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| Open AccessA membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat
Winter wheat cultivar Forno harbors a race-specific leaf rust resistance locus Lr14a, but the causative gene is unknown. Here, the authors show that Lr14a encodes a membrane-localized protein containing ankyrin repeats and Lr14a-containing segments have been introgressed into the bread wheat gene pool multiple times.
- Markus C. Kolodziej
- , Jyoti Singla
- & Beat Keller
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Article
| Open AccessArabidopsis ACINUS is O-glycosylated and regulates transcription and alternative splicing of regulators of reproductive transitions
AtACINUS is an Arabidopsis homolog of a mammalian splicing regulator and previously found to be O-GlcNAcyated. Here Bi et al. characterize the interactors and targets of AtACINUS, show it is required for development and stress responses and provide evidence that its O-glycosylation affects alternative splicing.
- Yang Bi
- , Zhiping Deng
- & Zhi-Yong Wang
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Article
| Open AccessMechanisms of feedback inhibition and sequential firing of active sites in plant aspartate transcarbamoylase
Aspartate transcarbamoylase acts in de novo pyrimidine biosynthesis and in plants is regulated by feedback inhibition via uridine 5-monophosphate (UMP). Here Bellin et al. describe the structural basis for this feedback inhibition, showing that UMP blocks the active site by binding to a plant specific UMP recognition loop.
- Leo Bellin
- , Francisco Del Caño-Ochoa
- & Santiago Ramón-Maiques
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Article
| Open AccessMultifunctional evolution of B and AGL6 MADS box genes in orchids
B class AP3/PI and AGL6-like MADS proteins determine lips and sepals/petals identities in orchids. Here, the authors characterize the extended function of OAP3/OPI/OAGL6 in regulating the specific structure of the lateral sepals, pigmentation/senescence of the perianth and abscission of the pedicel.
- Hsing-Fun Hsu
- , Wei-Han Chen
- & Chang-Hsien Yang
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Article
| Open AccessThe singularity response reveals entrainment properties of the plant circadian clock
Phase response curves reveal how biological clocks respond to stimuli applied during different circadian phases but can be costly to produce. Here Masuda et al. show that phase response curves for plants can be reconstructed by monitoring how a desynchronized population responds to a single stimulus.
- Kosaku Masuda
- , Isao T. Tokuda
- & Hirokazu Fukuda
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Article
| Open AccessGenetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis
The establishment of symbiotic interaction between Aeschynomene evenia and photosynthetic bradyrhizobia doesn’t involve the canonical Nod factors and infection threads. Here, the authors assemble the draft genome of A. evenia and identify a receptor-like kinase in mediating the symbiotic interaction.
- Johan Quilbé
- , Léo Lamy
- & Jean-François Arrighi
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Article
| Open AccessPh2 encodes the mismatch repair protein MSH7-3D that inhibits wheat homoeologous recombination
In the allohexaploid genome of wheat, meiotic recombination between homoeologues is suppressed through the action of several loci. Here, the authors report the cloning of the long sought-after gene Ph2 and show its function in reduction of homoeologous recombination.
- Heïdi Serra
- , Radim Svačina
- & Pierre Sourdille
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Article
| Open AccessPlasma membrane H+-ATPase overexpression increases rice yield via simultaneous enhancement of nutrient uptake and photosynthesis
Improved utilisation of nitrogen and carbon could boost agricultural productivity. Here Zhang et al. show that overexpression of a single gene, encoding the plasma membrane H+ -ATPase 1 OSA1, is able to increase both carbon fixation via photosynthesis and nitrogen assimilation via ammonium uptake in rice.
- Maoxing Zhang
- , Yin Wang
- & Yiyong Zhu
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Article
| Open AccessGenomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism
Figs and their wasp pollinators are a classic example of coevolution. By assembling and analysing genomes from across the Ficus clade, authors suggest that fig hybridization driven by pollinator host-switching in this obligate pollination system, is more common than previously thought.
- Gang Wang
- , Xingtan Zhang
- & Jin Chen
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Article
| Open AccessRole of an ancient light-harvesting protein of PSI in light absorption and photoprotection
LHCR proteins are ancient chlorophyll a-binding antennas that evolved in diverse algae of the red lineage. Here Lu et al. characterize a red lineage LHCR mutant and show reduced oxidative damage in high light but attenuated growth under low light, thus demonstrating how LHCR proteins impact the balance between photoprotection and light harvesting.
