Plant sciences articles within Nature Communications

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  • Article
    | Open Access

    The shoot apical meristem of flowering plants transitions from forming leaves to floral organs. Here Higo et al. show that DNA methylation of many transposons that are hypermethylated in gametes is established in the SAM before flowering, suggesting it protects against harmful transposition long before germ cell differentiation.

    • Asuka Higo
    • , Noriko Saihara
    •  & Hiroyuki Tsuji

  • Article
    | Open Access

    Transposable element insertion polymorphisms (TIPs) are a potential source of large effect alleles. Here, the authors use genome resequencing data for 602 tomato accessions together with transcriptomic and extensive phenotypic information to investigate the contribution of TIPs to tomato diversity.

    • Marisol Domínguez
    • , Elise Dugas
    •  & Leandro Quadrana

  • Article
    | Open Access

    Floral phenotypes impact interactions between plants and pollinators. Here, the authors show that Moricandia arvensis displays discrete seasonal plasticity in floral phenotype, with large, lilac flowers attracting long-tongued bees in spring and small, rounded, white flowers attracting generalist pollinators in summer.

    • José M. Gómez
    • , Francisco Perfectti
    •  & Rubén Torices

  • Article
    | Open Access

    An insufficient amount of pollen transfer by pollinators (pollen limitation) could reduce plant reproduction in human-impacted landscapes. Here the authors conduct a global meta-analysis and find that pollen limitation is high in urban environments and depends of plant traits such as pollinator dependency.

    • Joanne M. Bennett
    • , Janette A. Steets
    •  & Tia-Lynn Ashman

  • Article
    | Open Access

    The significance of protein nanoclustering in cell polarization is unclear. Here Pan et al. show that auxin-induced TMK1/sterol nanoclustering as well as microtubule-based positive feedback regulation of the TMK1/sterol nanoclusters is critical for cell polarity formation in Arabidopsis.

    • Xue Pan
    • , Linjing Fang
    •  & Zhenbiao Yang

  • Article
    | Open Access

    Exopolysaccharides (EPS) are perceived by legumes and regulate symbiosis with rhizobia. Here the authors describe the structure of the Lotus EPS receptor, EPR3 and show that it has atypical βαββ and βαβ folds that represent a structural signature for a unique class of EPS receptors in the plant kingdom.

    • Jaslyn E. M. M. Wong
    • , Kira Gysel
    •  & Kasper R. Andersen

  • Article
    | Open Access

    Ralstonia solanacearum evades plant immunity by producing an atypical flagellin protein, thus causing bacterial wilt disease. Here, Wei et al. show that soybean has evolved a divergent flagellin receptor that recognises R. solanacearum flagellin and enhances wilt resistance when transferred to other plants.

    • Yali Wei
    • , Alexandra Balaceanu
    •  & Alberto P. Macho

  • Article
    | Open Access

    Wild teas are considered as valuable resource for studying domestication and breeding. Here, Zhang et al. report genome of wild tea DASZ and transcriptome of 217 accessions, which clarify pedigree of Chinese tea cultivars and show tea may not have undergone long-term artificial directional selection on flavor-related metabolites.

    • Weiyi Zhang
    • , Youjun Zhang
    •  & Weiwei Wen

  • Article
    | Open Access

    Strigolactones are a newly identified, but incompletely characterized class of plant hormones play crucial roles in plant development. Here the authors show that strigolactones prevent an auxin feedback-effect on PIN-FORMED (PIN) polarity and trafficking, thereby regulating vascular tissue formation and regeneration.

    • Jing Zhang
    • , Ewa Mazur
    •  & Jiří Friml

  • Article
    | Open Access

    Chinese chestnut is widely cultivated for nut production and harbors value as a genetic resource for restoration of American and European chestnut trees destroyed by chestnut blight. Here, the authors reveal the genomic basis of homoploid hybrid speciation within Castanea spp. and find the nonrandom distribution of reproductive barrier loci based on a high-quality reference genome.

    • Yongshuai Sun
    • , Zhiqiang Lu
    •  & Hui Ma

  • Article
    | Open Access

    There is mixed evidence for how temperature affects diversification rates. Here, authors use a supermatrix of nearly 20,000 rosid species, comprising almost a quarter of flowering plants, to show that tropical groups are older and speciated twice as slowly as their counterparts from cooler climates.

    • Miao Sun
    • , Ryan A. Folk
    •  & Robert P. Guralnick

  • Article
    | Open Access

    Epigenetic regulation can silence transposons and maintain gene expression. Here the authors survey Arabidopsis mutants defective in epigenetic regulation and show ectopic activation of thousands of cryptic TSSs and altered expression of nearby genes demonstrating the importance of suppressing spurious transcription.

