Article
|
Open Access
Featured
-
-
Article
| Open AccessDisentangling the genetic basis of rhizosphere microbiome assembly in tomato
Genetics factors involved in rhizosphere microbiomes assembly remain largely elusive. Here, the authors integrate microbiomics and quantitative plant genetics to reveal genetic loci associated with specific microbes and rhizobacterial traits underlying microbiome assembly in tomato.
- Ben O. Oyserman
- , Stalin Sarango Flores
- & Jos M. Raaijmakers
-
Article
| Open AccessIdentifying plant genes shaping microbiota composition in the barley rhizosphere
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere. Here, the authors report QTLs and the associated candidate genes underlying rhizosphere microbiome composition in barley.
- Carmen Escudero-Martinez
- , Max Coulter
- & Davide Bulgarelli
-
Article
| Open AccessThe 3D architecture of the pepper genome and its relationship to function and evolution
The organization of chromatin into self-interacting domains is universal among eukaryotic genomes. Here, the authors report a reference-grade pepper genome assembly and use this reference to help describe the relationship among 3D chromatin conformation, chromatin function, and gene expression.
- Yi Liao
- , Juntao Wang
- & Changming Chen
-
Article
| Open AccessA role for ascorbate conjugates of (+)-catechin in proanthocyanidin polymerization
Proanthocyanidins are natural polymers of flavan-3-ols produced by plants. Here the authors provide genetic and biochemical evidence for the involvement of ascorbate linked flavan-3-ol oligomers in the extension of the proanthocyanidin chain.
- Keji Yu
- , Richard A. Dixon
- & Changqing Duan
-
Article
| Open AccessChIP-Hub provides an integrative platform for exploring plant regulome
A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states.
- Liang-Yu Fu
- , Tao Zhu
- & Dijun Chen
-
Article
| Open AccessA highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants
The plant xylem microbiota remains understudied. Here, the authors characterise the xylem microbiota in maize plants finding that some bacteria carried N fixing genes. By using synthetic communities the authors confirm that xylem inhabiting and N fixing bacteria provide the host plant with N.
- Liyu Zhang
- , Meiling Zhang
- & Chao Ai
-
Article
| Open AccessPhysiological adaptive traits are a potential allele reservoir for maize genetic progress under challenging conditions
Phenomic and genomic approaches are required to evaluate the progress of breeding strategies. Here, the authors analyse 65 years of genetic progress in maize, showing that breeders have selected traits with stable effects on yield whereas not for adaptive traits key for climate change adaptation.
- Claude Welcker
- , Nadir Abusamra Spencer
- & François Tardieu
-
Article
| Open AccessDrought-exposure history increases complementarity between plant species in response to a subsequent drought
Using experimental communities of grassland species, this study shows that drought-exposure history can accelerate recovery from subsequent drought through increased niche complementarity between species. This transgenerational effect may enhance the sustainability of biodiversity and ecosystem functioning in a future with more frequent droughts.
- Yuxin Chen
- , Anja Vogel
- & Bernhard Schmid
-
Article
| Open AccessA Catharanthus roseus Fe(II)/α-ketoglutarate-dependent dioxygenase catalyzes a redox-neutral reaction responsible for vindolinine biosynthesis
Catharanthus roseus is the source for anticancer drug vinblastine and other medicinal monoterpenoid indole alkaloids. Here the authors characterize an Fe/2OG dioxygenase, vindolinine synthase, which catalyzes an unusual redox-neutral reaction leading to alkaloid diversity.
- Jasmine Ga May Eng
- , Mohammadamin Shahsavarani
- & Yang Qu
-
Article
| Open AccessA functionally conserved STORR gene fusion in Papaver species that diverged 16.8 million years ago
The STORR gene fusion event is a key step in the evolution of benzylisoquinoline alkaloid metabolism in opium poppy. Here, the authors combine phylogenetic, transcriptomic, metabolomic, biochemical and genomic analyses to show the STORR gene fusion occurred only once between 16.8-24.1 million years ago in Papaver species.
- Theresa Catania
- , Yi Li
- & Ian A. Graham
-
Article
| Open AccessPOWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean
In soybean production, level of seed protein frequently shows a negative correlation with seed oil content and yield. Here, the authors report a CCT gene pleiotropically regulates these traits and the selection of larger seeds determining allele leads to higher oil content but lower protein content in soybean cultivars.
