Molecular Plant

Article	Citations
TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data	7689
TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining	320
The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation	275
WheatOmics: A platform combining multiple omics data to accelerate functional genomics studies in wheat	192
Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level	158
Toxic metals and metalloids: Uptake, transport, detoxification, phytoremediation, and crop improvement for safer food	156
Two gap-free reference genomes and a global view of the centromere architecture in rice	154
Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China	146
A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era	143
Single-Cell Transcriptome Analysis in Plants: Advances and Challenges	143
Plant cytochrome P450 plasticity and evolution	138
High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat	137
Transcriptional landscape of rice roots at the single-cell resolution	135
Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing	135
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes	134
Lipid Metabolism: Critical Roles in Male Fertility and Other Aspects of Reproductive Development in Plants	128
The Chromosome-Level Genome Sequence of the Autotetraploid Alfalfa and Resequencing of Core Germplasms Provide Genomic Resources for Alfalfa Research	127
MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle	125
Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus	120
A 2-kb Mycovirus Converts a Pathogenic Fungus into a Beneficial Endophyte for Brassica Protection and Yield Enhancement	118
A Comprehensive Online Database for Exploring ∼20,000 Public Arabidopsis RNA-Seq Libraries	112
Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae	103
Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations	101
Variation in cis-regulation of a NAC transcription factor contributes to drought tolerance in wheat	100
A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis	99

Zinc in plants: Integrating homeostasis and biofortification	98
Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome	98
Arabidopsis N6-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies	97
Highly efficient heritable genome editing in wheat using an RNA virus and bypassing tissue culture	95
Transcriptional activation and phosphorylation of OsCNGC9 confer enhanced chilling tolerance in rice	94
A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding	92
The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution	91
Plant Immune Mechanisms: From Reductionistic to Holistic Points of View	91
The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future	89
The miR319-Targeted GhTCP4 Promotes the Transition from Cell Elongation to Wall Thickening in Cotton Fiber	88
Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity	85
Protein Quality Control in Plant Organelles: Current Progress and Future Perspectives	84
Plant adaptation to low phosphorus availability: Core signaling, crosstalks, and applied implications	83
CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis	82
Interspecific plant interaction via root exudates structures the disease suppressiveness of rhizosphere microbiomes	82
The GW2-WG1-OsbZIP47 pathway controls grain size and weight in rice	80
High-efficiency and multiplex adenine base editing in plants using new TadA variants	78
Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction	77
The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold	76
Nitric oxide regulation of plant metabolism	74
Lipidomic Analysis Reveals the Importance of GIPCs in Arabidopsis Leaf Extracellular Vesicles	74
Control of Plant Growth and Defense by Photoreceptors: From Mechanisms to Opportunities in Agriculture	71
ζ-Carotene Isomerase Suppresses Tillering in Rice through the Coordinated Biosynthesis of Strigolactone and Abscisic Acid	71
Creation and judicious application of a wheat resistance gene atlas	70
Nematode-Encoded RALF Peptide Mimics Facilitate Parasitism of Plants through the FERONIA Receptor Kinase	70
Hydrogen sulfide-linked persulfidation of ABI4 controls ABA responses through the transactivation of MAPKKK18 in Arabidopsis	70
CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement	70
Counteraction of ABA-Mediated Inhibition of Seed Germination and Seedling Establishment by ABA Signaling Terminator in Arabidopsis	70
The receptor-like cytoplasmic kinase RIPK regulates broad-spectrum ROS signaling in multiple layers of plant immune system	70
Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives	69
Nutrient–hormone relations: Driving root plasticity in plants	69
A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice	69
Hybrid speciation via inheritance of alternate alleles of parental isolating genes	68
Development of a widely targeted volatilomics method for profiling volatilomes in plants	68
