Transcriptomic, epigenomic and physiological comparisons reveal key factors for different manganese tolerances in three Chenopodium ambrosioides L. populations.

[1]  P. Suprasanna,et al.  Comprehensive mechanisms of heavy metal toxicity in plants, detoxification, and remediation. , 2023, Journal of hazardous materials.

[2]  Hanchao Zhang,et al.  Genetic and epigenetic variation separately contribute to range expansion and local metalliferous habitat adaptation during invasions of Chenopodium ambrosioides into China. , 2022, Annals of botany.

[3]  I. Smýkalová,et al.  Molecular Mechanisms Underlying Flax (Linum usitatissimum L.) Tolerance to Cadmium: A Case Study of Proteome and Metabolome of Four Different Flax Genotypes , 2022, Plants.

[4]  Fabian Tobar-Tosse,et al.  Whole‐genome DNA methylation patterns of Oryza sativa (L.) and Oryza glumaepatula (Steud) genotypes associated with aluminum response , 2022, Plant direct.

[5]  Hanchao Zhang,et al.  Reactive Oxygen Species Partly Mediate DNA Methylation in Responses to Different Heavy Metals in Pokeweed , 2022, Frontiers in Plant Science.

[6]  M. Skórka,et al.  The Implication of Manganese Surplus on Plant Cell Homeostasis: A Review , 2022, Journal of Plant Growth Regulation.

[7]  Yahua Chen,et al.  Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process , 2022, Microbiome.

[8]  D. Podar,et al.  The role of roots and rhizosphere in providing tolerance to toxic metals and metalloids. , 2021, Plant, cell & environment.

[9]  Qingfeng Wang,et al.  Distinct methylome patterns contribute to ecotypic differentiation in the growth of the storage organ of a flowering plant (sacred lotus) , 2021, Molecular ecology.

[10]  Liang Zhang,et al.  Targeted and nontargeted metabolomics analysis for determining the effect of storage time on the metabolites and taste quality of keemun black tea. , 2021, Food chemistry.

[11]  Yan Huang,et al.  Transcriptome analysis of cadmium‐treated Brassica varieties reveals different expression pattern , 2021 .

[12]  Xueli Cao,et al.  Untargeted metabolomics coupled with chemometrics approach for Xinyang Maojian green tea with cultivar, elevation and processing variations. , 2021, Food chemistry.

[13]  R. Bell,et al.  Variation of Cicer Germplasm to Manganese Toxicity Tolerance , 2020, Frontiers in Plant Science.

[14]  Chen Zhu,et al.  Genome-wide investigation of DNA methylation dynamics reveals a critical role of DNA demethylation during the early somatic embryogenesis of Dimocarpus longan Lour. , 2020, Tree physiology.

[15]  Margaret H. Frank,et al.  TBtools - an integrative toolkit developed for interactive analyses of big biological data. , 2020, Molecular plant.

[16]  E. Peiter,et al.  Manganese in Plants: From Acquisition to Subcellular Allocation , 2020, Frontiers in Plant Science.

[17]  Chongling Yan,et al.  Uptake, biotransformation and physiological response of TBBPA in mangrove plants after hydroponics exposure. , 2020, Marine pollution bulletin.

[18]  C. Jin,et al.  Inhibition of DNA demethylation enhances plant tolerance to cadmium toxicity by improving iron nutrition. , 2019, Plant, cell & environment.

[19]  M. Seki,et al.  Histone Modifications Form Epigenetic Regulatory Networks to Regulate Abiotic Stress Response1[OPEN] , 2019, Plant Physiology.

[20]  Guodao Liu,et al.  Advances in the Mechanisms of Plant Tolerance to Manganese Toxicity , 2019, International journal of molecular sciences.

[21]  Mingquan Guo,et al.  Antioxidant and Anti-Inflammatory Activities of the Crude Extracts of Moringa oleifera from Kenya and Their Correlations with Flavonoids , 2019, Antioxidants.