    • Ngoc Tu Le
    • , Yoshiko Harukawa
    •  & Hidetoshi Saze

  • Article
    | Open Access

    CLE and CEP peptides regulate rhizobial symbiosis in legumes to balance the benefits of nitrogen fixation with the metabolic costs of nodule production. Here Laffont et al. show that cytokinin and bacterial Nod factors induce Medicago CEP7 which acts antagonistically to CLE13 to fine-tune nodulation.

    • Carole Laffont
    • , Ariel Ivanovici
    •  & Florian Frugier

  • Article
    | Open Access

    MicroRNA2118 induces the production of phased small interfering RNAs (phaisRNAs) in plants. Here the authors show that rice miR2118 is required for both male and female fertility and supports the production of atypical U-rich 21 nt phasiRNAs that are abundant in anther walls.

    • Saori Araki
    • , Ngoc Tu Le
    •  & Reina Komiya

  • Article
    | Open Access

    Some plants produce toxic isothiocyanates that protect them against pathogens. Here, Chen et al. show that the plant pathogenic fungus Sclerotinia sclerotiorum converts isothiocyanates into non-toxic compounds via glutathione conjugation and, more effectively, via hydrolysis to amines using an isothiocyanate hydrolase.

    • Jingyuan Chen
    • , Chhana Ullah
    •  & Daniel G. Vassão

  • Article
    | Open Access

    It is unclear whether rapid global change will lead to unexpected trait combinations. In this global meta-analysis on vascular plants, Cui et al. show that, although within-species responses do not always follow the leaf economic spectrum, the slopes of interspecific trait relationships are robust to rapid environmental change.

    • Erqian Cui
    • , Ensheng Weng
    •  & Jianyang Xia

  • Article
    | Open Access

    Sieve element differentiation in Arabidopsis roots requires two antagonistic regulators of auxin efflux, BRX and PAX. Here the authors show that together they coordinate sieve element formation by preventing cell fate bistability emerging from AUX1-mediated competition for auxin between neighboring cells.

    • Bernard Moret
    • , Petra Marhava
    •  & Kirsten H. W. ten Tusscher

  • Article
    | Open Access

    Hydroxyglutarate synthase (HglS) converts 2-oxoadipate to D-2- hydroxyglutarate during lysine catabolism in bacteria. Here the authors use structural and biochemical approaches to show that HglS acts via successive decarboxylation and intramolecular hydroxylation and that homologous enzymes catalyze the final step of lysine catabolism in plants.

    • Mitchell G. Thompson
    • , Jacquelyn M. Blake-Hedges
    •  & Jay D. Keasling

  • Article
    | Open Access

    Small RNAs act to regulate gene or transposon activity during plant development. Here, the authors show that maize Dicer-like 5 is required for 24-nt phased, secondary small interfering RNA production in anthers and that dicer-like 5 mutants show abnormal tapetal development and temperature-sensitive sterility.

    • Chong Teng
    • , Han Zhang
    •  & Virginia Walbot

  • Article
    | Open Access

    Grapevine is one of a few ancestrally dioecious crops that are reverted to hermaphroditism during domestication. Here, the authors identify candidate genes related to male- and female-sterility in grapes and describe the genetic process that led to hermaphroditism during domestication.

    • Mélanie Massonnet
    • , Noé Cochetel
    •  & Dario Cantu

  • Article
    | Open Access

    Reduction of pollen grain number is widespread in selfing plants, but the determining gene is unknown. Here, the authors show that a ribosome-biogenesis factor encoding gene RDP1 is responsible for adaptive reduction of male gamete number in Arabidopsis thaliana.

    • Takashi Tsuchimatsu
    • , Hiroyuki Kakui
    •  & Kentaro K. Shimizu

  • Article
    | Open Access

    Mediator is a multiprotein complex required to activate gene transcription by RNAPII. Here, the authors report that MED12 and MED13 are conditional positive regulators that facilitate the expression of genes depleted in active chromatin marks and the induction of gene expression in response to environmental stimuli in Arabidopsis.

    • Qikun Liu
    • , Sylvain Bischof
    •  & Steven E. Jacobsen

  • Article
    | Open Access

    B chromosomes are supernumerary chromosomes exhibiting dramatic differences between different organs in same species. Here, the authors show programmed B chromosome elimination in goatgrass starts at the onset of embryo differentiation by nondisjunction of chromatids, anaphase lagging, and ends with the degradation of micronucleated DNA.

    • Alevtina Ruban
    • , Thomas Schmutzer
    •  & Andreas Houben

  • Article
    | Open Access

    Comprehensive epigenomic maps of various rice varieties are still unavailable. Here, the authors report the development of eChIP as a fast and low-input upgrade of regular plant ChIP-seq protocol for epigenome analysis of 20 rice varieties and annotate over 80% of the genome with different epigenome properties for transcriptional regulation.

