The genome of stress tolerant crop wild relative Paspalum vaginatum leads to increased biomass productivity in the crop Zea mays
暂无分享,去创建一个
S. Shu | J. Schmutz | R. O’Malley | J. Jenkins | K. Barry | Toshihiro Obata | C. Daum | A. Lipzen | P. Qi | Bin Yu | K. Devos | Cindy Chen | L. Berry | Bangjun Zhou | Chi Zhang | Laura Sandor | Christopher Plott | Huihui Yu | Ronan C. O’Malley | B. Sigmon | Guangchao Sun | Nishikant Wase | James c. Schnable | Yuko Yoshinga | Thomas Gottilla | Ashley Foltz | Anna Lipzen | C. Plott
[1] U. Ludewig,et al. Adjusting plant nutrient acquisition to fluctuating availability: transcriptional co-regulation of the nitrate and phosphate deprivation responses in roots , 2021, Journal of experimental botany.
[2] Ming-guo Zhou,et al. Mechanism of validamycin A inhibiting DON biosynthesis and synergizing with DMI fungicides against Fusarium graminearum , 2021, Molecular plant pathology.
[3] Mark R. Marten,et al. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1 , 2021, Autophagy.
[4] M. Paul,et al. Trehalose 6-phosphate signalling and impact on crop yield , 2020, Biochemical Society transactions.
[5] Xuan Zeng,et al. A Rice Autophagy Gene OsATG8b Is Involved in Nitrogen Remobilization and Control of Grain Quality , 2020, Frontiers in Plant Science.
[6] W. Huh,et al. The trehalose-6-phosphate phosphatase Tps2 regulates ATG8 transcription and autophagy in Saccharomyces cerevisiae , 2020, Autophagy.
[7] M. Fujita,et al. Trehalose Protects Maize Plants from Salt Stress and Phosphorus Deficiency , 2019, Plants.
[8] D. Bassham,et al. Combating stress: the interplay between hormone signaling and autophagy in plants. , 2019, Journal of experimental botany.
[9] Toshihiro Obata,et al. Metabolic Dynamics of Developing Rice Seeds Under High Night-Time Temperature Stress , 2019, Front. Plant Sci..
[10] S. Thomine,et al. Autophagy and Nutrients Management in Plants , 2019, Cells.
[11] R. Sekhon,et al. Sugar Partitioning and Source-Sink Interaction are Key Determinants of Leaf Senescence in Maize. , 2019, Plant, cell & environment.
[12] J. Schmutz,et al. High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome , 2019, Scientific Reports.
[13] Steven B. Cogill,et al. Comparative transcriptome profiling provides insights into plant salt tolerance in seashore paspalum (Paspalum vaginatum) , 2019, BMC Genomics.
[14] Qiang Liu,et al. Overexpression of maize sucrose non-fermenting-1-related protein kinase 1 genes, ZmSnRK1s, causes alteration in carbon metabolism and leaf senescence in Arabidopsis thaliana. , 2019, Gene.
[15] H. Matsui,et al. Functional identification of a rice trehalase gene involved in salt stress tolerance. , 2019, Gene.
[16] Hui Zhang,et al. The genome of broomcorn millet , 2019, Nature Communications.
[17] N. Killiny,et al. Exogenous GABA is quickly metabolized to succinic acid and fed into the plant TCA cycle , 2019, Plant signaling & behavior.
[18] S. Signorelli,et al. Autophagy in Plants: Both a Puppet and a Puppet Master of Sugars , 2019, Front. Plant Sci..
[19] Jie Zhou,et al. BZR1 Mediates Brassinosteroid-Induced Autophagy and Nitrogen Starvation in Tomato1 , 2018, Plant Physiology.
[20] R. Vierstra,et al. Maize multi-omics reveal roles for autophagic recycling in proteome remodelling and lipid turnover , 2018, Nature Plants.
[21] J. Peñuelas,et al. Root exudate metabolomes change under drought and show limited capacity for recovery , 2018, Scientific Reports.
[22] Tamar Avin-Wittenberg. Autophagy and its role in plant abiotic stress management. , 2018, Plant, cell & environment.
[23] James C. Schnable,et al. Parallel natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize , 2018 .
[24] Brent S. Pedersen,et al. GOATOOLS: A Python library for Gene Ontology analyses , 2018, Scientific Reports.
[25] Carolyn J. Lawrence-Dill,et al. Response to Persistent ER Stress in Plants: A Multiphasic Process That Transitions Cells from Prosurvival Activities to Cell Death[OPEN] , 2018, Plant Cell.