- Yandu Lu
- , Qinhua Gan
- & Krishna K. Niyogi
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Article
| Open AccessPerception of a divergent family of phytocytokines by the Arabidopsis receptor kinase MIK2
Secreted peptides and cell-surface localized receptor kinases allow plants to modify growth and development according to external cues. Here, Rhodes et al. show that the MIK2 receptor perceives the SERINE RICH ENDOGENOUS PEPTIDE (SCOOP) family of phytocytokines and is capable of recognising Fusarium-derived SCOOP-like peptides.
- Jack Rhodes
- , Huanjie Yang
- & Cyril Zipfel
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Article
| Open AccessExpansion within the CYP71D subfamily drives the heterocyclization of tanshinones synthesis in Salvia miltiorrhiza
Salvia miltiorrhiza is a medicinal plant that can produce the bioactive tanshinones. Here, the authors report the improved genome assembly and reveal the possible roles of three CYP71Ds in catalyzing the reactions leading to the formation of the characteristic furan D-ring of transhinones.
- Ying Ma
- , Guanghong Cui
- & Luqi Huang
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Article
| Open AccessComprehensive genomic resources related to domestication and crop improvement traits in Lima bean
Lima bean is an important crop for improving food security in Latin America and elsewhere. Here, the authors assemble its genome, conduct population genomics analysis using genotyping-by-sequencing data, and identify differentially expressed genes between two pod developmental stages.
- Tatiana Garcia
- , Jorge Duitama
- & Maria Isabel Chacón-Sánchez
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Article
| Open AccessLong-term single-cell imaging and simulations of microtubules reveal principles behind wall patterning during proto-xylem development
Plant cell wall formation is directed by cortical microtubules, which produce complex patterns needed to support xylem vessels. Here, the authors perform live-cell imaging and simulations of Arabidopsis cells during proto-xylem differentiation to show how local microtubule dynamics control pattern formation.
- René Schneider
- , Kris van’t Klooster
- & Staffan Persson
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Article
| Open AccessLEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate
Pioneer transcription factors access their DNA binding motifs in closed chromatin and often act in cell fate reprogramming. Here, Jin et al. present biochemical evidence for a pioneer factor in plants and show that LFY promotes floral cell fate and locally unlocks chromatin by displacing histone H1 and recruiting SWI/SNF chromatin remodelers.
- Run Jin
- , Samantha Klasfeld
- & Doris Wagner
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Article
| Open AccessLife history, climate and biogeography interactively affect worldwide genetic diversity of plant and animal populations
A global analysis of population-level variation in genetic diversity for 727 plant and animal species finds that biogeography, life history traits and climate are important for predicting the distribution of local genetic diversity, and should be considered together when assessing the local conservation status of species.
- H. De Kort
- , J. G. Prunier
- & S. Blanchet
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Article
| Open AccessA network-based framework for shape analysis enables accurate characterization of leaf epidermal cells
While cell shape is crucial for function and development of organisms, versatile frameworks for cell shape quantification, comparison, and classification remain underdeveloped. Here, the authors use a network-based framework for Arabidopsis leaf epidermal cell shape characterization and classification.
- Jacqueline Nowak
- , Ryan Christopher Eng
- & Zoran Nikoloski
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Article
| Open AccessA wheat cysteine-rich receptor-like kinase confers broad-spectrum resistance against Septoria tritici blotch
Septoria tritici blotch (STB) is a devastating foliar disease affecting worldwide wheat production. Here, the authors report a cysteine-rich receptor-like kinase that can confer resistance to Zymoseptoria tritici, the pathogen that causes STB, and slow penetration and intercellular growth of the pathogen.
- Cyrille Saintenac
- , Florence Cambon
- & Thierry Langin
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Article
| Open AccessMale fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function
Active DNA demethylation is required for sexual reproduction in plants, but the underlying mechanisms are unknown. Here, the authors show that the DNA glycosylases DEMETER and REPRESSOR OF SILENCING 1 enable the DNA demethylation-dependent activation of genes involved in pollen tube progression.
- Souraya Khouider
- , Filipe Borges
- & Daniel Bouyer
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Article
| Open AccessChromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis
Ophiorrhiza pumila is a medicinal plant that can produce the anti-cancer monoterpene indole alkaloid (MIA) camptothecin. Here, the authors report its genome assembly and propose a working model for MIA evolution and biosynthesis through comparative genomics, synteny, and metabolic gene cluster analyses.
