Featured
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Article
| Open AccessRewiring of a KNOXI regulatory network mediated by UFO underlies the compound leaf development in Medicago truncatula
This study reveals a pathway in which the transformation of trifoliate leaves into pinnate-like pentafoliate leaves is regulated by the conserved regulators of floral development (MtUFO) and leaf development (MtKNOXI) in M. truncatula.
- Zhichao Lu
- , Juanjuan Zhang
- & Chuanen Zhou
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Article
| Open AccessDecoding early stress signaling waves in living plants using nanosensor multiplexing
Upon stress, plants activate a signaling cascade leading to resistance or stress adaptation. Here, Ang & Saju et al. use sensor multiplexing to elucidate the interplay between H2O2 and SA signaling as plants mount stress-specific defense responses.
- Mervin Chun-Yi Ang
- , Jolly Madathiparambil Saju
- & Rajani Sarojam
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Article
| Open AccessTwo orthogonal differentiation gradients locally coordinate fruit morphogenesis
The coordination of cellular behaviors is essential for proper organogenesis. Here the authors show that fruit development in Arabidopsis is governed by time-shifted differentiation gradients that act locally along two perpendicular organ axes.
- Andrea Gómez-Felipe
- , Elvis Branchini
- & Daniel Kierzkowski
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Article
| Open AccessA distal enhancer guides the negative selection of toxic glycoalkaloids during tomato domestication
This study identified a distal enhancer GE1, which acts as the key regulator controlling steroidal glycoalkaloids metabolism by modulating the GAME gene cluster and guides negative selection of steroidal glycoalkaloids production during tomato domestication.
- Feng Bai
- , Peng Shu
- & Mingchun Liu
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Article
| Open AccessThe thylakoid proton antiporter KEA3 regulates photosynthesis in response to the chloroplast energy status
Thylakoid K+/H+ exchange by KEA3 optimizes photosynthesis during light fluctuations. Here, the authors show that a combination of stromal pH, ATP, ADP and NADP+, NADPH induces structural re-arrangements required for KEA3 regulation in vivo.
- Michał Uflewski
- , Tobias Rindfleisch
- & Ute Armbruster
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Article
| Open AccessAutophagy-mediated degradation of integumentary tapetum is critical for embryo pattern formation
A seed consists of an embryo, endosperm, and seed coat. Here the authors show that autophagy plays a crucial role in regulating timely programmed cell death in the innermost seed coat, thereby influencing embryo pattern formation and seed viability.
- Lin-lin Zhao
- , Ru Chen
- & Peng Zhao
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Review Article
| Open AccessDevelopmental timing in plants
Plants exhibit reproducible timing of developmental events at multiple scales, from switches in cell identity to maturation of the whole plant. Using simplified models to convey key concepts, we review how timing mechanisms interact with the environment to control cyclical and progressive developmental transitions.
- Enrico Coen
- & Przemyslaw Prusinkiewicz
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Article
| Open AccessBee-pollination promotes rapid divergent evolution in plants growing in different soils
In nature, soil, pollinators, and herbivores are the main drivers of plant adaptation and diversification. This study reveals that the interaction between soil and biotic pollination causes divergent evolution where pollinators play a key role, leading to strong divergence among plants in different soils.
- Thomas Dorey
- & Florian P. Schiestl
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Article
| Open AccessDefects in the cell wall and its deposition caused by loss-of-function of three RLKs alter root hydrotropism in Arabidopsis thaliana
Plants have evolved strategies to protect root tips from the damage of stresses. Chang et al., show that root tips are covered with wax, which can efficiently protect root tips from osmotic stress and alter root hydrotropism in Arabidopsis.
- Jinke Chang
- , Xiaopeng Li
- & Jia Li
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Article
| Open AccessAn ARF gene mutation creates flint kernel architecture in dent maize
The mutation of ARFTF17 results in the development of flint kernel architecture in dent maize by reducing excessive pericarp length. This discovery holds significant potential for enhancing grain quality in elite, high-yielding dent maize hybrids.
