Plant sciences articles within Nature Communications

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  • Article
    | Open Access

    Single fluorescent protein biosensors are susceptible to expression and instrumental artifacts. Here Ast et al. describe a dual fluorescent protein design whereby a reference fluorescent protein is nested within a reporter fluorescent protein to control for such artifacts while preserving sensitivity and dynamic range.

    • Cindy Ast
    • , Jessica Foret
    •  & Wolf B. Frommer

  • Article
    | Open Access

    Plants employ developmental strategies to avoid shade and compete with neighbors for light. Here, Xie et al. show that phytochrome-interacting factors, which are regulated in a light-dependent manner, directly repress MIR156 genes and promote the expression of SPL genes to enhance shade-avoidance responses.

    • Yurong Xie
    • , Yang Liu
    •  & Haiyang Wang

  • Article
    | Open Access

    Plants are able to prime anti-herbivore defenses in response to olfactory cues of insect pests. Here, Helms et al. identify the insect pheromone E,S-conophthorin produced by the goldenrod gall fly as the specific chemical component that elicits this priming response in goldenrod plants.

    • Anjel M. Helms
    • , Consuelo M. De Moraes
    •  & Mark C. Mescher

  • Article
    | Open Access

    The fossil record of flowers is limited, necessitating other approaches to understanding floral evolution. Here, Sauquet and colleagues reconstruct the characteristics and diversification of ancient angiosperm flowers by combining models of flower evolution with an extensive database of extant floral traits.

    • Hervé Sauquet
    • , Maria von Balthazar
    •  & Jürg Schönenberger

  • Article
    | Open Access

    The DOG1 protein is a major regulator of seed dormancy in Arabidopsis. Here, Née et al. provide evidence that DOG1 can interact with the type 2C protein phosphatases AHG1 and AHG3 and that this represents the convergence point of the DOG1-regulated dormancy pathway and signalling by the plant hormone abscisic acid.

    • Guillaume Née
    • , Katharina Kramer
    •  & Wim J. J. Soppe

  • Article
    | Open Access

    Multiple plastid-derived signals have been proposed but not shown to move to the nucleus to promote plant acclimation to fluctuating light. Here the authors use a fluorescent hydrogen peroxide sensor to provide evidence that H2O2 is transferred directly from chloroplasts to nuclei to control nuclear gene expression.

    • Marino Exposito-Rodriguez
    • , Pierre Philippe Laissue
    •  & Philip M. Mullineaux

  • Article
    | Open Access

    Phytoplankton and plant plastids have distinct evolutionary origins and membrane organization. Here Floriet al. show that diatom photosynthetic complexes spatially segregate into interconnected subdomains within loose thylakoid stacks enabling fast diffusion of electron carriers and efficient photosynthesis

    • Serena Flori
    • , Pierre-Henri Jouneau
    •  & Giovanni Finazzi

  • Article
    | Open Access

    Ethylene is a plant hormone that promotes fruit ripening. Here, the authors identify pyrazinamide, a drug used to treat tuberculosis, as an inhibitor of ethylene biosynthesis inArabidopsis thalianaand present the crystal structure of its active form (pyrazinecarboxylic acid) bound to ACC oxidase.

    • Xiangzhong Sun
    • , Yaxin Li
    •  & Hongwei Guo

  • Article
    | Open Access

    The phytohormone auxin is sensed by SCFTIR1-AUX/IAA receptors leading to AUX/IAA repressor ubiquitylation and turnover. Here the authors show that IAA6 and IAA19 differ in their ubiquitylation and turnover dynamics, differentially contributing to auxin sensing and enabling discrimination of auxin concentrations.

    • Martin Winkler
    • , Michael Niemeyer
    •  & Luz Irina A. Calderón Villalobos

  • Article
    | Open Access

    Variation among wild relatives of crop plants can be used to identify genes underlying traits of agronomic importance. Here, the authors show that a modified mapping-by-sequencing approach can rapidly identify the genetic basis for viral resistance in sugar beet using wild beet populations in their natural habitat.