[26] Jukon Kim,et al. A Nitrogen Molecular Sensing System, Comprised of the ALLANTOINASE and UREIDE PERMEASE 1 Genes, Can Be Used to Monitor N Status in Rice , 2018, Front. Plant Sci..
[27] M. Paul,et al. Trehalose 6-Phosphate Regulates Photosynthesis and Assimilate Partitioning in Reproductive Tissue , 2018, Plant Physiology.
[28] P. Carillo. GABA Shunt in Durum Wheat , 2018, Front. Plant Sci..
[29] F. Fritschi,et al. Post-silking carbon partitioning under nitrogen deficiency revealed sink limitation of grain yield in maize , 2018, Journal of experimental botany.
[30] M. Paul,et al. Exogenous trehalose improves growth under limiting nitrogen through upregulation of nitrogen metabolism , 2017, BMC Plant Biology.
[31] Iddo Friedberg,et al. Maize GO Annotation—Methods, Evaluation, and Review (maize‐GAMER) , 2017, bioRxiv.
[32] P. Raymer,et al. Ploidy Level and Genetic Diversity in the Genus Paspalum, Group Disticha , 2017 .
[33] He-Jin Lee,et al. Is trehalose an autophagic inducer? Unraveling the roles of non-reducing disaccharides on autophagic flux and alpha-synuclein aggregation , 2017, Cell Death and Disease.
[34] Feng Luo,et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads , 2017, Nature Methods.
[35] D. Bassham,et al. SnRK1 activates autophagy via the TOR signaling pathway in Arabidopsis thaliana , 2017, PloS one.
[36] G. Schnitkey. Fertilizer Costs in 2017 and 2018 , 2017 .
[37] L. M. Lagrimini,et al. The role of Tre6P and SnRK1 in maize early kernel development and events leading to stress-induced kernel abortion , 2017, BMC Plant Biology.
[38] Rebecca L. Roston,et al. Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize[OPEN] , 2017, Plant Cell.
[39] F. Rolland,et al. The SnRK1 Energy Sensor in Plant Biotic Interactions. , 2016, Trends in plant science.
[40] Li Li,et al. Trehalose, sucrose and raffinose are novel activators of autophagy in human keratinocytes through an mTOR-independent pathway , 2016, Scientific Reports.
[41] Lior Pachter,et al. Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.
[42] T. Vyn,et al. Maize Plant Resilience to N Stress and Post-silking N Capacity Changes over Time: A Review , 2016, Front. Plant Sci..
[43] Xiuren Zhang,et al. Trehalose Accumulation Triggers Autophagy during Plant Desiccation. , 2015, PLoS genetics.
[44] L. M. Lagrimini,et al. Differential Role for Trehalose Metabolism in Salt-Stressed Maize[OPEN] , 2015, Plant Physiology.
[45] S. Kelly,et al. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy , 2015, Genome Biology.
[46] L. M. Lagrimini,et al. Expression of trehalose-6-phosphate phosphatase in maize ears improves yield in well-watered and drought conditions , 2015, Nature Biotechnology.
[47] R. Vierstra,et al. Autophagic Recycling Plays a Central Role in Maize Nitrogen Remobilization , 2015, Plant Cell.
[48] S. Kojima,et al. Autophagy Supports Biomass Production and Nitrogen Use Efficiency at the Vegetative Stage in Rice1[OPEN] , 2015, Plant Physiology.
[49] Katharina J. Hoff,et al. BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS , 2016, Bioinform..
[50] Chao Xie,et al. Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.
[51] W. Huber,et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.
[52] A. von Haeseler,et al. IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.
[53] Paul Theodor Pyl,et al. HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.
[54] Mark Stitt,et al. Trehalose metabolism in plants. , 2014, The Plant journal : for cell and molecular biology.
[55] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[56] M. Abbas,et al. Drought Resistance Strategies of Seashore Paspalum Cultivars at Different Mowing Heights , 2014 .
[57] W. Bond,et al. Diversification of C(4) grasses (Poaceae) does not coincide with their ecological dominance. , 2014, American journal of botany.
[58] Alexandros Stamatakis,et al. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..
[59] Aaron A. Klammer,et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.
[60] H. Di,et al. Nitrogen losses from the soil/plant system: a review , 2013 .
[61] M. Paul,et al. Inhibition of SnRK1 by metabolites: tissue-dependent effects and cooperative inhibition by glucose 1-phosphate in combination with trehalose 6-phosphate. , 2013, Plant physiology and biochemistry : PPB.