[22]  Yi Li,et al.  Manganese tolerance and accumulation characteristics of a woody accumulator Camellia oleifera , 2019, Environmental Science and Pollution Research.

[23]  Kaile Sun,et al.  The maize bHLH transcription factor bHLH105 confers manganese tolerance in transgenic tobacco. , 2019, Plant science : an international journal of experimental plant biology.

[24]  M. Ozturk,et al.  Heavy metal stress and responses in plants , 2019, International Journal of Environmental Science and Technology.

[25]  M. B. Bitonti,et al.  Cadmium and/or copper excess induce interdependent metal accumulation, DNA methylation, induction of metal chelators and antioxidant defences in the seagrass Zostera marina. , 2019, Chemosphere.

[26]  S. Jacobsen,et al.  A DNA methylation reader complex that enhances gene transcription , 2018, Science.

[27]  M. Rao,et al.  Early responses to manganese (Mn) excess and its relation to antioxidant performance and organic acid exudation in barley cultivars , 2018 .

[28]  Yongsheng Liu,et al.  The WRKY transcription factor, WRKY13, activates PDR8 expression to positively regulate cadmium tolerance in Arabidopsis. , 2018, Plant, cell & environment.

[29]  H. Rennenberg,et al.  Physiological and molecular mechanisms of heavy metal accumulation in nonmycorrhizal versus mycorrhizal plants. , 2018, Plant, cell & environment.

[30]  Xue-hong Zhang,et al.  Simultaneous hyperaccumulation of cadmium and manganese in Celosia argentea Linn. , 2018, International journal of phytoremediation.

[31]  Brent S. Pedersen,et al.  GOATOOLS: A Python library for Gene Ontology analyses , 2018, Scientific Reports.

[32]  Guillaume Echevarria,et al.  A global database for plants that hyperaccumulate metal and metalloid trace elements. , 2018, The New phytologist.

[33]  Jebi Sudan,et al.  Plant epigenetic mechanisms: role in abiotic stress and their generational heritability , 2018, 3 Biotech.

[34]  F. Dakora,et al.  Nature and mechanisms of aluminium toxicity, tolerance and amelioration in symbiotic legumes and rhizobia , 2018, Biology and Fertility of Soils.

[35]  K. Iwasaki,et al.  Rice reduces Mn uptake in response to Mn stress , 2018, Plant signaling & behavior.

[36]  Ben P. Williams,et al.  Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit , 2017, Nature Communications.

[37]  Changhua Zhu,et al.  Hydrilla verticillata employs two different ways to affect DNA methylation under excess copper stress. , 2017, Aquatic toxicology.

[38]  Y. Qi,et al.  Long-term manganese-toxicity-induced alterations of physiology and leaf protein profiles in two Citrus species differing in manganese-tolerance. , 2017, Journal of plant physiology.

[39]  K. Iwasaki,et al.  The Tonoplast-Localized Transporter MTP8.2 Contributes to Manganese Detoxification in the Shoots and Roots of Oryza sativa L. , 2017, Plant & cell physiology.

[40]  Qiuhong Chen,et al.  Hydrogen-rich water pretreatment alters photosynthetic gas exchange, chlorophyll fluorescence, and antioxidant activities in heat-stressed cucumber leaves , 2017, Plant Growth Regulation.

[41]  A. R. Reis,et al.  Physiological highlights of manganese toxicity symptoms in soybean plants: Mn toxicity responses. , 2017, Plant physiology and biochemistry : PPB.

[42]  Jianhua Zhang,et al.  WRKY transcription factors in plant responses to stresses. , 2017, Journal of integrative plant biology.

[43]  P. Zhuang,et al.  Influences of calcium silicate on chemical forms and subcellular distribution of cadmium in Amaranthus hypochondriacus L. , 2017, Scientific Reports.

[44]  Youko Oono,et al.  Variation of DNA methylation patterns associated with gene expression in rice (Oryza sativa) exposed to cadmium. , 2016, Plant, cell & environment.

