Featured
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Article
| Open AccessPhylotranscriptomic insights into a Mesoproterozoic–Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae)
“Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”
- Zheng Hou
- , Xiaoya Ma
- & Bojian Zhong
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Article
| Open AccessNew recognition specificity in a plant immune receptor by molecular engineering of its integrated domain
Plant NLR proteins trigger immune responses upon recognition of pathogen effectors. Here the authors show that the integrated decoy domain of the rice NLR RGA5 can be engineered to trigger immune responses upon binding a non-cognate effector.
- Stella Cesari
- , Yuxuan Xi
- & Thomas Kroj
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Article
| Open AccessUsing CRISPR-Kill for organ specific cell elimination by cleavage of tandem repeats
How double strand breaks (DSBs) are repaired within the plant 45S rDNA repeats is unclear. Here, the authors show that Cas9-mediated DSBs in 45S rDNA are mainly repaired by cNHEJ and describe CRISPR-Kill as a tool for organ-specific cell elimination by targeting functional repetitive DNA in Arabidopsis.
- Angelina Schindele
- , Fabienne Gehrke
- & Holger Puchta
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Article
| Open AccessExtracellular vesiculo-tubular structures associated with suberin deposition in plant cell walls
Suberizing plant cells export suberin monomers outside of the cell to form a hydrophobic barrier. Here the authors propose a role for extracellular vesiculo-tubular structures in the deposition of suberin monomers.
- Damien De Bellis
- , Lothar Kalmbach
- & Marie Barberon
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Article
| Open AccessParallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages
Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.
- Andrea Fulgione
- , Célia Neto
- & Angela M. Hancock
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Article
| Open AccessA peroxisomal heterodimeric enzyme is involved in benzaldehyde synthesis in plants
Benzaldehyde is a simple aromatic aldehyde that attracts pollinators, has antifungal properties and contributes to flavor in many plants. Here the authors show that benzaldehyde is synthesized in petunia via the benzoic acid β-oxidative pathway by a peroxisomal heterodimeric enzyme consisting of α and β subunits.
- Xing-Qi Huang
- , Renqiuguo Li
- & Natalia Dudareva
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Article
| Open AccessApoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature
Arabidopsis root hair growth is enhanced at low temperatures. Here the authors show that the class III peroxidases PRX62 and PRX69 modulate ROS homeostasis and cell wall characteristics, and promote root hair elongation at low temperature.
- Javier Martínez Pacheco
- , Philippe Ranocha
- & José M. Estevez
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Article
| Open AccessNorway spruce postglacial recolonization of Fennoscandia
Contrasting theories exist regarding how Norway spruce recolonized Fennoscandia after the last glaciation. Here, the authors provide evidences from sedimentary ancient DNA and modern population genomics to support that Norway spruce was present in southern Fennoscandia shortly after deglaciation and the early Holocene migration from the east.
- Kevin Nota
- , Jonatan Klaminder
- & Laura Parducci
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Article
| Open AccessDNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development
Our understanding of the extent of involvement of DNA methylation in genome-wide gene regulation and plant developmental control is incomplete. Here, the authors knock out all five known DNA methyltransferases and show the developmental and gene expression changes in the DNA methylation-free Arabidopsis plants.
- Li He
- , Huan Huang
- & Jian-Kang Zhu
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Article
| Open AccessPhylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere
Fagaceae are diverse family including trees of ecological and economic importance. This phylogenomic analysis of nuclear and plastid genomes reconstructs evolutionary history and finds evidence of multiple adaptive introgression events in this important plant family.
- Biao-Feng Zhou
- , Shuai Yuan
- & Baosheng Wang
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Article
| Open AccessGenotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1
Pattern-triggered immunity is activated by recognition of microbe-derived structures by host pattern recognition receptors. Here the authors use a genotype-by sequencing approach to show that bacterial translation initiation factor 1 triggers PTI in Arabidopsis thaliana after recognition by the RLP32 receptor.
