The methylome is altered for plants in a high CO2 world: Insights into the response of a wild plant population to multigenerational exposure to elevated atmospheric [CO2]
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[1] O. Paun,et al. Current research frontiers in plant epigenetics: an introduction to a Virtual Issue , 2020, The New phytologist.
[2] A. Iqbal,et al. Untangling the molecular mechanisms and functions of nitrate for improving nitrogen use efficiency. , 2020, Journal of the science of food and agriculture.
[3] L. Ziska,et al. Rising Atmospheric CO2 Lowers Concentrations of Plant Carotenoids Essential to Human Health: Meta-analysis. , 2019, Molecular nutrition & food research.
[4] Mary Gehring. Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming? , 2019, The New phytologist.
[5] G. Taylor,et al. FACE facts hold for multiple generations; Evidence from natural CO2 springs , 2018, Global change biology.
[6] Chi Zhang,et al. PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files , 2018, Bioinform..
[7] O. Bossdorf,et al. Structure, stability and ecological significance of natural epigenetic variation: a large-scale survey in Plantago lanceolata. , 2018, The New phytologist.
[8] S. Sultan,et al. Context-Dependent Developmental Effects of Parental Shade Versus Sun Are Mediated by DNA Methylation , 2018, Front. Plant Sci..
[9] A. Makino,et al. New insights into the cellular mechanisms of plant growth at elevated atmospheric carbon dioxide concentrations. , 2018, Plant, cell & environment.
[10] P. Zalar,et al. Occultifur mephitis f.a., sp. nov. and other yeast species from hypoxic and elevated CO2 mofette environments. , 2018, International journal of systematic and evolutionary microbiology.
[11] D. W. Markman,et al. Ecoevolutionary Dynamics of Carbon Cycling in the Anthropocene. , 2018, Trends in ecology & evolution.
[12] Ibtisam Al-Harrasi,et al. Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula) , 2018, BMC Genomics.
[13] L. Freschi,et al. Recurrent water deficit causes epigenetic and hormonal changes in citrus plants , 2017, Scientific Reports.
[14] Peter A. Crisp,et al. The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress1[OPEN] , 2017, Plant Physiology.
[15] J. Lämke,et al. Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants , 2017, Genome Biology.
[16] Axel Fischer,et al. GeSeq – versatile and accurate annotation of organelle genomes , 2017, Nucleic Acids Res..
[17] Xiaofeng Cao,et al. Context and Complexity: Analyzing Methylation in Trinucleotide Sequences. , 2017, Trends in plant science.
[18] G. Bonan,et al. Stomatal Function across Temporal and Spatial Scales: Deep-Time Trends, Land-Atmosphere Coupling and Global Models1[OPEN] , 2017, Plant Physiology.
[19] Sonja J. Prohaska,et al. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward , 2017, bioRxiv.
[20] W. Ye,et al. Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress , 2017, BMC Genomics.
[21] D. Zivkovic,et al. Methylome evolution in plants , 2016, Genome Biology.
[22] V. Colot,et al. Plant Transgenerational Epigenetics. , 2016, Annual review of genetics.
[23] Touati Benoukraf,et al. Whole genome DNA methylation: beyond genes silencing , 2016, Oncotarget.
[24] Patrick Mardulyn,et al. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. , 2016, Nucleic acids research.
[25] R. Wing,et al. DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses , 2016, Nature Communications.
[26] Richard J. Edwards,et al. Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA‐Seq transcriptome , 2016, Global change biology.
[27] P. Reich,et al. Adaptation to elevated CO2 in different biodiversity contexts , 2016, Nature Communications.
[28] L. Luo,et al. Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism , 2016, PloS one.
[29] Robert J. Schmitz,et al. Widespread natural variation of DNA methylation within angiosperms , 2016, Genome Biology.
[30] Hao Wu,et al. Differential methylation analysis for BS-seq data under general experimental design , 2016, Bioinform..
[31] Guangsheng Zhou,et al. Elevated-CO2 Response of Stomata and Its Dependence on Environmental Factors , 2016, Front. Plant Sci..
[32] Sergio Alan Cervantes-Pérez,et al. Phosphate starvation induces DNA methylation in the vicinity of cis-acting elements known to regulate the expression of phosphate–responsive genes , 2016, Plant signaling & behavior.
[33] Philip N Benfey,et al. Unique cell-type specific patterns of DNA methylation in the root meristem , 2016, Nature Plants.
[34] Steven R. Eichten,et al. DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity , 2016, bioRxiv.