[45]  Jie Lei,et al.  Effects of manganese on the microstructures of Chenopodium ambrosioides L., A manganese tolerant plant , 2016, International journal of phytoremediation.

[46]  M. Gu,et al.  Manganese Toxicity in Sugarcane Plantlets Grown on Acidic Soils of Southern China , 2016, PloS one.

[47]  M. Li,et al.  A newly found manganese hyperaccumulator—Polygonum lapathifolium Linn. , 2016, International journal of phytoremediation.

[48]  Xuan Lan Thi Hoang,et al.  Role of Ethylene and Its Cross Talk with Other Signaling Molecules in Plant Responses to Heavy Metal Stress1 , 2015, Plant Physiology.

[49]  K. Borowiak,et al.  RELATIONS BETWEEN MN CONCENTRATION AND YIELD, NUTRIENT, WATER STATUS, AND GAS EXCHANGE PARAMETERS OF TOMATO , 2015 .

[50]  Siyuan Zhu,et al.  Genome-wide transcriptomic profiling of ramie (Boehmeria nivea L. Gaud) in response to cadmium stress. , 2015, Gene.

[51]  Xiuli Wu,et al.  Root transcriptome analysis on the grape genotypes with contrast translocation pattern of excess manganese from root to shoot , 2015, Plant and Soil.

[52]  G. Pan,et al.  The Dynamics of DNA Methylation in Maize Roots under Pb Stress , 2014, International journal of molecular sciences.

[53]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[54]  K Ito,et al.  Application of ggplot2 to Pharmacometric Graphics , 2013, CPT: pharmacometrics & systems pharmacology.

[55]  D. Salt,et al.  Arabidopsis thaliana Yellow Stripe1-Like4 and Yellow Stripe1-Like6 localize to internal cellular membranes and are involved in metal ion homeostasis , 2013, Front. Plant Sci..

[56]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[57]  W. Durka,et al.  Scoring and analysis of methylation‐sensitive amplification polymorphisms for epigenetic population studies , 2013, Molecular ecology resources.

[58]  I. Brunner,et al.  Aluminum exclusion and aluminum tolerance in woody plants , 2013, Front. Plant Sci..

[59]  A. Pérez-Figueroa.  msap: a tool for the statistical analysis of methylation‐sensitive amplified polymorphism data , 2013, Molecular ecology resources.

[60]  O. Acevedo-Sandoval,et al.  Impacts of Manganese Mining Activity on the Environment: Interactions Among Soil, Plants, and Arbuscular Mycorrhiza , 2013, Archives of Environmental Contamination and Toxicology.

[61]  Yongli Xu,et al.  Vacuolar membrane transporters OsVIT1 and OsVIT2 modulate iron translocation between flag leaves and seeds in rice. , 2012, The Plant journal : for cell and molecular biology.

[62]  B. Kolano,et al.  Distribution of 5S and 35S rRNA gene sites in 34 Chenopodium species (Amaranthaceae) , 2012 .

[63]  Rod Peakall,et al.  GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update , 2012, Bioinform..

[64]  X. Sheng,et al.  Assessment of bacterial communities and characterization of lead-resistant bacteria in the rhizosphere soils of metal-tolerant Chenopodium ambrosioides grown on lead-zinc mine tailings. , 2012, Chemosphere.

[65]  J. Xia,et al.  OsYSL6 Is Involved in the Detoxification of Excess Manganese in Rice1[W][OA] , 2011, Plant Physiology.

[66]  K. Hirschi,et al.  Plant cation/H+ exchangers (CAXs): biological functions and genetic manipulations. , 2011, Plant biology.

[67]  Chuan-Yun Li,et al.  KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases , 2011, Nucleic Acids Res..

[68]  N. Furuno,et al.  A novel vanadium transporter of the Nramp family expressed at the vacuole of vanadium-accumulating cells of the ascidian Ascidia sydneiensis samea. , 2011, Biochimica et biophysica acta.

