water

Summary Abscisic acid (ABA) is a crucial regulator of plant growth, while vacuolar malate accumulation is pivotal for determining fruit taste and flavor. However, the relationship between ABA signaling and malate metabolism remains poorly understood. Here, we show that the ABA‐modulated auxin response factor 2 (ARF2)‐multidrug and toxic compound extrusion protein like 1 (MdMATEL1)/cytosolic NAD‐dependent

Summary Recent studies have shown a linear relationship between solar‐induced Chl fluorescence (SIF) and gross primary productivity (GPP) at large scales. However, this relationship diverges at finer leaf scales, particularly in tropical forests with complex canopy structures. To address this issue, we assessed seasonal and intracanopy variations in leaf energy partitioning in central Amazonian forests

Since the Devonian era 450 million years ago, most terrestrial plants have formed mutualistic associations with a group of soil fungi known as arbuscular mycorrhizal fungi (AMF) that provide benefits ranging from improved mineral nutrition to increased tolerance of biotic and abiotic stresses (Marro et al., 2022; Shi et al., 2023; Fiorilli et al., 2024). This symbiosis constitutes a unique biological

SummaryCarnivorous plants secrete digestive enzymes for prey degradation. Although carnivorous plants have a polyphyletic origin and evolved several times independently, they surprisingly co‐opted similar digestive enzymes during convergent evolution. However, despite having similar digestive enzymes, the mode of their regulation strongly differs across different phylogenetic lineages. But what factors

SummaryEnvironmental changes and their effects are among the most pressing topics of today's ecological research. Shrublands, although widespread across the globe, remain understudied in this respect. We conducted a global meta‐analysis of 81 shrubland sites subjected to experimental warming, shifts in precipitation (e.g. increased precipitation and drought), and nitrogen addition to quantify seven

Summary In terrestrial plants, seeds often germinate and initiate early development in the darkness under layers of soil. Soil overlay promotes ethylene accumulation to maintain the hook until the seedlings reach the soil surface. During this phase of etiolated growth and soil emergence, seedlings perceive changing light fluence. Coordinated interplay of the ethylene and light signaling pathways ensures

Summary Flavonoids are valuable metabolites produced by legumes, including Medicago truncatula, and play crucial roles in signaling communication during legume–rhizobium symbiosis. Isoflavone reductase proteins (IFRs) are involved in the biosynthesis of isoflavones and plant defense regulation. However, their role in symbiotic nitrogen fixation remains mostly elusive. Here, 13 putative IFR gene family

Summary We investigated the impact of leaf color variation on herbivory, testing current hypotheses indicating that leaf color could influence herbivory through bottom‐up control (by signaling leaf quality and defenses) or top‐down control (by attracting predators). A comprehensive phylogenetic meta‐analysis was conducted to assess the effects of leaf color on defense traits, leaf palatability, herbivore

SummaryPolyploidy plays a major role in diversification and speciation of almost all plants. Separately, the microbiome is recognized for its ubiquitous role in plant functioning. Despite the importance of both processes, we lack a synthetic picture of their reciprocal relationship. I forge this missing linkage by presenting the ways in which plant polyploidy can shape the microbiome and how the microbiome

Summary Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification

SummaryParasitic plants, those that directly acquire resources from other plants, are distributed across all biomes on earth. They can be restricted to a single host, or they can be generalists, but with preferences. Tristerix corymbosus (Loranthaceae) is a native generalist hemiparasite in Chile but infests many nonnative tree species and appears to suppress them more than its native hosts, indicating

Summary Ungulate herbivory, a widespread and complex disturbance, shapes grassland biodiversity and functions primarily through three mechanisms: defoliation, trampling, and excreta return. However, the specific effects of these mechanisms on soil biodiversity and community assembly remain unclear. We conducted a 4‐yr factorial experiment in the Eurasian steppe to investigate how defoliation, trampling

Summary Crassulacean acid metabolism (CAM) photosynthesis has independently evolved many times in arid‐adapted plant lineages. Cistanthe cachinalensis (Montiaceae), a desert annual, can upregulate CAM facultatively upon stress such as drought. Few studies, however, consider life history stages when measuring CAM activity or its facultative onset. To test the effect of drought and flowering on photosynthetic

Summary Phytoplasmas are specialized phloem‐limited bacteria that cause diseases on various crops, resulting in significant agricultural losses. This research focuses on the jujube witches' broom (JWB) phytoplasma and investigates the host‐manipulating activity of the effector SJP39. We found that SJP39 directly interacts with the plant transcription factor bHLH87 in the nuclei. SJP39 stabilizes the

Summary In response to chilling, plants undergo a variety of metabolic changes, including structural modifications of sphingolipids, which have an important but poorly understood effect on cold tolerance. Here, we used biochemical, molecular, cell biological, and genetic approaches to investigate the mechanism of cold‐induced sphingolipid regulation. Chilling stress affected sphingolipid metabolism

Summary Plants have evolved sophisticated strategies to cope with various environmental stresses. Recent studies have provided insights into the mechanisms of rapid cold stress response through key components including OST1, ICE1, HOS1, and CBFs. However, the mechanisms by which plants modulate the intensity of their cold tolerance in response to fluctuating temperatures remain largely unexplored.

SummaryIn arbuscular mycorrhizal (AM) fungi, only c. 370 species have been formally described despite these fungal organisms having coevolved with plants for hundreds of millions of years. In contrast to this, dozens of thousands of species are known for many fungal lineages with shorter evolutionary timescales. This Viewpoint highlights some plausible reasons for these striking discrepancies in species

Summary Alternative splicing is essential for plants, enabling a single gene to produce multiple transcript variants to boost functional diversity and fine‐tune responses to environmental and developmental cues. Arabidopsis thaliana At‐RS31, a plant‐specific splicing factor in the Serine/Arginine‐rich (SR) protein family, responds to light and the Target of Rapamycin (TOR) signalling pathway, yet its

Summary RNA editing in plant organelles is widely regarded as a neutral corrective mechanism, yet it persists as a complex, energetically costly process, requiring numerous nuclear‐encoded pentatricopeptide repeat proteins. Ferns are the most diverse lineage of land plants that uniquely retain both cytidine‐to‐uridine (C‐to‐U) and uridine‐to‐cytidine (U‐to‐C) Berget RNA editing in their plastomes,

Summary Genetic load can reduce fitness and hinder adaptation. While its genetic underpinnings are well established, the influence of environmental variation on genetic load is less well characterized, as is the relationship between genetic load and putatively adaptive genetic variation. This study examines the interplay among climate, species range dynamics, adaptive variation, and mutational load

Summary Eclepins are root‐secreted compounds that induce the hatching of cyst nematodes. Solanoeclepin A (SEA) and B (SEB) have been isolated as potent hatching factors for potato cyst nematodes (PCNs). SEB is biosynthesized in roots, released into the rhizosphere, and converted into SEA by soil microorganisms. However, given that SEB and SEA exhibit comparable hatching‐inducing activity toward PCNs

SummaryGlobal forest restoration initiatives provide an important chance to recover biodiversity and enhance forest functions and services. Over recent decades, functional diversity (FD) has been regarded as a key driver of the positive relationships between biodiversity and ecosystem functioning (BEF). Despite extensive observations on the associations between tree FD and various forest ecosystem

Summary With the intensification of global warming, there is an urgent need to develop crops with enhanced heat tolerance. Pearl millet, as a typical C4 heat‐tolerant crop, has mechanisms of heat tolerance at the cellular level which remain unclear. Constructed single‐cell transcriptomic landscape of pearl millet leaves under heat stress and normal conditions, comprising 20 589 high‐quality cells classified

Summary Cauline leaf development represents an intermediate phase between vegetative and reproductive stages. While extensive research has been conducted on the genetic and environmental factors that determine cauline leaf number, less attention has been given to the regulation of their morphology and the establishment of cauline leaf identity. In this study, we report that miR156‐targeted SQUAMOSA

Summary Low oxygen signalling in plants is important in development and stress responses. Measurement of oxygen levels in plant cells and tissues is hampered by a lack of chemical tools with which to reliably detect and quantify endogenous oxygen availability. We have exploited hypoxia‐activated fluorescent probes to visualise low oxygen (hypoxia) in plant cells and tissues. We applied 4‐nitrobenzyl

Summary In Arabidopsis thaliana, REDUCED LATERAL ROOT FORMATION (RLF), a cytochrome b5‐like heme‐binding domain (Cytb5‐HBD) protein, is necessary for proper lateral root (LR) formation. Whereas the other Cytb5‐HBD proteins in A. thaliana regulate different metabolic reactions, RLF is unique as it specifically regulates organ development. However, it remains unknown whether heme binding to RLF is necessary

Summary BRASSINOSTEROID INSENSITIVE1‐ASSOCIATED RECEPTOR KINASE 1 (BAK1)‐INTERACTING RECEPTOR‐LIKE KINASE (BIR) proteins are negative regulators of cell death and defense against microbes in Arabidopsis thaliana. Here, we demonstrate that the members of the BIR family function as negative regulators of antiviral resistance in Arabidopsis. We show that during tobacco rattle virus (TRV) infection, BIR1

Zou et al. 2024. Genetic and epigenetic reprogramming in response to internal and external cues by induced transposon mobilization in Moso bamboo. New Phytologist 244: 1916–1930, doi: 10.1111/nph.20107. On the title page of the article, the author name Muthusamy Ramakrishnan was incorrectly spelled at publication. This has now been corrected. We apologise for this error.