Phenylpropanoid Derivatives Are Essential Components of Sporopollenin in Vascular Plants	67
Molecular Basis of Disease Resistance and Perspectives on Breeding Strategies for Resistance Improvement in Crops	67
An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion	66
A compressed variance component mixed model for detecting QTNs and QTN-by-environment and QTN-by-QTN interactions in genome-wide association studies	65
Chromosome-Level Reference Genome and Population Genomic Analysis Provide Insights into the Evolution and Improvement of Domesticated Mulberry (Morus alba)	65
A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis	65
Primary carbohydrate metabolism genes participate in heat-stress memory at the shoot apical meristem of Arabidopsis thaliana	64
The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis	64
HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing	63
Major episodes of horizontal gene transfer drove the evolution of land plants	63
Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia–legume symbiosis	63
A transceptor–channel complex couples nitrate sensing to calcium signaling in Arabidopsis	63
The landscape of gene–CDS–haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic improvement	62
Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline	62
MPK14-mediated auxin signaling controls lateral root development via ERF13-regulated very-long-chain fatty acid biosynthesis	62
An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops	61

Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding	61
An alternative, zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants	61
Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield	61
GmCRY1s modulate gibberellin metabolism to regulate soybean shade avoidance in response to reduced blue light	60
Targeted mutagenesis of POLYAMINE OXIDASE 5 that negatively regulates mesocotyl elongation enables the generation of direct-seeding rice with improved grain yield	60
Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes	60
Efficient Gene Targeting in Maize Using Inducible CRISPR-Cas9 and Marker-free Donor Template	60
Rice metabolic regulatory network spanning the entire life cycle	59
Pho-view of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling	59
The OsNAC23-Tre6P-SnRK1a feed-forward loop regulates sugar homeostasis and grain yield in rice	58
Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex	57
Cell wall β-1,4-galactan regulated by the BPC1/BPC2-GALS1 module aggravates salt sensitivity in Arabidopsis thaliana	56
Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204	56
N-terminal truncated RHT-1 proteins generated by translational reinitiation cause semi-dwarfing of wheat Green Revolution alleles	56
Genome editing mediated by SpCas9 variants with broad non-canonical PAM compatibility in plants	56
Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway	55
Parallel selection of distinct Tof5 alleles drove the adaptation of cultivated and wild soybean to high latitudes	55
An inferred functional impact map of genetic variants in rice	55
ITPK1 is an InsP6/ADP phosphotransferase that controls phosphate signaling in Arabidopsis	55
Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution	55
Bph30 confers resistance to brown planthopper by fortifying sclerenchyma in rice leaf sheaths	54
Unraveling the 3D Genome Architecture in Plants: Present and Future	54
Orphan Crops and their Wild Relatives in the Genomic Era	54
A natural variation in Ribonuclease H-like gene underlies Rht8 to confer “Green Revolution” trait in wheat	54
Phytophthora Effectors Modulate Genome-wide Alternative Splicing of Host mRNAs to Reprogram Plant Immunity	54
PlantscRNAdb: A database for plant single-cell RNA analysis	54
Cloning and functional characterization of Rht8, a “Green Revolution” replacement gene in wheat	54
Innovations in Agriculture and Food Supply in Response to the COVID-19 Pandemic	53
Mobilizing Crop Biodiversity	53
Citrus Pan-Genome to Breeding Database (CPBD): A comprehensive genome database for citrus breeding	53
A Synthetic Photorespiratory Shortcut Enhances Photosynthesis to Boost Biomass and Grain Yield in Rice	53
The YDA-MKK4/MKK5-MPK3/MPK6 Cascade Functions Downstream of the RGF1-RGI Ligand–Receptor Pair in Regulating Mitotic Activity in Root Apical Meristem	52
Enhancing the light reactions of photosynthesis: Strategies, controversies, and perspectives	52
Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield	52
Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation	51
Hybrid Rubisco with Complete Replacement of Rice Rubisco Small Subunits by Sorghum Counterparts Confers C4 Plant-like High Catalytic Activity	51
From Green Super Rice to green agriculture: Reaping the promise of functional genomics research	51
The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation	50