[69]  Hanbo Chen,et al.  VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R , 2011, BMC Bioinformatics.

[70]  J. Pittman,et al.  Dissecting Pathways Involved in Manganese Homeostasis and Stress in Higher Plant Cells , 2010 .

[71]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[72]  S. Doncheva,et al.  Silicon amelioration of manganese toxicity in Mn-sensitive and Mn-tolerant maize varieties , 2009 .

[73]  Steve Horvath,et al.  WGCNA: an R package for weighted correlation network analysis , 2008, BMC Bioinformatics.

[74]  Thomas D. Schmittgen,et al.  Analyzing real-time PCR data by the comparative CT method , 2008, Nature Protocols.

[75]  Zhujun Zhu,et al.  Effects of exogenous salicylic acid on manganese toxicity, element contents and antioxidative system in cucumber , 2008 .

[76]  J. Pittman,et al.  ECA3, a Golgi-Localized P2A-Type ATPase, Plays a Crucial Role in Manganese Nutrition in Arabidopsis1[C][W][OA] , 2007, Plant Physiology.

[77]  Edward S. Buckler,et al.  TASSEL: software for association mapping of complex traits in diverse samples , 2007, Bioinform..

[78]  Lokesh Kumar,et al.  Mfuzz: A software package for soft clustering of microarray data , 2007, Bioinformation.

[79]  W. Maksymiec.  Signaling responses in plants to heavy metal stress , 2007, Acta Physiologiae Plantarum.

[80]  Zhujun Zhu,et al.  Combined Effects of Excess Mn and Low pH on Oxidative Stress and Antioxidant Enzymes in Cucumber Roots , 2006 .

[81]  I. E. Woodrow,et al.  In vivo localization of manganese in the hyperaccumulator Gossia bidwillii (Benth.) N. Snow & Guymer (Myrtaceae) by cryo-SEM/EDAX. , 2006, Plant, cell & environment.

[82]  S. Thomine,et al.  Mobilization of vacuolar iron by AtNRAMP3 and AtNRAMP4 is essential for seed germination on low iron , 2005, The EMBO journal.

[83]  K. Hirschi,et al.  Functional and regulatory analysis of the Arabidopsis thaliana CAX2 cation transporter , 2004, Plant Molecular Biology.

[84]  Dianmo Li,et al.  Invasive species in China — an overview , 2001, Biodiversity & Conservation.

[85]  V. Velikova,et al.  Oxidative stress and some antioxidant systems in acid rain-treated bean plants Protective role of exogenous polyamines , 2000 .

[86]  G. Gadd,et al.  Mutants of Saccharomyces cerevisiae defective in vacuolar function confirm a role for the vacuole in toxic metal ion detoxification. , 1997, FEMS microbiology letters.

[87]  J. Ruiz-Herrera,et al.  Differences in DNA methylation patterns are detectable during the dimorphic transition of fungi by amplification of restriction polymorphisms , 1997, Molecular and General Genetics MGG.

[88]  A. Wellburn,et al.  Determinations of total carotenoids and chlorophylls a and b of leaf extracts in different solvents , 1983 .

[89]  Sumira Jan,et al.  Heavy Metal ATPase (HMA2, HMA3, and HMA4) Genes in Hyperaccumulation Mechanism of Heavy Metals , 2016 .

[90]  M. Filek,et al.  Response of chloroplasts of tolerant and sensitive wheat genotypes to manganese excess: structural and biochemical properties , 2016, Acta Physiologiae Plantarum.

[91]  D. Paterson,et al.  Synchrotron-based Techniques Shed Light on Mechanisms of Plant Sensitivity and 17 Tolerance to High Manganese in the Root Environment , 2015 .

[92]  Lei Jie,et al.  Germplasm collections and manganese tolerance mechanisms of manganese hyperaccumulator plants. , 2011 .

[93]  A. van Dorsselaer,et al.  Early manganese‐toxicity response in Vigna unguiculata L. – a proteomic and transcriptomic study , 2008, Proteomics.