- Amit Rai
- , Hideki Hirakawa
- & Mami Yamazaki
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Article
| Open AccessSequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants
The nucleolus organizing region (NOR) consists of multiple, highly repetitive rDNA genes. Here Sims et al. use both long- and short-read sequencing to determine the organization and sequence of Arabidopsis NOR2 rDNA and show that different rRNA gene variants are integrated into translating ribosomes in a tissue-specific manner.
- Jason Sims
- , Giovanni Sestini
- & Peter Schlögelhofer
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Article
| Open AccessInositol pyrophosphates promote the interaction of SPX domains with the coiled-coil motif of PHR transcription factors to regulate plant phosphate homeostasis
Plants regulate phosphate homeostasis via the interaction of PHR transcription factors with SPX receptors bound to inositol pyrophosphate signaling molecules. Here the authors show that inositol pyrophosphate-bound SPX interacts with the coiled-coil domain of PHR, which regulates the oligomerization and activity of the transcription factor.
- Martina K. Ried
- , Rebekka Wild
- & Michael Hothorn
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Article
| Open AccessH2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots
Polycomb Group complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3. Here, the authors show that H2AK121ub marks less accessible but transcriptionally permissive chromatin, while H3K27me3 enforces a repressed transcriptionally less-permissive state.
- Xiaochang Yin
- , Francisco J. Romero-Campero
- & Yue Zhou
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Article
| Open AccessRETRACTED ARTICLE:The Arabidopsis NOT4A E3 ligase promotes PGR3 expression and regulates chloroplast translation
NOT4 proteins associate with ribosomes and are required for co-translational quality control in yeast and animals. Here, Bailey et al. show that Arabidopsis NOT4A positively regulates the expression of the nuclear encoded pentatricopeptide repeat (PPR) protein PGR3 and is required for ribosome biogenesis and mRNA translation in the chloroplast.
- Mark Bailey
- , Aiste Ivanauskaite
- & Daniel J. Gibbs
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Article
| Open AccessDirect energy transfer from photosystem II to photosystem I confers winter sustainability in Scots Pine
Evergreen conifers rely on ‘sustained quenching’ to protect their photosynthetic machinery during long, cold winters. Here, Bag et al. show that direct energy transfer (spillover) from photosystem II to photosystem I triggered by loss of grana stacking in chloroplast is the major component of sustained quenching in Scots pine.
- Pushan Bag
- , Volha Chukhutsina
- & Stefan Jansson
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Article
| Open AccessCondensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts
Introducing the pyrenoid-based CO2-concentrating mechanism of green algae into crops could greatly improve photosynthesis. Here, the authors show that expression of the algal linker protein EPYC1 and a plant-algal hybrid Rubisco in Arabidopsis chloroplasts leads to formation of a phase separated algal-like proto-pyrenoid.
- Nicky Atkinson
- , Yuwei Mao
- & Alistair J. McCormick
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Article
| Open AccessCloning of wheat keto-acyl thiolase 2B reveals a role of jasmonic acid in grain weight determination
It has been reported that several phytohormones are involved in the regulation of grain weight, but the role of jasmonic acids (JA) remains elusive. Here, via bulked segregant analysis (BSA)-based cloning, the authors show keto-acyl thiolase 2B involved in β-oxidation during JA synthesis is a positive regulator of wheat grain weight.
- Yun Chen
- , Yan Yan
- & Jin-Ying Gou
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Article
| Open AccessArabidopsis calcium-dependent protein kinase 3 regulates actin cytoskeleton organization and immunity
Remodelling of the actin cytoskeleton occurs during plant immune responses to pathogens. Here Lu et al. show that this process requires the calcium-dependent kinase CPK3 which phosphorylates actin depolymerizing factor 4 and is required for both PAMP and effector-triggered immunity in Arabidopsis.
- Yi-Ju Lu
- , Pai Li
- & Brad Day
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Article
| Open AccessPeroxisomes form intralumenal vesicles with roles in fatty acid catabolism and protein compartmentalization in Arabidopsis
Peroxisomes are organelles compartmentalising metabolic reactions such as the breakdown of fats, and are commonly thought of as single membrane-bound compartments. Here the authors show that Arabidopsis peroxisomes contain extensive internal vesicles that form from the bounding membrane in an ESCRT-dependent process.
- Zachary J. Wright
- & Bonnie Bartel
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Article
| Open AccessCoupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis
Histone 3 Lys 27 trimethylation (H3K27me3) mediates epigenetic silencing of gene expression. Here, Zhang et al. show that in Arabidopsis, the BAH-domain H3K27me3-reader protein AIPP3 forms a complex with PHD proteins and CPL2, a plant-specific Pol II phosphatase, to inhibit Pol II activity by dephosphorylation.