    • Lun Zhao
    • , Liang Xie
    •  & Xingwang Li

  • Article
    | Open Access

    Increasing grain yield needs to be put in the context of environmental stress. Here, the authors reveal that a UDP-glucosyltransferase is associated with regulation of rice grain size, abiotic stress tolerance, flavonoid-mediated auxin signaling, and redirection of carbon flux to flavonoid glycosides synthesis.

    • Nai-Qian Dong
    • , Yuwei Sun
    •  & Hong-Xuan Lin

  • Article
    | Open Access

    The association between leguminous plants and rhizobial bacteria is a paradigmatic example of a symbiosis driven by metabolic exchanges. Here, diCenzo et al. report the reconstruction and modelling of a genome-scale metabolic network of the plant Medicago truncatula nodulated by the bacterium Sinorhizobium meliloti.

    • George C. diCenzo
    • , Michelangelo Tesi
    •  & Marco Fondi

  • Article
    | Open Access

    Gene isoforms result from variable transcription start sites (TSSs) and polyadenylation sites (PASs) at the end of transcripts. Here, the authors perform transcript isoform sequencing and find widespread promoter- proximal transcriptional termination in Arabidopsis, suggesting this may represent a checkpoint that regulates plant gene expression.

    • Quentin Angelo Thomas
    • , Ryan Ard
    •  & Sebastian Marquardt

  • Article
    | Open Access

    Snow algae bloom along the coast of Antarctica and are likely to be biogeochemically important. Here, the authors produced the first map of such blooms, show that they are driven by warmer temperatures and proximity to birds and mammals, and are likely to increase given projected climate changes.

    • Andrew Gray
    • , Monika Krolikowski
    •  & Matthew P. Davey

  • Article
    | Open Access

    Alfalfa is an important forage crop, but genetic improvement is challenging due to the lack of a reference genome and an efficient genome editing protocol. Here, the authors report the chromosome-level assembly of the autotetraploid genome and a CRISPR/Cas9-based transgene-free genome editing protocol.

    • Haitao Chen
    • , Yan Zeng
    •  & Qiang Qiu

  • Article
    | Open Access

    One of the major photosynthetic light-harvesting complexes (LHCs) are fucoxanthin chlorophyll a/c-binding proteins (FCPs), which are present in diatoms, a major group of algae. Here, the authors present the cryo-EM structure of the photosystem I-FCP (PSI-FCPI) supercomplex isolated from the marine centric diatom Chaetoceros gracilis that contains 16 FCPI subunits surrounding the PSI core and discuss possible excitation energy transfer pathways.

    • Ryo Nagao
    • , Koji Kato
    •  & Fusamichi Akita

  • Article
    | Open Access

    TRANSPARENT TESTA19 (TT19) encodes a glutathione S-transferase which functions in anthocyanin stabilization and vacuolar transport. Here, by tt19 suppressor screening, the authors show that RDR6/SGS3/DCL4 siRNA pathway constituents synergistically interact with components of the flavonoid pathway to control carbon metabolism.

    • Nan Jiang
    • , Aimer Gutierrez-Diaz
    •  & Erich Grotewold

  • Article
    | Open Access

    Cytosolic ion gradients in growing pollen tubes are thought to be required for polar growth. Here the authors show that the Arabidopsis plasma membrane H+ ATPases, AHA6, AHA8, and AHA9, maintain tip-to-shank proton gradients, oscillations in cytosolic pH and actin organization to enable pollen tube elongation.

    • Robert D. Hoffmann
    • , Maria Teresa Portes
    •  & Michael Palmgren

  • Article
    | Open Access

    Auxin-mediated recruitment of AUX/IAAs by the F-box protein TIR1 prompts rapid AUX/IAA ubiquitylation and degradation. By resolving auxin receptor topology, the authors show that intrinsically disordered regions near the degrons of two Aux/IAA proteins reinforce complex assembly and position Aux/IAAs for ubiquitylation.

    • Michael Niemeyer
    • , Elena Moreno Castillo
    •  & Luz Irina A. Calderón Villalobos

  • Article
    | Open Access

    Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.

    • Shujun Ou
    • , Jianing Liu
    •  & Doreen Ware

  • Article
    | Open Access

    Plant metacaspases mediate immune response following activation by Ca2+. Here, via crystallography and functional analyses, the authors show that a linker domain in Arabidopsis Metacaspase 4 blocks substrate access to the active site but is cleaved multiple times in the presence of Ca2+ to allow enzyme activation.

    • Ping Zhu
    • , Xiao-Hong Yu
    •  & Qun Liu

  • Article
    | Open Access

    WUSCHEL is a homeodomain transcription factor that is essential for stem cell maintenance in the plant shoot apical meristem. Here, via structural and biochemical approaches, Sloan et al. show that strong WUSCHEL binding to preferential target motifs can be attributed to dimer formation that stabilizes DNA binding.

    • Jeremy Sloan
    • , Jana P. Hakenjos
    •  & Jan U. Lohmann

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