[62] R. Feil,et al. Overexpression of the Trehalase Gene AtTRE1 Leads to Increased Drought Stress Tolerance in Arabidopsis and Is Involved in Abscisic Acid-Induced Stomatal Closure1[W][OA] , 2013, Plant Physiology.
[63] U. Sonnewald,et al. Maize Source Leaf Adaptation to Nitrogen Deficiency Affects Not Only Nitrogen and Carbon Metabolism But Also Control of Phosphate Homeostasis1[W][OA] , 2012, Plant Physiology.
[64] A. Fernie,et al. The use of metabolomics to dissect plant responses to abiotic stresses , 2012, Cellular and Molecular Life Sciences.
[65] Justin N. Vaughn,et al. Reference genome sequence of the model plant Setaria , 2012, Nature Biotechnology.
[66] Anne Guiboileau,et al. Autophagy machinery controls nitrogen remobilization at the whole-plant level under both limiting and ample nitrate conditions in Arabidopsis. , 2012, The New phytologist.
[67] Haiyan Zhang,et al. ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments. , 2012, Biochemical and biophysical research communications.
[68] Jeremy D. DeBarry,et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity , 2012, Nucleic acids research.
[69] David M. Goodstein,et al. Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..
[70] A. Igiri,et al. Growth of seashore paspalum, ( Paspalum vaginatum L ) in soil contaminated with crude petroleum oil , 2011 .
[71] M. Matsui,et al. Growth Arrest by Trehalose-6-Phosphate: An Astonishing Case of Primary Metabolite Control over Growth by Way of the SnRK1 Signaling Pathway1[C][W][OA] , 2011, Plant Physiology.
[72] M. Frith,et al. Adaptive seeds tame genomic sequence comparison. , 2011, Genome research.
[73] M. Hajirezaei,et al. Root exudation of sugars, amino acids, and organic acids by maize as affected by nitrogen, phosphorus, potassium, and iron deficiency , 2011 .
[74] J. Fisahn,et al. Photosynthesis and metabolism interact during acclimation of Arabidopsis thaliana to high irradiance and sulphur depletion. , 2010, Plant, cell & environment.
[75] Remco R. Bouckaert,et al. DensiTree: making sense of sets of phylogenetic trees , 2010, Bioinform..
[76] Hongdong Xiao,et al. Effect of silicon on chilling-induced changes of solutes, antioxidants, and membrane stability in seashore paspalum turfgrass , 2010, Acta Physiologiae Plantarum.
[77] Wanchen Li,et al. Cloning and Characterization of Functional Trehalose-6-Phosphate Synthase Gene in Maize , 2010, Journal of Plant Biology.
[78] Sai Guna Ranjan Gurazada,et al. Genome sequencing and analysis of the model grass Brachypodium distachyon , 2010, Nature.
[79] Jiping Chen,et al. The responses of Arabidopsis thaliana to cadmium exposure explored via metabolite profiling. , 2010, Chemosphere.
[80] Dawn H. Nagel,et al. The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.
[81] D. Cordell,et al. The story of phosphorus: Global food security and food for thought , 2009 .
[82] M. Stitt,et al. Adjustment of growth and central metabolism to a mild but sustained nitrogen-limitation in Arabidopsis. , 2009, Plant, cell & environment.
[83] P. J. Andralojc,et al. Inhibition of SNF1-Related Protein Kinase1 Activity and Regulation of Metabolic Pathways by Trehalose-6-Phosphate1[W][OA] , 2009, Plant Physiology.
[84] Mihaela M. Martis,et al. The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.
[85] W. Winiwarter,et al. How a century of ammonia synthesis changed the world , 2008 .
[86] R. Vierstra,et al. The ATG Autophagic Conjugation System in Maize: ATG Transcripts and Abundance of the ATG8-Lipid Adduct Are Regulated by Development and Nutrient Availability1[W][OA] , 2008, Plant Physiology.
[87] Filip Rolland,et al. A central integrator of transcription networks in plant stress and energy signalling , 2007, Nature.
[88] Gerard Talavera,et al. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. , 2007, Systematic biology.
[89] Yiwei Jiang,et al. Broadband Spectral Reflectance Models of Turfgrass Species and Cultivars to Drought Stress , 2007 .
[90] Philip Mancus. Nitrogen Fertilizer Dependency and Its Contradictions: A Theoretical Exploration of Social‐Ecological Metabolism* , 2007 .
[91] John A. Hamilton,et al. The TIGR Rice Genome Annotation Resource: improvements and new features , 2006, Nucleic Acids Res..
[92] A. Fernie,et al. Gas chromatography mass spectrometry–based metabolite profiling in plants , 2006, Nature Protocols.
[93] Thomas Ragg,et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements , 2006, BMC Molecular Biology.