- Haihai Wang
- , Yongcai Huang
- & Yongrui Wu
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Article
| Open AccessA fungal core effector exploits the OsPUX8B.2–OsCDC48-6 module to suppress plant immunity
Plant ubiquitin regulatory domain-containing proteins (PUX) play vital roles in CDC48-mediated protein quality control processes. Here Shi et al. show that a conserved core Magnaporthe oryzae effector (MoNLE1) can specially target the rice PUX protein OsPUX8B.2 and interfere with host immune responses.
- Xuetao Shi
- , Xin Xie
- & Wende Liu
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Article
| Open AccessA double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice
Drought is one of the major abiotic stresses affecting rice growth and development. Here, the authors identify a dsRNA-binding protein positively regulates rice drought resistance through promoting stability of OsNCED4 mRNAs, transcript of a key gene for the biosynthesis of abscisic acid, via protein phase separation.
- Huaijun Wang
- , Tiantian Ye
- & Lizhong Xiong
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Article
| Open AccessSwitching action modes of miR408-5p mediates auxin signaling in rice
miR408-5p typically regulates target IAA30 via translation repression, but switches to cleaving IAA30 mRNA under high auxin conditions. miR393, miR156, miR408-5p and their targets could hierarchically act in auxin pathway and regulate leaf inclination.
- Fuxi Rong
- , Yusong Lv
- & Liang Wu
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Article
| Open AccessDynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.
- Chao Fang
- , Ning Jiang
- & Jiming Jiang
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Article
| Open AccessWheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein
Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. Here, the authors report the cloning of powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima encoding a mixed lineage kinase domain-like (MLKL) protein.
- Huanhuan Li
- , Wenqiang Men
- & Wenxuan Liu
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Article
| Open AccessIn-section Click-iT detection and super-resolution CLEM analysis of nucleolar ultrastructure and replication in plants
Application of correlative light and electron microscopy (CLEM) in plants remains challenging. Here, the authors use Click-iT chemistry as a tool for CLEM, due to its unique properties in resin permeability and super-resolution microscopy. They use this approach to study cellular physiology in Arabidopsis.
- Michal Franek
- , Lenka Koptašíková
- & Jíří Fajkus
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Article
| Open AccessGenetic gains underpinning a little-known strawberry Green Revolution
Cultivated strawberry is a hybrid species with a 250-year domestication history. Here, the authors use genomic prediction and a historically important breeding population to show that the introduction of photoperiod-insensitive hybrids and genetic gains from breeding have been catalysts for a strawberry Green Revolution.
- Mitchell J. Feldmann
- , Dominique D. A. Pincot
- & Steven J. Knapp
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Article
| Open AccessDynamics of extrachromosomal circular DNA in rice
Comparing to other biological systems, our understanding of plant extrachromosomal circular DNA (eccDNA) is limited. Here, the authors profile eccDNA from six rice tissues and investigate eccDNA characteristics, formation mechanisms, distribution, and functional implications.
- Jundong Zhuang
- , Yaoxin Zhang
- & Tingting Lu
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Article
| Open AccessArchitecture of symbiotic dinoflagellate photosystem I–light-harvesting supercomplex in Symbiodinium
Here the authors determine the cryoEM structure of Symbiodinium photosystem I, revealing a distinct architecture and pigment network of this light-harvesting supercomplex.
- Long-Sheng Zhao
- , Ning Wang
- & Yu-Zhong Zhang
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Article
| Open AccessThe spliceosome-associated protein CWC15 promotes miRNA biogenesis in Arabidopsis
CWC15 is a spliceosome-associated protein in Arabidopsis. Here the authors reports a multifaceted role of CWC15 in promoting microRNA (miRNA) biogenesis by binding to miRNA promoters and interacting with microprocessor components.