- Li Fan
- , Katja Fröhlich
- & Thorsten Nürnberger
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Article
| Open AccessMechanosensory trichome cells evoke a mechanical stimuli–induced immune response in Arabidopsis thaliana
Plant immunity can be induced by pathogen signals or environmental cues. Here, the authors show that plant leaves use trichomes to sense incoming raindrops and trigger basal defence responses to protect against subsequent microbial infection.
- Mamoru Matsumura
- , Mika Nomoto
- & Yasuomi Tada
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Article
| Open AccessArabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading
MicroRNAs regulate gene expression through RNA cleavage or translation repression. Here the authors show that RBV, an evolutionarily conserved WD40 domain protein, acts to promote MIR transcription, pri-miRNA processing and miRNA loading into AGO1.
- Chao Liang
- , Qiang Cai
- & Xuemei Chen
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Comment
| Open AccessBreeding future crops to feed the world through de novo domestication
By the end of this century, a 50% increase in agricultural productivity is required to feed the world. Recent studies have demonstrated de novo domestication of wild plants as a new crop breeding strategy to meet future food challenges.
- Hong Yu
- & Jiayang Li
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Article
| Open AccessSex-linked deubiquitinase establishes uniparental transmission of chloroplast DNA
Most sexual organisms ensure that organelles are inherited from a single parent. Here, the authors describe OTU2p, a Chlamydomonas deubiquitinase that drives uniparental organelle inheritance without gametic dimorphism by preventing proteasome-mediated degradation exclusively in gametes of the plus mating type.
- Sunjoo Joo
- , Thamali Kariyawasam
- & Jae-Hyeok Lee
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Article
| Open AccessTwo zinc finger proteins with functions in m6A writing interact with HAKAI
The components of m6A writer and their interactions are still far from fully understood. Here, the authors identify two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, as components of the Arabidopsis m6A writer complex, and show that hiz2 mutant plants have an 85% reduction in m6A abundance and severe developmental defects.
- Mi Zhang
- , Zsuzsanna Bodi
- & Rupert G. Fray
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Article
| Open AccessNatural variation in Glume Coverage 1 causes naked grains in sorghum
Low glume coverage is the preferred for easy threshing in grain production, but the genetic basis remains unclear. Here, the authors report the gene GC1, which encodes an atypical G protein γ subunit, negatively regulates sorghum glume coverage and the naturally truncated alleles can be useful in the naked grain breeding.
- Peng Xie
- , Sanyuan Tang
- & Qi Xie
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Article
| Open AccessHSL1 and BAM1/2 impact epidermal cell development by sensing distinct signaling peptides
HAESA and HSL2 are receptors for IDA/IDL-family signaling peptides in plants. Here the authors show that HSL1, previously shown to recognize CLE9, preferentially binds IDA/IDL peptides and regulates leaf epidermal patterning independently of CLE peptides.
- Andra-Octavia Roman
- , Pedro Jimenez-Sandoval
- & Julia Santiago
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Article
| Open AccessLocal and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis
In plant genomes, both mCG and H3K9me2/mCH are important for silencing transposable elements (TEs). Here, the authors show that establishment of mCH is abolished in both TE and active genes when mCG is lost and targeting efficiency of mCH depends on relative levels of mCG within the genome.
- Taiko Kim To
- , Chikae Yamasaki
- & Tetsuji Kakutani
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Article
| Open AccessGenomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat
The connection between expression variation and phenotypic diversity in the populations of polyploid crops remains elusive. Here, the authors reveal the impact of genetic variants leading to biased expression of homoeologous genes in hexaploid wheat on agronomic traits.
- Fei He
- , Wei Wang
- & Eduard Akhunov
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Article
| Open AccessPervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants
The small size (≤15-nt) of micorexons poses difficulties for genome annotation and identification using standard RNA sequence mapping approaches. Here, the authors develop computational pipelines to discover and predict microexons in plants and reveal diverse evolutionary trajectories via genomewide microexon modeling.