    • Gina G. Capistrano-Gossmann
    • , D. Ries
    •  & F. J. Kopisch-Obuch

  • Article
    | Open Access

    Targeted homologous recombination between parental chromosomes could facilitate precision breeding of crop plants. Here, Filler Hayutet al. show that CRISPR-Cas9 can be used to induce DNA double strand breaks in somatic tissue and achieve targeted recombination between homologs at an endogenous locus in tomato.

    • Shdema Filler Hayut
    • , Cathy Melamed Bessudo
    •  & Avraham A. Levy

  • Article
    | Open Access

    Iron is an essential micronutrient for plants and a lack of iron availability limits crop yield in many parts of the world. Here the authors show that natural variation in root growth ofArabidopsis plants under iron deficiency can be caused by allelic variation at the FRO2locus.

    • Santosh B. Satbhai
    • , Claudia Setzer
    •  & Wolfgang Busch

  • Article
    | Open Access

    Spinach is an economically important vegetable crop but previous genomic resources were of limited use for comparative and functional analyses. Here, Xuet al. present a high quality draft spinach genome and transcriptome data for multiple Spinaciaaccessions providing insight into Caryophyllales genome evolution.

    • Chenxi Xu
    • , Chen Jiao
    •  & Quanhua Wang

  • Article
    | Open Access

    De-domestication is the process by which cultivated plants adopt characteristics similar to that of their wild predecessors. Here Qiuet al. re-sequence de-domesticated weedy rice and matched cultivated varieties and identify genetic variants indicative of convergent evolution across multiple de-domestication events.

    • Jie Qiu
    • , Yongjun Zhou
    •  & Yongliang Lu

  • Article
    | Open Access

    Fully quantifying the influence of vegetation on atmospheric chemistry remains challenging. Here, the authors show that forest canopy shading and turbulence significantly modify air pollution throughout the atmospheric boundary layer, and must be taken into account in models of the atmosphere.

    • P. A. Makar
    • , R. M. Staebler
    •  & Q. Zheng

  • Article
    | Open Access

    A metabolon is a complex of sequential metabolic enzymes that channels substrates directly between enzymes, thus optimizing metabolic flux. Here Zhanget al. provide protein interaction and isotope dilution data that support the existence of a metabolon that channels both citrate and fumarate in the plant TCA cycle.

    • Youjun Zhang
    • , Katherine F. M. Beard
    •  & Toshihiro Obata

  • Article
    | Open Access

    Low Pi availability inhibits primary root growth, but the sensory mechanisms are not known. Here the authors uncover a signalling pathway regulating Pi-mediated root growth inhibition inArabidopsis, involving the transcription factor STOP1, its direct target ALMT1, a malate channel, and ferroxidase LPR1.

    • Coline Balzergue
    • , Thibault Dartevelle
    •  & Thierry Desnos

  • Article
    | Open Access

    The male-sterilems2 mutant has facilitated commercial production of wheat for over 40 years. Here, Xia et al. map Ms2and describe how a retrotransposon insertion event in the regulatory element of an orphan gene is associated with expression in anthers and development of male sterility.

    • Chuan Xia
    • , Lichao Zhang
    •  & Xiuying Kong

  • Article
    | Open Access

    The plant circadian clock regulates numerous developmental processes such as seasonal growth and flowering time. Here Ritteret al. identify two transcription factors, FRS7 and FRS12, which interact to form a repressor complex that regulates clock output partially by controlling the expression of GIGANTEA and PIF4.

    • Andrés Ritter
    • , Sabrina Iñigo
    •  & Alain Goossens

  • Article
    | Open Access

    Plant cryptochromes are regulated by blue-light dependent phosphorylation. Here the authors map thein vivo phosphorylation sites of Arabidopsiscryptochrome 2 and identify four closely related kinases that act to both activate and destabilize the receptor in response to blue light.

    • Qing Liu
    • , Qin Wang
    •  & Chentao Lin

  • Article
    | Open Access

    Plastoquinone (PLQ) shuttles electrons between photosystem II (PSII) and cytochrome b6f. Here the authors perform molecular dynamics simulations and propose that PLQ enters the exchange cavity of PSII by a promiscuous diffusion mechanism whereby three different channels each act as entry and exit points.