Unraveling a genetic roadmap for improved taste in the domesticated apple	50
The RING E3 ligase CLG1 targets GS3 for degradation via the endosome pathway to determine grain size in rice	50
The LEAFY floral regulator displays pioneer transcription factor properties	50
Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions	50
Two VOZ transcription factors link an E3 ligase and an NLR immune receptor to modulate immunity in rice	50
RGF1-RGI1, a Peptide-Receptor Complex, Regulates Arabidopsis Root Meristem Development via a MAPK Signaling Cascade	49
A reciprocal inhibitory module for Pi and iron signaling	48
GSK3-mediated stress signaling inhibits legume–rhizobium symbiosis by phosphorylating GmNSP1 in soybean	48
A reactive oxygen species burst causes haploid induction in maize	47
CLE14 functions as a “brake signal” to suppress age-dependent and stress-induced leaf senescence by promoting JUB1-mediated ROS scavenging in Arabidopsis	46
Persulfidation-induced structural change in SnRK2.6 establishes intramolecular interaction between phosphorylation and persulfidation	46
Arabidopsis CHLOROPHYLLASE 1 protects young leaves from long-term photodamage by facilitating FtsH-mediated D1 degradation in photosystem II repair	46
Glycosylation of N-hydroxy-pipecolic acid equilibrates between systemic acquired resistance response and plant growth	46
Coordination of plant growth and abiotic stress responses by tryptophan synthase β subunit 1 through modulation of tryptophan and ABA homeostasis in Arabidopsis	46
Pathogen-inducible OsMPKK10.2-OsMPK6 cascade phosphorylates the Raf-like kinase OsEDR1 and inhibits its scaffold function to promote rice disease resistance	45
A transcription factor STOP1-centered pathway coordinates ammonium and phosphate acquisition in Arabidopsis	45
Genome Editing Enables Next-Generation Hybrid Seed Production Technology	45
The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat	44
Normal Structure and Function of Endothecium Chloroplasts Maintained by ZmMs33-Mediated Lipid Biosynthesis in Tapetal Cells Are Critical for Anther Development in Maize	44
Decreasing nitrogen assimilation under drought stress by suppressing DST-mediated activation of Nitrate Reductase 1.2 in rice	44
A near-complete assembly of an Arabidopsis thaliana genome	43
Genomic insights into the fast growth of paulownias and the formation of Paulownia witches' broom	43
The blue light receptor CRY1 interacts with GID1 and DELLA proteins to repress GA signaling during photomorphogenesis in Arabidopsis	43
IIIVmrMLM: The R and C++ tools associated with 3VmrMLM, a comprehensive GWAS method for dissecting quantitative traits	42
Genome architecture and tetrasomic inheritance of autotetraploid potato	42
ESCRT-I Component VPS23A Sustains Salt Tolerance by Strengthening the SOS Module in Arabidopsis	42
Regulation of the stability and ABA import activity of NRT1.2/NPF4.6 by CEPR2-mediated phosphorylation in Arabidopsis	42
The Ghd7 transcription factor represses ARE1 expression to enhance nitrogen utilization and grain yield in rice	41
Warm temperature compromises JA-regulated basal resistance to enhance Magnaporthe oryzae infection in rice	41
Pandemics of People and Plants: Which Is the Greater Threat to Food Security?	41
Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus	41
A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root	41
The miR166–SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato	40
Ectopic expression of VRT-A2 underlies the origin of Triticum polonicum and Triticum petropavlovskyi with long outer glumes and grains	39
Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects	39
A cell wall-localized NLR confers resistance to Soybean mosaic virus by recognizing viral-encoded cylindrical inclusion protein	39
Molecular basis underlying rice tiller angle: Current progress and future perspectives	38
Dynamic changes of phosphatidylinositol and phosphatidylinositol 4-phosphate levels modulate H+-ATPase and Na+/H+ antiporter activities to maintain ion homeostasis in Arabidopsis under salt stress	38
WheatGmap: a comprehensive platform for wheat gene mapping and genomic studies	37
Activation of Mitochondrial orf355 Gene Expression by a Nuclear-Encoded DREB Transcription Factor Causes Cytoplasmic Male Sterility in Maize	37
Redox sensor QSOX1 regulates plant immunity by targeting GSNOR to modulate ROS generation	37
Pyramiding favorable alleles in an elite wheat variety in one generation by CRISPR-Cas9-mediated multiplex gene editing	37

Bract suppression regulated by the miR156/529-SPLs-NL1-PLA1 module is required for the transition from vegetative to reproductive branching in rice	37
Dynamic spatial reorganization of BSK1 complexes in the plasma membrane underpins signal-specific activation for growth and immunity	37
Transcriptional Regulation of Lipid Catabolism during Seedling Establishment	37