- Bangjun Zhou
- , Huihui Yu
- & Bin Yu
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Article
| Open AccessFungal community composition predicts forest carbon storage at a continental scale
Soil microbial diversity and composition is thought to play a major role in elemental cycling. Here, the authors analyse a large dataset of soil microbiome and carbon data from European forests and find that soil fungal community composition is a strong predictor of carbon storage.
- Mark A. Anthony
- , Leho Tedersoo
- & Colin Averill
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Article
| Open AccessSpatiotemporal formation of glands in plants is modulated by MYB-like transcription factors
The spatiotemporal formation of glands in tomato trichomes is regulated by two MYB-like transcription factors, named as GCR1 and 2, whose expression is tightly restricted by SlTOE1B. GCR1 and 2 inhibit gland formation by repressing LFS expression.
- Jiang Chang
- , Shurong Wu
- & Shuang Wu
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Article
| Open AccessBiosynthesis of the highly oxygenated tetracyclic core skeleton of Taxol
Despite intensive investigation, stepwise reactions from diol to Taxol tetracyclic core skeleton remain unclear. Here, authors fill this gap by identifying two P450s and confirming the reaction order.
- Chengshuai Yang
- , Yan Wang
- & Zhihua Zhou
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Article
| Open AccessNatural variation in OsMYB8 confers diurnal floret opening time divergence between indica and japonica subspecies
Florets of indica rice open earlier than japonica rice, hindering utilization of the cross subspecies heterosis. Here, the authors show that an OsMYB8-OsJAR1 module regulates diurnal floret opening time divergences between the two subspecies.
- Yajun Gou
- , Yueqin Heng
- & Rongxin Shen
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Article
| Open AccessA transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination
Japonica rice generally has greater capacity for low temperatures germination (LTG) than indica rice. Here, the authors report an E2 ubiquitin-conjugating enzyme-encoding gene OsUBC12 can increase LTG in japonica rice by negatively regulate ABA signaling via promoting the proteasomal degradation of OsSnRK1.1.
- Chuanzhong Zhang
- , Hongru Wang
- & Jun Fang
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Article
| Open AccessCopine proteins are required for brassinosteroid signaling in maize and Arabidopsis
Brassinosteroids play vital role in plant growth and development. Here, the authors demonstrate that the plasma membrane-associated copine proteins are new components required for the receptor complex functioning in BR signaling in maize and Arabidopsis.
- Teng Jing
- , Yuying Wu
- & Mingyue Gou
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Article
| Open AccessNatural variation of STKc_GSK3 kinase TaSG-D1 contributes to heat stress tolerance in Indian dwarf wheat
Indian dwarf wheat (Triticum sphaerococcum) is thermotolerant, but the underlying mechanism is unclear. Here, the authors report the cloning of the heat tolerance gene encoding a STKc_GSK3 kinase and its variation affects phosphorylation level of downstream TaPIF4 in determining thermotolerance.
- Jie Cao
- , Zhen Qin
- & Mingming Xin
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Article
| Open AccessA root cap-localized NAC transcription factor controls root halotropic response to salt stress in Arabidopsis
This study reports that the SOMBRERO, a root cap-localized transcription factor, determines root halotropic response to salt stress via spatiotemporally modulating AUX1-depdenent auxin redistribution in the root tip.
- Lulu Zheng
- , Yongfeng Hu
- & Yi Han
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Article
| Open AccessNatural variation in BnaA9.NF-YA7 contributes to drought tolerance in Brassica napus L
Rapeseed production is often threatened by drought stress. Here, the authors report transcription factor BnaA9.NFYA7 negatively regulates rapeseed drought tolerance through ABA signal transduction pathway via feedback inhibition of the expression of BnaABF3/4s-related genes.
- Jia Wang
- , Lin Mao
- & Liezhao Liu
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Article
| Open AccessPsAF5 functions as an essential adapter for PsPHB2-mediated mitophagy under ROS stress in Phytophthora sojae
ROS is an important defense means against pathogens for host. Here the authors show that PsAF5 functions as a mitophagy adapter and regulates mitochondrial homeostasis in Phytophthora sojae under ROS stress, which is crucial for its infection.
- Wenhao Li
- , Hongwei Zhu
- & Xili Liu
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Article
| Open AccessQuantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing
The understanding of pathogenicity in quantitative plant pathosystems remains limited. This study reveals the genetic architecture of quantitative pathogenicity traits in a significant fungal plant pathogen, shedding light on potential evolutionary mechanisms involved in host adaptation.
- Reda Amezrou
- , Aurélie Ducasse
- & Thierry C. Marcel
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Article
| Open AccessA genomic toolkit for winged bean Psophocarpus tetragonolobus
Winged bean is a tropical legume that can produce similar level of seed protein to soybean. Here, the authors report the genome assembly, population genetics, QTL mapping of the plant architecture, protein content and phytonutrients for this species.
- Wai Kuan Ho
- , Alberto Stefano Tanzi
- & Sean Mayes
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Article
| Open AccessNonpathogenic Pseudomonas syringae derivatives and its metabolites trigger the plant “cry for help” response to assemble disease suppressing and growth promoting rhizomicrobiome
Upon pathogen attack, plants can trigger the “cry for help” response and assemble beneficial rhizobacteria. Here, the authors use nonpathogenic Pseudomonas syringae DC3000 derivatives to elicit a similar “cry for help” response as the wild-type pathogenic DC3000 in Arabidopsis.
- Yunpeng Liu
- , Huihui Zhang
- & Ruifu Zhang
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Article
| Open AccessAttenuation of phytofungal pathogenicity of Ascomycota by autophagy modulators
Woo et al. report new autophagy inhibitors identified through a high-throughput chemical screening using a BRET-based assay and an ATG8 synthetic sensor, that function as safe and effective fungicides against broad fungal pathogens.
- Jongchan Woo
- , Seungmee Jung
- & Savithramma P. Dinesh-Kumar
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Article
| Open AccessSynthetic microbe-to-plant communication channels
The soil microbiome communicates with plant roots using a chemical language. Here, using p-coumaroyl-homoserine lactone as the synthetic communication signal, the authors demonstrate programmable microbe-to-plant communication from the sender in the soil bacteria to a receiver in the plant.
- Alice Boo
- , Tyler Toth
- & Christopher A. Voigt
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Article
| Open AccessGeographic range of plants drives long-term climate change
The geographic spread of plants exerted an important control over ancient climate change by modifying continental weathering and carbon burial rates. This effect is investigated using a new coupled vegetation-climate-biogeochemical model.
- Khushboo Gurung
- , Katie J. Field
- & Benjamin J. W. Mills
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Article
| Open AccessCore clock genes adjust growth cessation time to day-night switches in poplar
Alique et al. show that poplar trees adjust their seasonal growth timing by finely tuning the daily expression level of the photoperiodic integrator FT2 through a mechanism governed by the circadian clock’s core genes.
- Daniel Alique
- , Arturo Redondo López
- & Mariano Perales
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Article
| Open AccessInterplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition
Seed germination in plants is a tightly controlled process relying on translation of stored RNAs. Here, Tremblay et al. show that nascent transcriptome and epigenome reprogramming are detected from initial stages of germination.
- Benjamin J. M. Tremblay
- , Cristina P. Santini
- & Julia I. Qüesta
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Article
| Open AccessGenomic evidence for rediploidization and adaptive evolution following the whole-genome triplication
Polyploidization-rediploidization process plays an important role in plant adaptive evolution. Here, the authors assemble the genomes of mangrove species Sonneratia alba and its inland relative Lagerstroemia speciosa, and reveal genomic evidence for rediploidization and adaptive evolution after the whole-genome triplication.