- Wolfgang Goettel
- , Hengyou Zhang
- & Yong-qiang Charles An
-
Article
| Open AccessCloning of the broadly effective wheat leaf rust resistance gene Lr42 transferred from Aegilops tauschii
The Aegilops tauschii-derived leaf rust resistance gene Lr42 has been widely used for breeding resistance wheat cultivars, but the molecular basis is unknown. Here, the authors show that Lr42 encodes an NLR-type of disease resistance gene by bulked segregant mapping in Ae. tauschii and confirm its function in common wheat.
- Guifang Lin
- , Hui Chen
- & Sanzhen Liu
-
Article
| Open AccessDosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize
The role of miRNAs in genome imbalance is unclear. Here, the authors show that cis miRNAs in aneuploids present a predominant gene-dosage effect, whereas trans miRNAs trend toward the inverse level by examining global miRNA modulation in haploid and diploid aneuploids with the varied dosage of multiple chromosomal segments in maize.
- Xiaowen Shi
- , Hua Yang
- & James A. Birchler
-
Article
| Open AccessIdentification of positive and negative regulators of antiviral RNA interference in Arabidopsis thaliana
Whether natural variations of plant virus resistance are enriched in genes of RNA interference pathway is unknown. Here, via genome-wide association studies, the authors identify regulators of the RDR6 and DCL2 antiviral pathways are involved in quantitative resistance to cucumber mosaic virus in Arabidopsis.
- Si Liu
- , Meijuan Chen
- & Shou-Wei Ding
-
Article
| Open AccessNitrogen represses haustoria formation through abscisic acid in the parasitic plant Phtheirospermum japonicum
Parasitic plants obtain nutrients from their hosts. Here the authors show that nitrogen sufficiency suppresses parasitism in the root parasite Phtheirospermum japonicum by increasing levels of the phytohormone ABA suggesting that the degree of parasitism is regulated by nutrient availability.
- Anna Kokla
- , Martina Leso
- & Charles W. Melnyk
-
Article
| Open AccessExact simulation of pigment-protein complexes unveils vibronic renormalization of electronic parameters in ultrafast spectroscopy
Multimode vibronic mixing in model photosynthetic systems revealed by numerically exact simulations is shown to strongly modify linear and non-linear optical responses and facilitate the persistence of coherent dynamics.
- F. Caycedo-Soler
- , A. Mattioni
- & M. B. Plenio
-
Article
| Open AccessA 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data
Single-cell transcriptomics allows gene expression heterogeneity to be assessed at cellular resolution but the original location of each cell is unknown. Here the authors combine single nuclei RNA-seq with 3D spatial reconstruction of floral meristems to link gene activities with morphology.
- Manuel Neumann
- , Xiaocai Xu
- & Jose M. Muino
-
Article
| Open AccessCooperative regulation of PBI1 and MAPKs controls WRKY45 transcription factor in rice immunity
The U-box type ubiquitin ligase PUB44 positively regulates pattern-triggered immunity in rice. Here the authors identify a PUB44 substrate whose degradation is required for activation of the WRKY45 transcription factor upon immune elicitation.
- Kota Ichimaru
- , Koji Yamaguchi
- & Tsutomu Kawasaki
-
Article
| Open AccessPOD1-SUN-CRT3 chaperone complex guards the ER sorting of LRR receptor kinases in Arabidopsis
Cargo transport from the ER to the Golgi is highly selective. Here the authors identify three secretory pathway localized proteins that regulate ER sorting of receptor kinases in Arabidopsis and are required to support pollen tube growth.
- Yong Xue
- , Jiang-Guo Meng
- & Wei-Cai Yang
-
Article
| Open AccessPolymer-coated carbon nanotube hybrids with functional peptides for gene delivery into plant mitochondria
The delivery of genetic material into plants is challenging due to the cell wall barrier. Here, the authors hybridize polymer-coated carbon nanotubes with functional peptides to deliver plasmid DNA cargo into intact plant mitochondria for transient expression and homologous recombination at high efficiency.