    • Floris J. Van Eerden
    • , Manuel N. Melo
    •  & Siewert J. Marrink

  • Article
    | Open Access

    High-quality reference genomes facilitate analysis of genome structure and variation. Here Duet al. create a near-complete assembly of the indicarice genome by combining single molecule sequencing with mapping data and fosmid sequences and identify genetic variants by comparison with other rice genomes.

    • Huilong Du
    • , Ying Yu
    •  & Chengzhi Liang

  • Article
    | Open Access

    Host genomes have evolved multiple silencing mechanisms to repress transposable element activity. Here Ikedaet al. show that the Arabidopsis MAIL1 and MAINgenes encode a retrotransposon-related plant mobile domain and define an alternative silencing pathway largely independent of DNA methylation and siRNAs.

    • Yoko Ikeda
    • , Thierry Pélissier
    •  & Olivier Mathieu

  • Article
    | Open Access

    Devices that harness electron flow from photosynthetic organisms generally compromise host photosynthesis. Here, the authors show that, by redesigning the QAsite of Photosystem II, it is possible to reroute electrons to an exogenous quinone while maintaining endogenous photosynthetic electron transfer in a green alga.

    • Han-Yi Fu
    • , Daniel Picot
    •  & Francis-André Wollman

  • Article
    | Open Access

    The dominant male-sterile geneMs2 has facilitated the release of hundreds of wheat-breeding lines and cultivars in China. Here Ni et al. describe the cloning of the Ms2 gene, which appears as an orphan gene in the Triticinae, and show that Ms2 can be used to confer male sterility in wheat, barley and Brachypodium.

    • Fei Ni
    • , Juan Qi
    •  & Daolin Fu

  • Article
    | Open Access

    The mechanistic coupling of cell growth and cell cycle control with cell size regulation in tissues is not well understood. Here, the authors show that within the shoot apical meristem of Arabidopsis cell size depends on developmental stage, genotype and environmental signals; however cell growth and cell division are cell-autonomously coordinated.

    • Angharad R. Jones
    • , Manuel Forero-Vargas
    •  & James A. H. Murray

  • Article
    | Open Access

    Genome assembly for many plant species can be challenging due to large size and high repeat content. Here, the authors usein vitroproximity ligation to assemble the genome of lettuce, revealing a family-specific triplication event and providing a comprehensive reference genome for a member of the Compositae.

    • Sebastian Reyes-Chin-Wo
    • , Zhiwen Wang
    •  & Richard W. Michelmore

  • Article
    | Open Access

    Symbiosis with nitrogen-fixing bacteria (rhizobia) aids the growth of many legume species, but may also restrict their ability to colonize new regions lacking suitable rhizobia. Here, the authors show that symbiotic legumes are indeed less likely to become established in new regions than their non-symbiotic relatives.

    • Anna K. Simonsen
    • , Russell Dinnage
    •  & Peter H. Thrall

  • Article
    | Open Access

    Peking-type and PI 88788-type soybeans are both used as sources of resistance against soybean cyst nematode. Here the authors show that in contrast to PI 88788-type resistance, whereGmSNAP18 acts in combination with two neighbouring genes, in Peking-type resistance GmSNAP18 acts with GmSHMT08to confer resistance.

    • Shiming Liu
    • , Pramod K. Kandoth
    •  & Khalid Meksem

  • Article
    | Open Access

    Low temperature is a major factor limiting productivity in rice. Here the authors show that theCTB4a gene confers cold tolerance to japonicavarieties adapted to cold habitats at the booting stage of development, and propose that CTB4a acts via an interaction with the beta subunit of ATP synthase.

    • Zhanying Zhang
    • , Jinjie Li
    •  & Zichao Li

  • Article
    | Open Access

    The N-end rule pathway targets substrate proteins for proteasomal degradation. Here, Whiteet al. show that ArabidopsisPLANT CYSTEINE OXIDASEs show dioxygenase activity producing Cys-sulfinic acid at the N-terminus of target proteins, which then act as direct substrates for arginyl transferase.