- Xiao Feng
- , Qipian Chen
- & Ziwen He
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Article
| Open AccessPorous borders at the wild-crop interface promote weed adaptation in Southeast Asia
Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.
- Lin-Feng Li
- , Tonapha Pusadee
- & Kenneth M. Olsen
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Article
| Open AccessPhosphorylation of plasma membrane H+-ATPase Thr881 participates in light-induced stomatal opening
Comprehensive phosphoproteomic analysis using guard cell protoplasts revealed that Thr881 phosphorylation in addition of a penultimate residue, Thr948 of plasma membrane H+-ATPase are important for its function and light-induced stomatal opening.
- Yuki Hayashi
- , Kohei Fukatsu
- & Toshinori Kinoshita
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Article
| Open AccessLight-induced stomatal opening requires phosphorylation of the C-terminal autoinhibitory domain of plasma membrane H+-ATPase
Light-induced stomatal opening is crucial for photosynthesis. Here the authors show that blue light triggers phosphorylation of two Thr residues in the C-terminal autoinhibitory domain of plasma membrane H+-ATPase, thereby promoting stomatal opening.
- Saashia Fuji
- , Shota Yamauchi
- & Atsushi Takemiya
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Article
| Open AccessCepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery
Cepharanthine is a secondary metabolite isolated from Stephania with a variety of medicinal properties. Here, the authors assembled three Stephania genomes, propose cepharanthine biosynthetic pathway, and assess the antiviral potential of cepharanthine-related metabolites.
- Liang Leng
- , Zhichao Xu
- & Shilin Chen
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Article
| Open AccessGenetic control of thermomorphogenesis in tomato inflorescences
Mechanisms underlying changes in inflorescence development in response to high ambient temperature remain unclear. Here, the authors report the cloning of the MIB2, encoding a homology of SPATULA, and its activation of CONSTANS-Like1 for determining tomato inflorescence branching at high ambient temperature.
- Shuai Sun
- , Zhiqiang Liu
- & Xia Cui
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Review Article
| Open AccessChoreographing root architecture and rhizosphere interactions through synthetic biology
Engineering the form and function of root systems and their associated microbiota could provide a means to mitigate adverse climate-driven effects. Here, the authors review the recent developments in plant and rhizobacterial synthetic biology and highlight engineering targets for applications in root systems and rhizosphere.
- Carin J. Ragland
- , Kevin Y. Shih
- & José R. Dinneny
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Article
| Open AccessEpiallelic variation of non-coding RNA genes and their phenotypic consequences
This study uncovers abundant DNA methylation variations of non-coding RNA genes in the natural Arabidopsis population and shows the importance of epigenetic variations in plant phenotypic plasticity and diversity.
- Jie Liu
- & Xuehua Zhong
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Article
| Open AccessChromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana
The role of the nuclear matrix in plant nuclei is unclear. Here the authors reveal that nuclear matrix-associated proteins act as a regulatory hub, recruiting both DNA and transcriptional repressors to the nuclear matrix
- Linhao Xu
- , Shiwei Zheng
- & Hua Jiang
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Article
| Open AccessPhosphorylation of Arabidopsis UVR8 photoreceptor modulates protein interactions and responses to UV-B radiation
This paper reports that the Arabidopsis UV-B photoreceptor UVR8 is phosphorylated in vivo and that phosphorylation of Serine 402 modifies UVR8 activity and promotes flavonoid biosynthesis, a key response to UV-B exposure.
- Wei Liu
- , Giovanni Giuriani
- & Gareth I. Jenkins
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Article
| Open AccessA mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice
Seed dormancy is the preferred trait in rice production as it can prevent preharvest sprouting. Here, the authors report that MODD (mediator of OsbZIP46 deactivation and degradation) negatively regulates seed dormancy by inhibiting the transcriptional activity of ABSCISIC ACID INSENSITIVES (ABIs).
- Naihui Guo
- , Shengjia Tang
- & Peisong Hu
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