- Yi-Zhe Zhang
- , Jianlong Yuan
- & Cheng-Guo Duan
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Article
| Open AccessDocking of acetyl-CoA carboxylase to the plastid envelope membrane attenuates fatty acid production in plants
In plants, light-dependent activation fatty acid synthesis (FAS) is mediated in part by acetyl-CoA carboxylase (ACCase). Here the authors identify a family of genes encoding carboxyltransferase interactors that attenuate FAS in the light by docking acetyl-CoA carboxylase to the plastid envelope.
- Yajin Ye
- , Krisztina Nikovics
- & Jay J. Thelen
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Review Article
| Open AccessRole of Raf-like kinases in SnRK2 activation and osmotic stress response in plants
A better understanding of how plants respond to osmotic stress could potentially help improve crop yields. Here Fàbregas et al. review the recent characterization of Raf-like kinases that act in both in ABA-dependent and -independent responses to osmotic stress.
- Norma Fàbregas
- , Takuya Yoshida
- & Alisdair R. Fernie
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Article
| Open AccessThe liverwort oil body is formed by redirection of the secretory pathway
Liverworts have a unique oil body organelle unrelated to lipid stores found in other eukaryotes. Here the authors show that oil body formation is analogous to that of cell plates, relying on periodic redirection of the secretory pathway and a syntaxin-1 homolog, and that oil bodies contribute to defence against herbivory.
- Takehiko Kanazawa
- , Hatsune Morinaka
- & Takashi Ueda
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Article
| Open AccessLight-driven formation of manganese oxide by today’s photosystem II supports evolutionarily ancient manganese-oxidizing photosynthesis
Photosynthetic formation of manganese (Mn) oxides from dissolved Mn ions was proposed to occur in ancestral photosystems before oxygenic photosynthesis evolved. Here, the authors provide evidence for this hypothesis by showing that photosystem II devoid of the Mn cluster oxidises Mn ions leading to formation of Mn-oxide nanoparticles.
- Petko Chernev
- , Sophie Fischer
- & Holger Dau
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Article
| Open AccessA grass-specific cellulose–xylan interaction dominates in sorghum secondary cell walls
Sorghum is a source of lignocellulosic biomass for the production of renewable fuels. Here the authors characterise the sorghum secondary cell wall using multi-dimensional magic angle spinning solid-state NMR and present a model dominated by interactions between three-fold screw xylan and amorphous cellulose.
- Yu Gao
- , Andrew S. Lipton
- & Jenny C. Mortimer
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Article
| Open AccessReproductive phasiRNAs regulate reprogramming of gene expression and meiotic progression in rice
21-nucleotide phased secondary siRNAs are expressed in the developing rice anthers during meiosis. Here, the authors show that phasiRNAs can cleave target mRNA and act to ensure the progression of meiosis and fertility in rice.
- Yu-Chan Zhang
- , Meng-Qi Lei
- & Yue-Qin Chen
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Article
| Open AccessThe role of mixed vibronic Qy-Qx states in green light absorption of light-harvesting complex II
The green component of the solar spectrum can efficiently drive natural photosynthesis, but the process has been little investigated due to the complexity of the excited states involved. Here the authors utilize polarization-dependent two-dimensional electronic-vibrational spectroscopy to define the origin and dynamics of these states in light-harvesting complex II.
- Eric A. Arsenault
- , Yusuke Yoneda
- & Graham R. Fleming
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Article
| Open AccessPhotosynthetic hydrogen production by droplet-based microbial micro-reactors under aerobic conditions
The development of techniques capable of orchestrating the assembly of living cells into multicellular ensembles with synergistic and function is challenge. Here, the authors construct algal or algal/bacterial cells-based core shell-like structure based on aqueous two-phase system for synergic photosynthetic H2 production.
- Zhijun Xu
- , Shengliang Wang
- & Stephen Mann
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Article
| Open AccessSubnuclear gene positioning through lamina association affects copper tolerance
The nuclear lamina regulates chromatin organization and gene positioning. Here the authors show that CROWDED NUCLEI proteins contribute to the meshwork lamina structure in Arabidopsis nuclei and regulate copper tolerance by promoting lamina association and expression of copper response genes.