- Huihui Yu
- , Mu Li
- & Chi Zhang
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Article
| Open AccessCotranslational N-degron masking by acetylation promotes proteome stability in plants
N-terminal protein acetylation is required for plant viability. Here the authors show that reducing N-terminal acetylation by NatA leads to an increase in global protein turnover that is facilitated by absent masking of a novel N-degron
- Eric Linster
- , Francy L. Forero Ruiz
- & Markus Wirtz
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Article
| Open AccessCoat proteins of necroviruses target 14-3-3a to subvert MAPKKKα-mediated antiviral immunity in plants
MAPK cascades play an important role in innate immunity. Here, the authors show that that beet black scorch virus activates MAPK signaling in Nicotiana benthamiana and the viral coat protein counteracts MAPK-mediated defence by competitively binding to a MAPKKKα interactor.
- Zongyu Gao
- , Dingliang Zhang
- & Yongliang Zhang
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Article
| Open AccessArabidopsis guard cell chloroplasts import cytosolic ATP for starch turnover and stomatal opening
Stomatal guard cells require ATP in order to fuel stomatal movements. Here the authors show that guard cell photosynthesis is limited, mitochondria are the main source of ATP and that guard cell chloroplasts import ATP via nucleotide transporters.
- Shey-Li Lim
- , Sabrina Flütsch
- & Boon Leong Lim
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Article
| Open AccessGenomic insights into the evolution of Echinochloa species as weed and orphan crop
Echinochloa is an important genus in the grass family as many of them are either problematic weeds or domesticated millets. Here, the authors assemble three polyploidy genomes in this genus using the diploid-assisted scaffolding method DipHic and provide genomic insights into the dual roles of some species as weeds and orphan crops.
- Dongya Wu
- , Enhui Shen
- & Chu-Yu Ye
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Article
| Open AccessGraph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
Increasing studies have suggested that single reference genome is insufficient to capture all variations in the genome. Here, the authors report a graph-based cucumber pan-genome by analyzing 12 chromosome-scale assemblies and reveal variations associated with agronomic traits and domestication.
- Hongbo Li
- , Shenhao Wang
- & Zhonghua Zhang
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Article
| Open AccessBuxus and Tetracentron genomes help resolve eudicot genome history
Gamma triplication arises via two whole-genome duplications early in eudicot history, but the relative timing of these is unclear. Here, the authors report the genomes of Buxales and Trochodendrales and reject the hypothesis of gamma arising via inter-lineage hybridization between ancestral eudicot lineages.
- Andre S. Chanderbali
- , Lingling Jin
- & Pamela S. Soltis
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Article
| Open AccessGeminiviruses employ host DNA glycosylases to subvert DNA methylation-mediated defense
Plants tightly regulate DNA methylation to regulate gene expression. Here, the authors show that the tomato yellow leaf curl China virus βC1 protein interacts with plant DNA glycosylases to promote demethylation of viral DNA and promote virulence.
- Xiaojian Gui
- , Chang Liu
- & Xueping Zhou
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Article
| Open AccessPhloem iron remodels root development in response to ammonium as the major nitrogen source
Ammonium affects plant root development through different mechanisms than nitrate. Here, the authors show that the Arabidopsis cell wall-localized ferroxidase LPR2 is required to attenuate root growth in response to ammonium.
- Xing Xing Liu
- , Hai Hua Zhang
- & Chong Wei Jin
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Article
| Open AccessCarbohydrate-aromatic interface and molecular architecture of lignocellulose
The plant biomass is a composite formed by a variety of polysaccharides and an aromatic polymer named lignin. Here, the authors use solid-state NMR spectroscopy to unveil the carbohydrate-aromatic interface that leads to the variable architecture of lignocellulose biomaterials.
- Alex Kirui
- , Wancheng Zhao
- & Tuo Wang
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Article
| Open AccessCitrus Huanglongbing is a pathogen-triggered immune disease that can be mitigated with antioxidants and gibberellin
Huanglongbing is a devastating disease of citrus, caused by phloem-colonizing bacteria. Here, the authors present evidence that the disease is the result of an exacerbated immune response to the infection, including production of reactive oxygen species, and that antioxidants and a growth-promoting hormone can mitigate disease symptoms.