[35] Diep Ganguly,et al. Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics , 2016, Science Advances.
[36] D. Siemens,et al. Epigenetics of drought-induced trans-generational plasticity: consequences for range limit development , 2015, AoB PLANTS.
[37] Robert D. Finn,et al. The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..
[38] Stuart A Casson,et al. Elevated CO2-Induced Responses in Stomata Require ABA and ABA Signaling , 2015, Current Biology.
[39] Mukesh Jain,et al. Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response , 2015, Scientific Reports.
[40] N. Ma,et al. Low temperature-induced DNA hypermethylation attenuates expression of RhAG, an AGAMOUS homolog, and increases petal number in rose (Rosa hybrida) , 2015, BMC Plant Biology.
[41] Evgeny M. Zdobnov,et al. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..
[42] Fátima Sánchez-Cabo,et al. GOplot: an R package for visually combining expression data with functional analysis , 2015, Bioinform..
[43] Emily M. Strait,et al. The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome , 2015, Genesis.
[44] Gunnar Rätsch,et al. DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation , 2015, eLife.
[45] M. Yandell,et al. Genome Annotation and Curation Using MAKER and MAKER‐P , 2014, Current protocols in bioinformatics.
[46] M. Hawkesford,et al. Complex phylogeny and gene expression patterns of members of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) in wheat , 2014, Journal of experimental botany.
[47] Robert J. Schmitz,et al. Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation1 , 2014, Plant Physiology.
[48] A. Zanobetti,et al. Increasing CO2 threatens human nutrition , 2014, Nature.
[49] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[50] R. Martienssen,et al. Transgenerational Epigenetic Inheritance: Myths and Mechanisms , 2014, Cell.
[51] K. Rice,et al. Contemporary evolution of an invasive grass in response to elevated atmospheric CO2 at a Mojave Desert FACE site , 2014, Ecology letters.
[52] Matthew Fraser,et al. InterProScan 5: genome-scale protein function classification , 2014, Bioinform..
[53] Mauricio O. Carneiro,et al. From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.
[54] Robert Gentleman,et al. Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..
[55] 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.
[56] Marc Lohse,et al. OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets , 2013, Nucleic Acids Res..
[57] Rikke Bagger Jørgensen,et al. Response to multi-generational selection under elevated [CO2] in two temperature regimes suggests enhanced carbon assimilation and increased reproductive output in Brassica napus L. , 2013, Ecology and evolution.
[58] Matthew D. Schultz,et al. Patterns of Population Epigenomic Diversity , 2013, Nature.
[59] Jian Wang,et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.
[60] Matthew D. Schultz,et al. 'Leveling' the playing field for analyses of single-base resolution DNA methylomes. , 2012, Trends in genetics : TIG.
[61] Anushya Muruganujan,et al. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees , 2012, Nucleic Acids Res..
[62] Francine E. Garrett-Bakelman,et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles , 2012, Genome Biology.
[63] B. Murray,et al. Variable changes in genome size associated with different polyploid events in Plantago (Plantaginaceae). , 2012, The Journal of heredity.
[64] L. Ziska,et al. Plant Responses to Elevated CO2 , 2012 .
[65] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[66] Davis J. McCarthy,et al. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation , 2012, Nucleic acids research.
[67] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[68] Matthew R. Haworth,et al. Stomatal control as a driver of plant evolution. , 2011, Journal of experimental botany.
[69] Felix Krueger,et al. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..
[70] K. Hikosaka,et al. Phenotypic and genetic differences in a perennial herb across a natural gradient of CO2 concentration , 2011, Oecologia.
[71] D. Crowell,et al. Identification of a Novel Abscisic Acid-Regulated Farnesol Dehydrogenase from Arabidopsis1[W][OA] , 2010, Plant Physiology.
[72] J. J. Jansen,et al. Stress-induced DNA methylation changes and their heritability in asexual dandelions. , 2010, The New phytologist.
[73] David J. Beerling,et al. Maximum leaf conductance driven by CO2 effects on stomatal size and density over geologic time , 2009, Proceedings of the National Academy of Sciences.
[74] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[75] Jian-Kang Zhu,et al. Epigenetic regulation of stress responses in plants. , 2009, Current opinion in plant biology.
[76] O. Gaggiotti,et al. A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective , 2008, Genetics.
[77] Sofia M. C. Robb,et al. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. , 2007, Genome research.
[78] I. Henderson,et al. Epigenetic inheritance in plants , 2007, Nature.
