Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the

Plants depend on the combined action of a shoot-root-soil system to maintain their anchorage to the soil. Mechanical failure of any component of this system results in lodging, a permanent and irreversible inability to maintain vertical orientation. Models of anchorage in grass crops identify the compressive strength of roots near the soil surface as the key determinant of resistance to lodging. Indeed

The phytohormone methyl jasmonate (MeJA) enhances plant cold stress tolerance, but the underlying mechanisms remain elusive. Here, we discovered that MeJA induces a transient Ca2+ influx and elevated cytoplasmic free Ca2+ ([Ca2+]cyt) levels during the watermelon (Citrullus lanatus) response to cold stress. Conversely, silencing jasmonic acid carboxyl methyltransferase (ClJMT), encoding an enzyme that

PLASTIDIAL STARCH PHOSPHORYLASE 1 (PHS1) is considered integral to starch synthesis, yet its role in transient starch synthesis in photosynthetic tissues remains unclear, as mutation of PHS1 in Arabidopsis (Arabidopsis thaliana) does not affect the metabolic profile of leaves. PHS1 activity is elevated in the starch branching enzyme sbe2.1 sbe2.2 double mutant, which lacks starch granules but retains

Drought severely impacts plant growth, yet moderate drought stress can stimulate the biosynthesis of active compounds in medicinal plants. However, the molecular regulators and mechanisms linking drought resistance with the accumulation of active compounds remain poorly understood. In this study, we identified the Dof transcription factor SmDof32 as a key regulator of both salvianolic acid biosynthesis

Chloroplast thylakoid membranes are the sites of the light reactions of photosynthesis. They are also thought to influence starch granule biogenesis via the thylakoid-anchored protein MAR-BINDING FILAMENT-LIKE PROTEIN 1 (MFP1), but mechanistic understanding is scarce. Here, we report an Arabidopsis (Arabidopsis thaliana) mutant affected in PHOTOSYSTEM II REACTION CENTER W (PsbW), an integral thylakoid

The biogenesis of Photosystem II is a complicated process requiring numerous auxiliary factors to assist in all steps of its assembly. The cyanobacterial protein Ycf39 forms a stress-induced complex with two small chlorophyll-binding, High-light-inducible proteins C and D (HliC and HliD), and has been reported to participate in the insertion of chlorophyll molecules into the central D1 subunit of Photosystem

Flowering and secondary growth are two important biological processes in plant development, and there is a close association between flowering and xylem expansion in stem and root secondary growth. Here, we report the discovery of NAC secondary wall thickening promoting factor 3 (BnaA9.NST3), a key regulator of secondary cell wall formation in xylem fiber cells that affects B. napus (Brassica napus

Grana are fundamental structural units of the intricate chloroplast membrane network. Investigating their nanomorphology is essential for understanding photosynthetic efficiency regulation. Here, we present GRANA (Graphical Recognition and Analysis of Nanostructural Assemblies), an AI-enhanced, user-friendly software tool that recognizes grana on thylakoid network electron micrographs and generates

Transcription factors control gene expression during development and in response to a broad range of internal and external stimuli. They regulate promoter activity by directly binding cis-regulatory elements in DNA. The angiosperm Arabidopsis (Arabidopsis thaliana) contains more than 1,500 annotated transcription factors, each containing a DNA-binding domain that is used to define transcription factor

The comprehensive annotation of regulatory elements in linear genomes is needed to elucidate the molecular mechanisms underlying chromatin loop formation in plants. Here, we characterized a novel family of conserved noncoding sequences (CNSs) in the rice (Oryza sativa) genome. These sequences, known as AT-rich pincer-like elements (APEs), are composed of 13-bp repeat unit arrays in a reverse-forward

Ornamental plants can generate higher economic value per unit area compared to traditional crops. Enhancing market share in the flower industry relies on cultivating varieties with exceptional ornamental traits. Petal size, a critical factor influencing flower shape and ornamental appeal, is a primary focus for horticultural breeding selection. In this article, we review recent advances in understanding

Mitochondria are an indispensable component of every plant cell and are inextricably linked to many vital functions. One of their key characteristics is that they have their own genome. This genome, although greatly reduced, encodes several essential genes. While this has been known for decades, until recently it has not been possible to study the mitochondrial genome and its function in detail due

A key aspect of enhancing photosynthesis is improving the kinetics of photochemical quenching recovery following environmental perturbation or stress. Salt stress exacerbates high light stress in cyanobacteria and leads to severe yield losses in crop plants. Genetic traits that confer salt tolerance without compromising photosynthetic performance are essential for improving photosynthesis under these

Asiatic hybrid lilies (Lilium spp.) are favored by consumers for their vibrant colors and diverse anthocyanin pigmentations. Although the regulation of anthocyanin accumulation by transcription factors has been explored, the role of HD-Zip proteins with ethylene-responsive element binding factor associated amphiphilic repression (EAR) motifs in modulating anthocyanin levels through histone acetylation

Ectomycorrhizal (ECM) fungi contribute to N, Pi, and water uptake in trees while obtaining carbohydrates from their host plants. However, the molecular mechanisms underlying N assimilation during ECM symbiosis remain unclear. In this study, we used RNA interference (RNAi) to silence the expression of genes encoding glutamine synthetase (GS) and NADP-glutamate dehydrogenase (GDH), which are key enzymes

In Arabidopsis thaliana, the POWDERY MILDEW RESISTANT4 (PMR4)/GLUCAN SYNTHASE LIKE5 (GSL5) callose synthase is required for pathogen-induced callose deposition in cell wall defense. Paradoxically, pmr4/gsl5 mutants exhibit strong resistance to both powdery and downy mildew. The powdery mildew resistance of pmr4/gsl5 has been attributed to upregulated salicylic acid (SA) signaling based on its dependance

C2H2-type zinc finger protein (ZFP) transcription factors influence root growth and development. However, their potential roles in inhibiting adventitious root (AR) and lateral root (LR) formation in trees remain unclear. Here, we report that the ABA-responsive C2H2-type zinc finger protein transcription factor (PuZFP1) regulates Populus ussuriensis root development to enhance drought tolerance. PuZFP1

Plant growth and development are precisely controlled by light and temperature during their life span. However, the mechanism by which photoperiod and seasonal changes influence the physiological response of day-neutral plants, such as tomato (Solanum lycopersicum), remains unclear. Here, we found that the tomato CONSTANS (CO) close homolog, CONSTANS-Like1 (SlCOL1), does not affect the flowering of

Cotton (Gossypium. spp) stem trichomes and seed fibers are unicellular epidermal hairs regulated by relevant molecular networks. Genetic analysis of the glabrous stem landrace (Palmeri37) of Gossypium hirsutum L. has pinpointed GL2-interacting-repressor 1 (GhGIR1D), featuring a RING-like zinc finger domain, as the candidate gene underlying the stem glabrous trait. Overexpressing and silencing experiments

Seed germination, a pivotal stage in plant growth, is governed by phytohormones such as gibberellic acid (GA) and influenced by phytochromes, which are key photoreceptors in plants. The N6-methyladenosine (m6A) RNA modification is fundamental to plant growth and development. However, the molecular mechanisms underlying the regulation of PHYTOCHROME B (phyB) and the function of m6A signaling in GA-mediated

Identifying plant molecular mechanisms that mediate root–substrate interactions might offer potential solutions to soil erosion, especially in crop fields, where agricultural practices lead to soil loss. Mutants of the Arabidopsis (Arabidopsis thaliana) ATP-Binding Cassette G 43 (ABCG43) transporter gene show enhanced root–substrate cohesion, even though their root micro- and macro-structures are similar

Sugar content is a key determinant of peach (Prunus persica) fruit quality, influencing taste, consumer preferences, and market value. However, the roles of Major Facilitator Superfamily (MFS) transporters in sugar metabolism and regulation remain largely unexplored. This study employed a combination of spatial metabolomics, quantitative genetics, transcriptomics, comparative genomics, and functional

The rate of residual water loss is a major determinant of plant survival during drought, yet how the major paths of residual water flow develop as leaves expand is poorly understood. Here, we tracked the rate of residual water loss, the compositional development of cuticular wax, stomatal differentiation, pore formation, and xylem development as leaves expand in two co-occurring, deciduous tree species

Seed germination is a critical developmental stage in the lifecycle of plants, and its regulation is essential for ensuring crop productivity, particularly under adverse environmental conditions. Here, we find that the Arabidopsis thaliana Pre-mRNA PROCESSING FACTOR 21 (PRP21) is crucial for regulating the abscisic acid (ABA) response and seed germination. Our RNA deep sequencing and poly(A) tag sequencing

Excessive symmetry in cryo-EM data processing can distort key structural details of bacterial microcompartments, highlighting the importance of balanced symmetry for accurate structural insights.

Callus formation and shoot regeneration are naturally triggered by stress and damage to the plant. They are also key components of tissue culture, which is crucial for gene editing, transformation, propagation, and other technologies in many species. Thus, the study of callus formation and shoot regeneration provides valuable insights into plant development. The transcription factor ENHANCER OF SHOOT

Plant clathrin and its adaptor protein complexes—adaptor protein complex-1 (AP-1) at the trans-Golgi network/early endosome (TGN/EE) and the adaptor protein complex-2 (AP-2) at the plasma membrane (PM)—function in clathrin-mediated trafficking (CMT). This study reports the role of CMT in regulating copper (Cu) tolerance in plants. We found that high concentrations of exogenous Cu treatment increase

Flowering plants adjust their reproductive period to ensure reproductive success. This involves a tight control of both flower initiation and the termination of the flowering period to optimize resource allocation for seed production. The end of flowering is marked by the cessation of flower production by the inflorescence meristems, which enter a dormant-like state known as proliferative arrest. This

Low silicon (Si) rice 1 (OsLsi1) is a key transporter mediating Si uptake in rice (Oryza sativa). It is polarly localized at the distal side of the root exodermis and endodermis. Although OsLsi1 is also permeable to other metalloids, such as boron (B), germanium (Ge), arsenic (As), antimony (Sb), and selenium (Se), the role of its polar localization in the uptake of these metalloids remains unclear

Genomic prediction has accelerated breeding processes and provided mechanistic insights into the genetic bases of complex traits. To further optimize genomic prediction, we assess the impact of genome assemblies, genotyping approaches, variant types, allelic complexities, polyploidy levels, and population structures on the prediction of 20 complex traits in switchgrass (Panicum virgatum L.), a perennial

DNA methylation, a conserved epigenetic mark in both plants and animals, plays a critical role in growth, development, and adaptability. This study explores the origin, evolution, and functional diversification of two key methyltransferase regulators, DNAJ domain-containing protein 1/2/3 (DNAJ1/2/3) and SU(VAR)3-9 HOMOLOG 1/3 (SUVH1/3), in plants. By analyzing genomic data from 21 algae and 86 land

The RNA-binding proteins (RBPs) encoded by the nucleus are essential for RNA metabolism in eukaryotes. Pentatricopeptide repeat (PPR) proteins, a large subset of RBPs, are essential for plant development and reproduction by participating in organellar RNA processing. Here, we identified an E-type PPR protein, PPR767, which functions in mitochondria. Knocking out PPR767 resulted in decreased plant height

The evolution of parasitic plants has been marked by a progressive relaxation of selective pressures associated with maintaining photosynthesis, resulting in a wide diversity in photosynthetic capacity within this group. In this study, we explored this diversity by examining several hemi- and holoparasitic plants, focusing on photoprotection. Our findings revealed a strongly conserved evolutionary

High rates of photosynthesis require abundant water delivered to the canopy to replace water lost to transpiration. In addition to water drawn immediately from the soil, stem capacitance has been identified as an additional water source, particularly during transient transpiration states. However, little information is available about the potential of roots to contribute to plant capacitance because

β-Caryophyllene is a key volatile sesquiterpene involved in plant defense and contributes to the characteristic aroma of pak choi (Brassica campestris). This study aimed to elucidate the regulatory landscape of β-caryophyllene biosynthesis in pak choi to understand the genetic and molecular mechanisms controlling the production of this volatile sesquiterpene. Among 61 germplasm accessions of pak choi

MicroRNAs (miRNAs) are key regulators of gene expression and typically processed from primary transcripts (pri-miRNAs). Recent discoveries highlight that certain pri-miRNAs also encode miRNA-encoded peptides (miPEPs), which influence miRNA function. However, the molecular mechanisms underlying miPEP activity, including the specific domains or essential amino acid residues required for their function

Diketopiperazines (DKPs) are chemically and functionally diverse cyclic dipeptides associated primarily with microbes. Few DKPs have been reported from plants and animals; the best characterized is cyclo(His-Pro), found in the mammalian central nervous system, where it arises from the proteolytic cleavage of a thyrotropin-releasing tripeptide hormone. Herein, we report the identification of cyclo(His-Pro)

Ever since the first transgenic plant emerged from a green clump of callus, grant proposals were erected upon grand ideas, visions of crop genetic engineering innovations positively impacting people and the planet. But how many of these actually came to fruition? More than three decades of journal articles articulate the discoveries of gene-trait connections and how they may be implemented to improve

The root system architecture (RSA) determines plant growth and yield. The characterization of optimal RSA and discovery of genetic loci or candidate genes that control root traits are therefore important research goals. However, the hidden nature of the root system makes it difficult to perform nondestructive, rapid analyses of RSA. In this study, we developed an automated, nondestructive, high-throughput

In photosynthetic organisms, genetic material is stored in the nucleus and the two cytoplasmic organelles: plastids and mitochondria. While both the nuclear and cytoplasmic genomes are essential for survival, the inheritance of these genomes is subject to distinct laws. Cytoplasmic inheritance differs fundamentally from nuclear inheritance through two unique processes: vegetative segregation and uniparental

The DYW deaminase domain catalyzes the conversion of cytidines (C) to uridines (U) in RNA editing of plant organelles. While the DYW subgroup contains a complete DYW deaminase domain at the C-terminus, the E2 and E+ subgroups rely on complementary deaminases, in which catalytic activity depends on interactions with short DYW proteins, such as DYW1, DYW2, and MITOCHONDRIAL EDITING FACTOR 8 (MEF8)/MITOCHONDRIAL

Catabolic conversions within the jasmonate pathway have substantial consequences on phytohormone signaling output. In dicots, the jasmonic acid oxidase (JAO) catabolic route leads to jasmonic acid (JA) hydroxylation, which limits its conjugation into bioactive jasmonoyl-isoleucine (JA-Ile). Here, we functionally characterized the JAO pathway in rice (Oryza sativa) and demonstrated its key function

The transition to reproductive development is a critical step in the plant lifecycle and relies on the integration of intrinsic and environmental signals. Several different pathways controlling flowering time function downstream of the perception of environmental cues such as day length (photoperiodic pathway) and seasonal temperature (vernalization and ambient temperature pathways). In addition, the

Phosphate (Pi) is essential for photosynthesis in the chloroplast of algae and plants. Pi homeostasis in the chloroplast is maintained by transporters from several families, whose identities in algae are largely unknown as compared to land plants. Here, we assess the role of the putative PHOSPHATE TRANSPORTER 4-9 from Chlamydomonas reinhardtii (CrPHT4-9) in maintaining chloroplast Pi homeostasis and

A thorough understanding of the biochemical, stomatal, and mesophyll components that limit photosynthetic induction is crucial for targeted improvement of crop productivity. However, compared with biochemical activation and stomatal conductance (gs), mesophyll conductance (gm) remains underexplored in induction studies. The fluorescence method (the variable J method) is a valid and widely accessible