- Wenxiu Ma
- , Zhiqian Pang
- & Nian Wang
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Article
| Open AccessThe pollen virome of wild plants and its association with variation in floral traits and land use
Pollen can be a vehicle for viral spread among plants. Here, Fetters et al. apply viral metagenomics to characterize the pollen virome of a diverse set of wild plants, find known and previously un-known viruses and show that wild plant species harbor more viruses when surrounded by less natural vegetation and when they have traits that promote increased plant-pollinator vector interactions.
- Andrea M. Fetters
- , Paul G. Cantalupo
- & Tia-Lynn Ashman
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Article
| Open AccessPHOSPHATE STARVATION RESPONSE transcription factors enable arbuscular mycorrhiza symbiosis
Arbuscular mycorrhiza support plant phosphate uptake. Here Das et al. show that PHR transcription factors permit arbuscular mycorrhiza symbiosis by promoting gene expression related to symbiosis development and maintenance.
- Debatosh Das
- , Michael Paries
- & Caroline Gutjahr
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Article
| Open AccessNitrogen nutrition contributes to plant fertility by affecting meiosis initiation
Nitrogen deficiency can cause floral abortion during reproductive development of rice. Here the authors show that when nitrogen is limited, rice plants require the ETFβ protein, which is involved in branched chain amino acid catabolism, to promote nitrogen reutilization and support the initiation of meiosis.
- Han Yang
- , Yafei Li
- & Zhukuan Cheng
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Article
| Open AccessActivation of the plant mevalonate pathway by extracellular ATP
Products of the mevalonate pathway support plant development. Here the authors show that the extracellular ATP receptor P2K1 phosphorylates mevalonate kinase and this affects the mevalonate pathway.
- Sung-Hwan Cho
- , Katalin Tóth
- & Gary Stacey
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Article
| Open AccessShared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota
Plants and algae associate with microbial communities that affect their growth and development. Here, the authors characterize the microbiota associated with a unicellular alga in soil, revealing extensive taxonomic and functional overlap with the root microbiota of land plants.
- Paloma Durán
- , José Flores-Uribe
- & Ruben Garrido-Oter
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Article
| Open AccessIdentification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood
2-(2-Phenylethyl)chromones (PECs) contribute to the distinctive fragrance of agarwood. Here the authors identify a diarylpentanoid-producing polyketide synthase from Aquilaria sinensis and show how it catalyzes PEC formation.
- Xiao-Hui Wang
- , Bo-Wen Gao
- & She-Po Shi
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Article
| Open AccessNuA4 and H2A.Z control environmental responses and autotrophic growth in Arabidopsis
Function of nucleosomal acetyltransferase of H4 (NuA4), one major complex of HAT, remains unclear in plants. Here, the authors generate mutants targeting two components of the putative NuA4 complex in Arabidopsis (EAF1 and EPL1) and show their roles in photosynthesis genes regulation through H4K5ac and H2A.Z acetylation.
- Tomasz Bieluszewski
- , Weronika Sura
- & Piotr A. Ziolkowski
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Article
| Open AccessDistinct mechanisms orchestrate the contra-polarity of IRK and KOIN, two LRR-receptor-kinases controlling root cell division
Protein polarization coordinates many plant developmental processes. Here the authors show that IRK and KOIN, two LRR-receptor-kinases polarized to opposite sides of cells in the root meristem, rely on distinct mechanisms to achieve polarity.
- Cecilia Rodriguez-Furlan
- , Roya Campos
- & Jaimie M. Van Norman
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Article
| Open AccessSignatures of selection in recently domesticated macadamia
Macadamia is a recently domesticated nut crop. Here, the authors report the genome assembly of Hawaiian cultivar ‘Kau’ and conduct population genomic analyses to reveal the origin of Hawaiian cultivars and the genomic basis for one-step operation for the clonal crop domestication.