- Simon Sau Yin Law
- , Geoffrey Liou
- & Keiji Numata
-
Article
| Open AccessArabidopsis cryptochrome 2 forms photobodies with TCP22 under blue light and regulates the circadian clock
Cryptochrome signaling has been reported to regulate circadian oscillations in plants. Here the authors show that CRY2 and the TCP22 transcription factors can form photobodies in a blue light dependent manner and induce expression of CCA1, a core component of the circadian oscillator.
- Weiliang Mo
- , Junchuan Zhang
- & Zecheng Zuo
-
Article
| Open AccessAgrobacterium expressing a type III secretion system delivers Pseudomonas effectors into plant cells to enhance transformation
Agrobacterium infection can cause defense responses in many plants, which leads to transformation recalcitrance. Here, the authors express type III secretion system in Agrobacterium to deliver effector proteins into plant cells to suppress host defense responses and thus enhance transformation in some plant species.
- Vidhyavathi Raman
- , Clemencia M. Rojas
- & Kirankumar S. Mysore
-
Article
| Open AccessDandelion pappus morphing is actuated by radially patterned material swelling
The dandelion pappus opens and closes reversibly to tune seed dispersal according to environmental moisture levels. Here the authors combined experiments with a computational model to show that pappus closure is coordinated by radially-patterned tissue swelling at the base of floral organs.
- Madeleine Seale
- , Annamaria Kiss
- & Naomi Nakayama
-
Article
| Open AccessCryo-EM structures of thylakoid-located voltage-dependent chloride channel VCCN1
VCCN1 is a plant homolog of bestrophin channels and tunes photoreaction as a voltage-gated anion channel at thylakoids. Here, authors report the cryo-EM structures and functional features of apple VCCN1, with insights into its activation mechanism.
- Tatsuya Hagino
- , Takafumi Kato
- & Osamu Nureki
-
Article
| Open AccessStructure of the Arabidopsis guard cell anion channel SLAC1 suggests activation mechanism by phosphorylation
The anion channel SLAC1 controls stomatal closure upon phosphoactivation. Here via structural analysis and electrophysiology, the authors propose an inhibition-release model where phosphorylation causes dissociation of a cytosolic plug from the SLAC1 transmembrane domains to induce conformational change in the pore-forming helices.
- Yawen Li
- , Yinan Ding
- & Linfeng Sun
-
Article
| Open AccessCompetition contributes to both warm and cool range edges
Using a field experiment, this study shows that both lowland and alpine plant species experience greater competitive effects and a reduced ability to coexist towards their elevation range edges due to increased niche overlap and competitive inequality. These findings suggest competition helps set both lower and upper elevation range limits.
- Shengman Lyu
- & Jake M. Alexander
-
Article
| Open AccessSpindle motility skews division site determination during asymmetric cell division in Physcomitrella
In plants, the site of asymmetric cell division (ACD) is generally thought to be determined by the preprophase band and the mitotic spindle is typically static. However, the authors show here that the moss Physcomitrella has motile mitotic spindles that can skew ACD in the absence of preprophase bands.
- Elena Kozgunova
- , Mari W. Yoshida
- & Gohta Goshima
-
Article
| Open AccessDichotomy of the BSL phosphatase signaling spatially regulates MAPK components in stomatal fate determination
In Arabidopsis, BSL1 localizes to the cell cortex and activates the MAPKK Kinase YDA to inhibit stomatal production. Here the authors show that three other BSL proteins BSL2, BSL3, and BSU1 act in the nucleus to deactivate MPK6 and promote stomatal formation.
- Xiaoyu Guo
- , Xue Ding
- & Juan Dong
-
Article
| Open AccessThe barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei
Leaf rust is an economically significant disease of barley. Here the authors describe cloning of the barley Rph3 leaf rust resistance gene and reveal it encodes a predicted transmembrane protein that is expressed upon infection by Rph3-avirulent Puccinia hordei isolates.
- Hoan X. Dinh
- , Davinder Singh
- & Mohammad Pourkheirandish
-
Article
| Open AccessLimits to reproduction and seed size-number trade-offs that shape forest dominance and future recovery
The relationships that control seed production in trees are key to understand evolutionary pressures that have shaped forests. A global synthesis of fecundity data reveals that while seed production is not constrained by a strict size-number trade-off, it is influenced by taxonomy and nutrient allocation.
- Tong Qiu
- , Robert Andrus
- & James S. Clark
-
Article
| Open AccessThe initial charge separation step in oxygenic photosynthesis
The photosystem II reaction center (PSII-RC) is a model system to understand the initial steps of photosynthesis, but its excited state dynamics is difficult to disentangle with most spectroscopic methods. Here the authors perform a two-dimensional electronic-vibrational spectroscopic study of PSII-RC, providing detailed insight into such dynamics and into the mechanism of charge separation.
- Yusuke Yoneda
- , Eric A. Arsenault
- & Graham R. Fleming
-
Article
| Open AccessA dirigent family protein confers variation of Casparian strip thickness and salt tolerance in maize
Most crops are farmed under high transpiring environments, but our understanding of transpiration-dependent salt tolerance (TDST) remains limited. Here, the authors report a dirigent family protein is responsible for TDST by affecting lignin deposition at Casparian strip barrier and transportation of Na+ across the endodermis.
- Yanyan Wang
- , Yibo Cao
- & Caifu Jiang
-
Article
| Open AccessA fungal extracellular effector inactivates plant polygalacturonase-inhibiting protein
Plants produce polygalacuturonase-inhibiting proteins (PGIPs) to counteract cell wall degradation by pathogenic microbes. Here the authors show that Sclerotinia sclerotiorum, a fungal pathogen that causes stem rot disease, secretes a PGIP-inactivating effector to diminish plant resistance.
- Wei Wei
- , Liangsheng Xu
- & Weidong Chen
-
Article
| Open AccessDeletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata
Unlike Panax species, which can produce dammarane-type saponins, Aralia elata can only synthesize oleananetype saponins. Here, the authors reveal that the loss of the dammaranediol synthase-encoding gene and tandem duplication of triterpene biosynthetic genes drive structural divergences of saponins between the two genera.
- Yu Wang
- , He Zhang
- & Yuhua Li
-
Article
| Open AccessA natural allele of OsMS1 responds to temperature changes and confers thermosensitive genic male sterility
Thermosensitive genic male-sterile (TGMS) lines are widely used for two-line hybrid rice breeding, but the mechanism of TGMS has not been fully elucidated. Here, the authors show that natural allele of the OsMS1 gene, encoding a histone binding PHD finger protein, responds to temperature change and confers TGMS in rice.
- Lunying Wu
- , Xiaohui Jing
- & Yunhai Li
-
Article
| Open AccessHigh-quality genome and methylomes illustrate features underlying evolutionary success of oaks
The genus Quercus (oaks) has diversified into over 450 species which often play dominant roles in the ecosystems in which they occur. Here the authors present a genome and methylome for a California endemic oak, Quercus lobata, and describe features relevant to its evolutionary success.
- Victoria L. Sork
- , Shawn J. Cokus
- & Steven L. Salzberg
-
Article
| Open AccessGenomic distances reveal relationships of wild and cultivated beets
While a large amount of genomic resources is available, the phylogeny of wild and cultivated beets remains unclear. Here, the authors use the k-mer-based Mash method to analyze resequenced genomes of 606 accessions of the genus Beta and reveal Greece as the domestication site of sugar beet.
- Felix L. Sandell
- , Nancy Stralis-Pavese
- & Juliane C. Dohm
-
Article
| Open AccessA pair of non-Mendelian genes at the Ga2 locus confer unilateral cross-incompatibility in maize
Unilaterial cross-incompatibility (UCI) systems are regulated by a male-female gene pair that are genetically linked, but no pair of the male and female determinants has been isolated so far. Here, the authors report the cloning of a pair of pectin methylesterases encoding genes at the Ga2 locus confer UCI in maize.
- Zhibin Chen
- , Zhaogui Zhang
- & Huabang Chen
-
Article
| Open AccessChromosome evolution and the genetic basis of agronomically important traits in greater yam
While greater yam provides food and income security for millions of people around the world, there are limited genomic resources available. Here, the authors report a chromosome-scale assembly of the greater yam genome as well as quantitative trait loci associated with anthracnose resistance and tuber traits.
- Jessen V. Bredeson
- , Jessica B. Lyons
- & Daniel S. Rokhsar
-
Article
| Open AccessGenomic evidence for homoploid hybrid speciation between ancestors of two different genera
Carpinus fangiana exhibits intermediate morphology between C. viminea and Ostrya rehderiana. Here, the authors report that Carpinus sect. Distegocarpus likely originate through homoploid hybrid speciation (HHS) during the early divergence between Carpinus and Ostrya through genomic analyses.