miR395-regulated sulfate metabolism exploits pathogen sensitivity to sulfate to boost immunity in rice	36
PhieCBEs: Plant High-Efficiency Cytidine Base Editors with Expanded Target Range	36
Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume	35
Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding	35
BnIR: A multi-omics database with various tools for Brassica napus research and breeding	35
Verticillium dahliae secretory effector PevD1 induces leaf senescence by promoting ORE1-mediated ethylene biosynthesis	35
Wheat leaf rust resistance gene Lr13 is a specific Ne2 allele for hybrid necrosis	35
Tanned or Sunburned: How Excessive Light Triggers Plant Cell Death	35
Optimized prime editing efficiently generates glyphosate-resistant rice plants carrying homozygous TAP-IVS mutation in EPSPS	34
A bacterial effector protein uncovers a plant metabolic pathway involved in tolerance to bacterial wilt disease	34
Natural variations of ZmSRO1d modulate the trade-off between drought resistance and yield by affecting ZmRBOHC-mediated stomatal ROS production in maize	34
Importers Drive Leaf-to-Leaf Jasmonic Acid Transmission in Wound-Induced Systemic Immunity	33
A virus-derived siRNA activates plant immunity by interfering with ROS scavenging	33
Construction of a high-density mutant population of Chinese cabbage facilitates the genetic dissection of agronomic traits	33
Tonoplast-associated calcium signaling regulates manganese homeostasis in Arabidopsis	33
Structure, biochemical function, and signaling mechanism of plant NLRs	33
Hetero-trans-β-Glucanase Produces Cellulose–Xyloglucan Covalent Bonds in the Cell Walls of Structural Plant Tissues and Is Stimulated by Expansin	33
A teosinte-derived allele of a MYB transcription repressor confers multiple disease resistance in maize	33
High-efficiency plastome base editing in rice with TAL cytosine deaminase	33
The origin and evolution of salicylic acid signaling and biosynthesis in plants	33
Regulation of Leaf Longevity by DML3-Mediated DNA Demethylation	33
DNNGP, a deep neural network-based method for genomic prediction using multi-omics data in plants	32
Breeding with dominant genic male-sterility genes to boost crop grain yield in the post-heterosis utilization era	32
The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize	32
The genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution	32
Engineering broad-spectrum resistance to bacterial blight by CRISPR-Cas9-mediated precise homology directed repair in rice	32
Cellulose synthesis in land plants	32
A potato late blight resistance gene protects against multiple Phytophthora species by recognizing a broadly conserved RXLR-WY effector	32
PDX1.1-dependent biosynthesis of vitamin B6 protects roots from ammonium-induced oxidative stress	32
Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq	31
Engineered biocontainable RNA virus vectors for non-transgenic genome editing across crop species and genotypes	31
Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit	31
DNA demethylases remodel DNA methylation in rice gametes and zygote and are required for reproduction	31
A cryptic inhibitor of cytokinin phosphorelay controls rice grain size	30
Loss of two families of SPX domain-containing proteins required for vacuolar polyphosphate accumulation coincides with the transition to phosphate storage in green plants	30
Brassinosteroids enhance salicylic acid-mediated immune responses by inhibiting BIN2 phosphorylation of clade I TGA transcription factors in Arabidopsis	30
The IBI1 Receptor of β-Aminobutyric Acid Interacts with VOZ Transcription Factors to Regulate Abscisic Acid Signaling and Callose-Associated Defense	29
Differentiation trajectories and biofunctions of symbiotic and un-symbiotic fate cells in root nodules of Medicago truncatula	29
A complete assembly of the rice Nipponbare reference genome	29
Speed vernalization to accelerate generation advance in winter cereal crops	29
High-temperature wheat leaf rust resistance gene Lr13 exhibits pleiotropic effects on hybrid necrosis	29
Ca2+-dependent successive phosphorylation of vacuolar transporter MTP8 by CBL2/3-CIPK3/9/26 and CPK5 is critical for manganese homeostasis in Arabidopsis	29
Nuclear translocation of OsMFT1 that is impeded by OsFTIP1 promotes drought tolerance in rice	29
Multiplex precision gene editing by a surrogate prime editor in rice	29
Direct acetylation of a conserved threonine of RIN4 by the bacterial effector HopZ5 or AvrBsT activates RPM1-dependent immunity in Arabidopsis	29
Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis	28
Reshaping of the Arabidopsis thaliana Proteome Landscape and Co-regulation of Proteins in Development and Immunity	28
DET1-mediated COP1 regulation avoids HY5 activity over second-site gene targets to tune plant photomorphogenesis	28
Long-distance blue light signalling regulates phosphate deficiency-induced primary root growth inhibition	28