- Jishan Lin
- , Wenping Zhang
- & Ray Ming
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Article
| Open AccessThe CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis
CLASSY (CLSY) proteins regulate DNA methylation at specific loci in the Arabidopsis genome. Here the authors show that the CLSYs also control tissue-specific DNA methylation, including at siren loci in ovules, and that the lack of an individual CLSYs can shift the epigenetic landscape between tissues.
- Ming Zhou
- , Ceyda Coruh
- & Julie A. Law
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Article
| Open AccessSYP72 interacts with the mechanosensitive channel MSL8 to protect pollen from hypoosmotic shock during hydration
Pollen grains undergo desiccation and rehydration prior to germination and must survive osmotic shock. Here the authors show that the Qc-SNARE protein SYP72 is required for the localization of the mechanosensitive channel MSL8 at the plasma membrane and to maintain viability during rehydration.
- Xuemei Zhou
- , Yifan Zheng
- & Peng Zhao
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Article
| Open AccessConnected function of PRAF/RLD and GNOM in membrane trafficking controls intrinsic cell polarity in plants
The polarly localized BASL protein controls asymmetric cell division during stomatal lineage development in Arabidopsis. Here, the authors show that BASL polarization depends on PRAF/RLD proteins that interact with GNOM and suggest a role for endosomal trafficking in establishing polarity.
- Lu Wang
- , Dongmeng Li
- & Juan Dong
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Article
| Open AccessThe 2018 European heatwave led to stem dehydration but not to consistent growth reductions in forests
Forest dynamics are monitored at large scales with remote sensing, but individual tree data are necessary for ground-truthing and mechanistic insights. This study on high temporal resolution dendrometer data across Europe reveals that the 2018 heatwave affected tree physiology and growth in unexpected way.
- Roberto L. Salomón
- , Richard L. Peters
- & Kathy Steppe
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Article
| Open AccessDynamics and mechanism of dimer dissociation of photoreceptor UVR8
UVR8 is a plant photoreceptor that dissociates into monomers after sensing UV. Here, via ultrafast spectroscopy and computational calculations, the authors describe the dynamics of charge separation and charge neutralization in UVR8 and describe how these unzip interactions at the dimer interface.
- Xiankun Li
- , Zheyun Liu
- & Dongping Zhong
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Article
| Open AccessThe genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes
Reports on the origin of European wine grapes are controversial. Here, the authors perform population genetics analyses on a large set of representative wine-making varieties and reveal a single domestication event at the origin of the entire germplasm followed by repeated introgression from wild populations.
- Gabriele Magris
- , Irena Jurman
- & Michele Morgante
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Article
| Open AccessOxicam-type non-steroidal anti-inflammatory drugs inhibit NPR1-mediated salicylic acid pathway
The plant defense hormone salicylic acid has structural similarity to oxicam-type non-steroidal antiinflammatories. Here the authors show oxicams, as well as endogenous salicylic acid, can alter cellular redox state and immune signaling without affecting the redox status of cysteines in NPR1.
- Nobuaki Ishihama
- , Seung-won Choi
- & Ken Shirasu
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Article
| Open AccessGenomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits
Spinach is a nutritious leafy vegetable growing worldwide. Here, the authors report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 accessions, and provide insights into spinach domestication and the genetic basis of agronomic traits.
- Xiaofeng Cai
- , Xuepeng Sun
- & Quanhua Wang
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Article
| Open AccessInterdependent iron and phosphorus availability controls photosynthesis through retrograde signaling
Iron deficiency induces chlorosis in plants but only when phosphate supply is sufficient. Here, the authors show that phosphate-dependency is governed by a ROS-mediated retrograde signaling pathway involving the PHT4;4 chloroplast ascorbate transporter and the bZIP58 nuclear transcription factor.
- Hye-In Nam
- , Zaigham Shahzad
- & Hatem Rouached
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