[94] Rolf Apweiler,et al. InterProScan: protein domains identifier , 2005, Nucleic Acids Res..
[95] D. Bassham,et al. Visualization of autophagy in Arabidopsis using the fluorescent dye monodansylcadaverine and a GFP-AtATG8e fusion protein. , 2005, The Plant journal : for cell and molecular biology.
[96] Ewan Birney,et al. Automated generation of heuristics for biological sequence comparison , 2005, BMC Bioinformatics.
[97] Charles L. Guy,et al. Exploring the Temperature-Stress Metabolome of Arabidopsis1[w] , 2004, Plant Physiology.
[98] M. Nguyen,et al. Phosphorus runoff from agricultural land and direct fertilizer effects: a review. , 2004, Journal of environmental quality.
[99] Oliver Fiehn,et al. A prominent role for the CBF cold response pathway in configuring the low-temperature metabolome of Arabidopsis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[100] Jianxin Ma,et al. Close split of sorghum and maize genome progenitors. , 2004, Genome research.
[101] A. V. Van Dijken,et al. Trehalose Mediated Growth Inhibition of Arabidopsis Seedlings Is Due to Trehalose-6-Phosphate Accumulation1[w] , 2004, Plant Physiology.
[102] K. Matsuoka,et al. 3-methyladenine inhibits autophagy in tobacco culture cells under sucrose starvation conditions. , 2004, Plant & cell physiology.
[103] Yiwei Jiang,et al. Assessment of low light tolerance of seashore paspalum and bermudagrass , 2004 .
[104] Stephen M. Mount,et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.
[105] A. Myers,et al. Mutational Analysis of the Pullulanase-Type Debranching Enzyme of Maize Indicates Multiple Functions in Starch Metabolism Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.007575. , 2003, The Plant Cell Online.
[106] Michael J. Sanderson,et al. R8s: Inferring Absolute Rates of Molecular Evolution, Divergence times in the Absence of a Molecular Clock , 2003, Bioinform..
[107] T. G. Owens,et al. Trehalose accumulation in rice plants confers high tolerance levels to different abiotic stresses , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[108] W. V. Baird,et al. Changes in Membrane Polar Lipid Fatty Acids of Seashore Paspalum in Response to Low Temperature Exposure , 2002 .
[109] M. Tollenaar,et al. Yield potential, yield stability and stress tolerance in maize , 2002 .
[110] L. Trenholm,et al. Wear Tolerance, Growth, and Quality of Seashore Paspalum in Response to Nitrogen and Potassium , 2001 .
[111] T. Boller,et al. Trehalose and trehalase in Arabidopsis. , 2001, Plant physiology.
[112] V. Solovyev,et al. Ab initio gene finding in Drosophila genomic DNA. , 2000, Genome research.
[113] Bingru Huang,et al. Drought-resistance mechanisms of seven warm-season turfgrasses under surface soil drying. I. Shoot response , 1997 .
[114] Ziheng Yang,et al. PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..
[115] C. Cardona,et al. Low temperature tolerance assessment in Paspalum , 1997 .
[116] K. van Dun,et al. Inhibition of Trehalase Activity Enhances Trehalose Accumulation in Transgenic Plants , 1997, Plant physiology.
[117] H. Iwamura,et al. Succinic and lactic acids as plant growth promoting compounds produced by rhizospheric Pseudomonas putida , 1993 .
[118] M. Daly,et al. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. , 1987, Genomics.
[119] R. Brouwer. Nutritive influences on the distribution of dry matter in the plant , 1962 .
[120] D. Lightfoot. Developing Crop Varieties with Improved Nutrient-Use Efficiency , 2018 .
[121] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[122] T. Hodkinson,et al. New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins. , 2012, The New phytologist.
[123] M. Udvardi,et al. Comparative metabolomics of drought acclimation in model and forage legumes. , 2012, Plant, cell & environment.
[124] W. Rooney,et al. Genome evolution in the genus Sorghum (Poaceae). , 2005, Annals of botany.
[125] T. Ericsson. Growth and shoot: root ratio of seedlings in relation to nutrient availability , 2004, Plant and Soil.
[126] Jonathan D. G. Jones,et al. Trehalose-6-phosphate synthase 1, which catalyses the first step in trehalose synthesis, is essential for Arabidopsis embryo maturation. , 2002, The Plant journal : for cell and molecular biology.
[127] T. Horiguchi,et al. Responses of secondary metabolism in plants to nutrient deficiency , 1997 .
[128] E. Kendall,et al. Trehalase activity in plant tissue cultures , 1990 .