- Zefu Wang
- , Minghui Kang
- & Jianquan Liu
-
Article
| Open AccessStructural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC–LH1 supercomplex
Bacterial photosynthesis reflects the early stages of the evolution of photosynthesis. Here, the authors present a systematic study of the cryo-EM structures of the dimeric light harvesting–reaction center complexes and assembly variants from Rhodobacter sphaeroides, which delineated a hierarchical assembly pathway and quinone transport routes of the dimeric photosynthetic RC–LH1 core complex.
- Peng Cao
- , Laura Bracun
- & Lu-Ning Liu
-
Article
| Open AccessReshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax
The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.
- Zhen-Hui Wang
- , Xin-Feng Wang
- & Lin-Feng Li
-
Article
| Open AccessAsymmetric structure of the native Rhodobacter sphaeroides dimeric LH1–RC complex
Rhodobacter sphaeroides is a model organism for studying bacterial photosynthesis. Here, the authors present structures of its native dimeric and a protein-U-lacking monomeric light-harvesting-reaction center complexes, which reveal asymmetric features for the dimer and an altered shape for the monomer.
- Kazutoshi Tani
- , Ryo Kanno
- & Zheng-Yu Wang-Otomo
-
Article
| Open AccessRadiationless mechanism of UV deactivation by cuticle phenolics in plants
Phenolics are abundant in plant cuticles. Here, via transient absorption spectroscopy and quantum chemical calculations, the authors propose a model by which cuticle phenolics provide photoprotection due to ultrafast and non-radiative excited state deactivation combined with fluorescence emission.
- Ana González Moreno
- , Abel de Cózar
- & Antonio Heredia
-
Article
| Open AccessROS homeostasis mediated by MPK4 and SUMM2 determines synergid cell death
Synergid cells undergo programmed cell death following pollen tube reception and successful fertilization. Here the authors show that premature synergid cell death is prevented by the mitogen activated protein kinase MPK4 and the R protein SUMM2 which maintain ROS homeostasis in Arabidopsis.
- Ronny Völz
- , William Harris
- & Yong-Hwan Lee
-
Article
| Open AccessStructural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Fucoxanthin chlorophyll a/c-binding proteins (FCPs) harvest light energy in diatoms. The authors analyzed a structure of PSII-FCPII supercomplex at high resolution by cryo-EM, which identified each FCP subunit and pigment network in the supercomplex.
- Ryo Nagao
- , Koji Kato
- & Jian-Ren Shen
-
Article
| Open AccessStructure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa
Photosystem I (PSI) harvest and transfer light energy into chemical energy in photosynthesis. Here, authors analyzed its tetrameric structure from a glaucophyte alga by cryo-EM, providing insights into an evolutionary turning-point of PSI.
- Koji Kato
- , Ryo Nagao
- & Jian-Ren Shen
-
Article
| Open AccessCyclophilin anaCyp40 regulates photosystem assembly and phycobilisome association in a cyanobacterium
Cyclophilins are proteins found in many organisms, where they can play roles as chaperones, in signal transduction, or other functions. Here, Yadav et al. show that a cyanobacterial cyclophilin is involved in stress responses and in assembly of photosynthetic complexes, and displays unique structural features.
- Shivam Yadav
- , Martin Centola
- & Enrico Schleiff
-
Article
| Open AccessA hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis
Cell division and expansion are carefully coordinated during organ growth. Here, the authors show that the SCL28 and SMOS1 transcription factors interact to regulate cyclin-dependent kinase inhibitors and promote cell size increase over division in Arabidopsis.
- Yuji Nomoto
- , Hirotomo Takatsuka
- & Masaki Ito
Browse broader subjects
Browse narrower subjects
- Biofuels
- Light responses
- Natural variation in plants
- Photosynthesis
- Plant biotechnology
- Plant breeding
- Plant cell biology
- Plant development
- Plant domestication
- Plant ecology
- Plant evolution
- Plant genetics
- Plant hormones
- Plant immunity
- Plant molecular biology
- Plant physiology
- Plant reproduction
- Plant signalling
- Plant stress responses
- Plant symbiosis
- Secondary metabolism
- Stomata
- Tropism