    • Mark D. White
    • , Maria Klecker
    •  & Emily Flashman

  • Article
    | Open Access

    Pollinators are thought to be a driver of plant diversification, but their effects are difficult to disentangle from those of other biotic and abiotic factors. Here, the authors let plants evolve under different pollination regimes and show rapid and divergent evolution of plant height, floral traits and mating system.

    • Daniel D. L. Gervasi
    •  & Florian P Schiestl

  • Article
    | Open Access

    The phenolic polymer lignin is thought to have contributed to adaptation of early land plants to terrestrial environments. Here Renaultet al. show that moss, which does not produce lignin, contains an ancestral phenolic metabolism pathway that produces a phenol-enriched cuticle and prevents desiccation.

    • Hugues Renault
    • , Annette Alber
    •  & Danièle Werck-Reichhart

  • Article
    | Open Access

    Miniature inverted-repeat transposable elements (MITEs) are common components of eukaryotic genomes. Here the authors show that a stowaway-like MITE in the 3′-untranslated region of the riceGhd2gene can suppress translation in a DCL3a-dependent manner representing a novel role for transposons in translation.

    • Jianqiang Shen
    • , Juhong Liu
    •  & Lizhong Xiong

  • Article
    | Open Access

    Brassinosteroid (BR) signalling regulates plant development via the BES1/BZR1 family of transcription factors. Here the authors show that BES1 activity can be modified by the drought-responsive RD26 transcription factor providing a molecular basis for the interaction between drought and BR signalling.

    • Huaxun Ye
    • , Sanzhen Liu
    •  & Yanhai Yin

  • Article
    | Open Access

    TheLotus japonicus LysM receptor kinase EPR3 perceives rhizobial exopolysaccharides to initiate infection of the root epidermis. Here the authors show that EPR3 also mediates infection thread progression in the root cortex and show that key transcription factors that regulate symbiosis specify the expression of Epr3.

    • Yasuyuki Kawaharada
    • , Mette W. Nielsen
    •  & Jens Stougaard

  • Article
    | Open Access

    Volatile organic compounds (VOC) emitted by vegetation influence cloud formation, yet the impact of environmental stresses remains little known. Here, manipulation experiments reveal insect infestation and heat stress are linked to induced VOC and constitutive VOC emissions shifts, respectively.

    • D. F. Zhao
    • , A. Buchholz
    •  & Th. F. Mentel

  • Article
    | Open Access

    Turnip mosaic virusinfection increases the performance of aphid vectors on host plants. Here the authors show that this phenomenon requires relocalization of a viral protease to host cell vacuoles and that this only occurs when aphids are present, suggesting a viral protein responds dynamically to a vector.

    • Aurélie Bak
    • , Andrea L. Cheung
    •  & Clare L. Casteel

  • Article
    | Open Access

    Cpf1 is a type V CRISPR effector protein that has different target and guide RNA requirements compared to Cas9, thus offering an addition tool for precision genome editing. Here Kimet al. show that Cpf1 ribonucleoprotein can be introduced into protoplasts and used for transgene-free gene editing in plants.

    • Hyeran Kim
    • , Sang-Tae Kim
    •  & Sang-Gyu Kim

  • Article
    | Open Access

    Population structure of the model plantArabidopsis thaliana is shaped by glacial refugia and recent admixture. Here the authors show that genetically distinct groups of A. thalianahave spread east-west across Europe since the most recent ice age, likely as a result of human activity.

    • Cheng-Ruei Lee
    • , Hannes Svardal
    •  & Magnus Nordborg

  • Article
    | Open Access

    Peptide hormones play versatile roles in plant development and environmental responses. Here the authors report the engineering of a synthetic plant peptide that acts on meristems through interaction with both the CLV1 and TDR/PXY receptors ofArabidopsis thaliana.

    • Yuki Hirakawa
    • , Hidefumi Shinohara
    •  & Naoyuki Uchida

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