Summary The evolutionary history of gymnosperms suggests that most species struggle in wet environments. However, baldcypress (Taxodium distichum var. distichum) thrives in wetlands, making it a prime candidate for studying flood tolerance in gymnosperms. Our study aimed to explore the genetic basis of this flood tolerance. We accomplished the first chromosome‐level genome assembly of baldcypress.

Summary Tiller angle is a critical architectural trait in rice (Oryza sativa), affecting planting density, light interception, and grain yield. While HEAT STRESS TRANSCRIPTION FACTOR 2D (HSFA2D) has been shown to regulate tiller angle via LAZY1 (LA1)‐mediated auxin distribution, the precise mechanisms governing this pathway remain elusive. We identified and characterized LA6, which encodes a heat shock

Summary Cleistogenes squarrosa is a pioneer tumble plant widely distributed across the Eurasian steppes. It achieves long‐distance wind dispersal through stem reshaping. However, the underlying ecological adaptation mechanisms of this dispersal strategy remain unexplored. Combining with field and laboratory observations, we revealed that four coordinated processes – plant phenology, cell wall development

What is the typical oxygen status of plant tissues? The answer, perhaps unsurprisingly, is ‘it depends’. A recent meta-analysis revealed that plant tissues may experience oxygen levels ranging from anoxia to hyperoxia exceeding 60 kPa oxygen partial pressure (pO2), depending on tissue type and the environmental conditions under which oxygen status is assessed (Herzog et al., 2023). Most studies included

Summary Evolutionarily conserved switch‐defective/sucrose nonfermentable (SWI/SNF) ATP‐dependent chromatin remodelling complexes (CRCs) alter nucleosome positioning and chromatin states, affecting gene expression to regulate important processes such as proper development and hormonal signalling pathways. We employed transcript profiling, chromatin immunoprecipitation (ChIP), mass spectrometry, yeast

Summary The phenomena of isolation‐by‐distance and isolation‐by‐time shapecontra mating patterns and population genetic processes, such as inbreeding and outbreeding depression, which influence progeny fitness. However, the effects of parental isolation in time on offspring fitness remain understudied, especially in combination with isolation‐by‐distance. We planted offspring from a common garden experiment

SummaryPlant invasions are biogeographical phenomena that may involve shifts in belowground plant–fungal interactions, such as the release from fungal pathogens or more beneficial interactions with mutualists in nonnative ranges. However, native and nonnative ranges are not uniform but environmentally heterogeneous, and plant–fungal interactions are strongly shaped by spatio‐environmental context.

Summary In most tree species, roots serve as major carbon (C) sinks, where C is depleted first when C assimilation is limited. Recent methodological advancements in sugar infusion allow for a better understanding of physiological processes alleviating root C limitation. We conducted a glasshouse experiment with maple (Acer pseudoplatanus L.) and pine (Pinus sylvestris L.) saplings that underwent defoliation

SummaryPopulations of diverse, unknown, and potentially pathogenic fungi and fungus‐like organisms are continuously introduced into new locations via asymptomatic infections (e.g. as endophytes or latent pathogens) within internationally traded live plants. Interactions between these asymptomatic fungi and novel recipient host trees can be unpredictable, and urban introductions may act as bridgeheads

Summary The mechanistic links between fire‐caused injuries and post‐fire tree mortality are poorly understood. Current hypotheses differentiate effects of fire on tree carbon balance and hydraulic function, yet critical uncertainties remain about the relative importance of each and how they interact. We utilize two prescribed burns with Douglas‐fir and ponderosa pine to examine: the relative evidence

Summary Acylsugars, specialized metabolites produced by trichomes of many solanaceous species, provide protection against biotic and abiotic stresses. Many acylsugar metabolic enzymes have been identified; however, regulatory factors remain unknown. Our multidisciplinary approaches identified LEAFLESS (APETALA 2/ ETHYLENE RESPONSE FACTOR (AP2/ERF) family member) as a positive regulator of acylsugar

SummaryAdvances in single‐cell and spatial omics technologies have revolutionised biology by revealing the diverse molecular states of individual cells and their spatial organization within tissues. The field of plant biology has widely adopted single‐cell transcriptome and chromatin accessibility profiling and spatial transcriptomics, which extend traditional cell biology and genomics analyses and

Introduction Ripening involves complex biochemical and molecular reprogramming, resulting in color, texture, aroma, and flavor changes to attract humans and other animals (Giovannoni et al., 2017). In climacteric fruits, this process is controlled by a myriad of phytohormones, predominantly ethylene (Li et al., 2021; Huang et al., 2022). To allow these changes, fruits constantly reshape their cellular

Summary Colorful petal patterns fulfill important functions and constitute excellent systems to illuminate the evolutionary processes that generate morphological diversity or instead support the repetitive emergence of similar forms. Here, we combined phylogenomic approaches, genetic manipulations, molecular techniques, and bee behavioral experiments to (i) solve the species relationships across the