- Yuki Sakamoto
- , Mayuko Sato
- & Sachihiro Matsunaga
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Article
| Open AccessGenome-enabled discovery of anthraquinone biosynthesis in Senna tora
Anthraquinones are aromatic polyketides and have been used for treating various diseases, but the biosynthetic pathway is unclear. Here, the authors assemble the genome of an anthraquinone-producing medicinal plant Senna tora and show the evidences that CHS-like genes may be involved in anthraquinone biosynthesis.
- Sang-Ho Kang
- , Ramesh Prasad Pandey
- & Jae Kyung Sohng
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Article
| Open AccessEvidences for a role of two Y-specific genes in sex determination in Populus deltoides
Dioecy has evolved independently from hermaphroditic ancestors in different plant lineages. Here, the authors assemble Populus deltoides male and female genomes, and show the putative roles of a femaleness gene and a maleness gene in sex determination, which suggests independent evolution in different poplar species.
- Liangjiao Xue
- , Huaitong Wu
- & Tongming Yin
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Article
| Open AccessMolecular variation in a functionally divergent homolog of FCA regulates flowering time in Arabidopsis thaliana
Natural variation represents valuable source for gene discovery. Here, the authors show that a homolog of Flowering Control Locus A (FCA) functions in an antagonistic manner to FCA in regulating Arabidopsis flowering time through interacting with CUL1-E3 and modulating FLC expression.
- Yunhe Wang
- , Zhen Tao
- & Peijin Li
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Article
| Open AccessTwo nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming
Plant pathogens secrete various effectors to manipulate host immunity. Here, Kim et al. describe two Magnaporthe oryzae effectors that translocate into the nuclei of infected rice cells and reprogram expression of immunity-associated genes, increasing susceptibility to hemibiotrophic pathogens.
- Seongbeom Kim
- , Chi-Yeol Kim
- & Yong-Hwan Lee
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Article
| Open AccessFIS1 encodes a GA2-oxidase that regulates fruit firmness in tomato
Fruit firmness is an important target for breeders and a key determinant of shelf life for many fruits. Here the authors show that mutating tomato FIS1, a GA2-oxidase, increases the concentration of bioactive gibberellins, enhances cutin and wax biosynthesis and increases fruit firmness.
- Ren Li
- , Shuai Sun
- & Xia Cui
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Article
| Open AccessA cellulose synthase-derived enzyme catalyses 3-O-glucuronosylation in saponin biosynthesis
Saponins such as glycyrrhizin, a natural sweetener found in licorice root, are a class of triterpenoids synthesized that are characterized by a glucoronic acid moiety at the C-3 position. Here the authors show that saponin glucuronosylation is catalyzed by cellulose-synthase like enzymes and reconstitute glycyrrhizin synthesisin yeast.
- Soo Yeon Chung
- , Hikaru Seki
- & Toshiya Muranaka
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Article
| Open AccessGenome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding
Solanum pimpinellifolium (SP) is the progenitor of cultivated tomato and an important germplasm. Here, the authors assemble SP genome, identify structural variants (SVs) by comparing with modern cultivar, reveal SVs associated with important breeding traits, and detect SVs harboring master regulators of fruit quality traits.
- Xin Wang
- , Lei Gao
- & Zhangjun Fei
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Article
| Open AccessPlant hairy roots enable high throughput identification of antimicrobials against Candidatus Liberibacter spp.
The putative causal agent of citrus greening Candidatus Liberibacter asiaticus (CLas) cannot be cultured, which hampers finding new therapies to control this devastating disease. Here, the authors show that hairy roots support CLas propagation and enable high throughput antimicrobial screening.
- Sonia Irigoyen
- , Manikandan Ramasamy
- & Kranthi K. Mandadi
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Article
| Open AccessOsChz1 acts as a histone chaperone in modulating chromatin organization and genome function in rice
Function of CHZ-domain proteins in multicellular eukaryotes remains unclear. Here, the authors characterize the sole CHZ-domain protein identified in rice and show that it functions as an H2A/H2A.Z-H2B chaperone in dynamic regulation of chromatin organization and genome function.
- Kangxi Du
- , Qiang Luo
- & Wen-Hui Shen
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Article
| Open AccessIntraspecific host variation plays a key role in virus community assembly
The factors that determine whether pathogens co-occur in a host are poorly understood, especially for plant viruses. Here the authors conduct field experiments with the plant Plantago lanceolata and its viruses, showing that viral co-occurrences are driven predominantly by environmental context and host genotype rather than viral interactions.
- Suvi Sallinen
- , Anna Norberg
- & Anna-Liisa Laine
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