[79] G. Taylor,et al. Elucidating genomic regions determining enhanced leaf growth and delayed senescence in elevated CO2. , 2006, Plant, cell & environment.
[80] D. Reich,et al. Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.
[81] Hongwen Huang,et al. Development and characterization of polymorphic microsatellite loci in endangered fern Adiantum reniforme var. sinense , 2006, Conservation Genetics.
[82] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[83] P. Gupta,et al. Linkage disequilibrium and association studies in higher plants: Present status and future prospects , 2005, Plant Molecular Biology.
[84] S. Long,et al. What have we learned from 15 years of free-air CO2 enrichment (FACE)? A meta-analytic review of the responses of photosynthesis, canopy properties and plant production to rising CO2. , 2004, The New phytologist.
[85] Ian Korf,et al. Gene finding in novel genomes , 2004, BMC Bioinformatics.
[86] C. N. Hewitt,et al. Impact of rising CO2 on emissions of volatile organic compounds: isoprene emission from Phragmites australis growing at elevated CO2 in a natural carbon dioxide spring† , 2004 .
[87] Hong Gil Nam,et al. Stress memory in plants: a negative regulation of stomatal response and transient induction of rd22 gene to light in abscisic acid-entrained Arabidopsis plants. , 2003, The Plant journal : for cell and molecular biology.
[88] Mario Stanke,et al. Gene prediction with a hidden Markov model and a new intron submodel , 2003, ECCB.
[89] F. Woodward,et al. The role of stomata in sensing and driving environmental change , 2003, Nature.
[90] Brad T. Sherman,et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.
[91] R. Matyášek,et al. Cytosine methylation of plastid genome in higher plants. Fact or artefact? , 2001, Plant science : an international journal of experimental plant biology.
[92] P. Pearson,et al. Atmospheric carbon dioxide concentrations over the past 60 million years , 2000, Nature.
[93] J. Ward,et al. Is atmospheric CO2 a selective agent on model C3 annuals? , 2000, Oecologia.
[94] A. Raschi,et al. The impact of elevated CO2 on growth and photosynthesis in Agrostis canina L. ssp. monteluccii adapted to contrasting atmospheric CO2 concentrations , 1997, Oecologia.
[95] K. Shinozaki,et al. Identification of a cis-regulatory region of a gene in Arabidopsis thaliana whose induction by dehydration is mediated by abscisic acid and requires protein synthesis , 1995, Molecular and General Genetics MGG.
[96] R. Olmstead,et al. Evidence for the polyphyly of the Scrophulariaceae based on Chloroplast rbcL and ndhF sequences , 1995 .
[97] C. Körner,et al. Long term effects of naturally elevated CO2 on mediterranean grassland and forest trees , 1994, Oecologia.
[98] A. Raschi,et al. Natural CO2 springs in Italy: a resource for examining long‐term response of vegetation to rising atmospheric CO2 concentrations , 1993 .
[99] S. Kalisz,et al. A LIFE‐HISTORY BASED STUDY OF POPULATION GENETIC STRUCTURE: SEED BANK TO ADULTS IN PLANTAGO LANCEOLATA , 1993, Evolution; international journal of organic evolution.
[100] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[101] K. Wolff,et al. Genetic variability in Plantago species in relation to their ecology , 1988, Theoretical and Applied Genetics.
[102] H. Harmens,et al. Gene flow in Plantago I. Gene flow and neighbourhood size in P. lanceolata1 , 1986, Heredity.
[103] Robert J. Schmitz,et al. Putting DNA methylation in context: from genomes to gene expression in plants. , 2017, Biochimica et biophysica acta. Gene regulatory mechanisms.
[104] Nicolas Dierckxsens,et al. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. , 2016, Nucleic acids research.
[105] W. Rappel,et al. CO2 Sensing and CO2 Regulation of Stomatal Conductance: Advances and Open Questions. , 2016, Trends in plant science.
[106] M. Andersson,et al. Molecular Basis of Variation in Stomatal Responsiveness to Elevated CO2 , 2015 .
[107] R Core Team,et al. R: A language and environment for statistical computing. , 2014 .
[108] Stewart J. Cohen,et al. Climate Change 2014: Impacts,Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group II to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change , 2014 .
[109] Bao Liu,et al. DNA cytosine methylation in plant development. , 2010, Journal of genetics and genomics = Yi chuan xue bao.
[110] S. Long,et al. Review Tansley Review , 2022 .
[111] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .