The methylome is altered for plants in a high CO 2 world: Insights into the response of a wild plant population to multigenerational exposure to elevated atmospheric [CO 2 ]

Current research frontiers in plant epigenetics: an introduction to a Virtual Issue

(2020) Mimmi C. Eriksson et al.   NEW PHYTOLOGIST

Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?

(2019) Mary Gehring   NEW PHYTOLOGIST

Rising Atmospheric CO 2 Lowers Concentrations of Plant Carotenoids Essential to Human Health: A Meta‐Analysis

(2019) Irakli Loladze et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Untangling the molecular mechanisms and functions of nitrate to improve nitrogen use efficiency

(2019) Asif Iqbal et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula)

(2018) Mahmoud W. Yaish et al.   BMC GENOMICS

Occultifur mephitis f.a., sp. nov. and other yeast species from hypoxic and elevated CO 2 mofette environments

(2018) Nataša Šibanc et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

New insights into the cellular mechanisms of plant growth at elevated atmospheric carbon dioxide concentrations

(2018) Dananjali Gamage et al.   PLANT CELL AND ENVIRONMENT

Ecoevolutionary Dynamics of Carbon Cycling in the Anthropocene

(2018) J. Grey Monroe et al.   TRENDS IN ECOLOGY & EVOLUTION

Structure, stability and ecological significance of natural epigenetic variation: a large-scale survey in Plantago lanceolata

(2018) Bence Gáspár et al.   NEW PHYTOLOGIST

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

FACE facts hold for multiple generations; Evidence from natural CO 2 springs

(2018) Jasmine M. Saban et al.   GLOBAL CHANGE BIOLOGY

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

Stomatal Function across Temporal and Spatial Scales: Deep-Time Trends, Land-Atmosphere Coupling and Global Models

(2017) Peter J. Franks et al.   PLANT PHYSIOLOGY

The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress

(2017) Diep R. Ganguly et al.   PLANT PHYSIOLOGY

Context and Complexity: Analyzing Methylation in Trinucleotide Sequences

(2017) Xianwei Song et al.   TRENDS IN PLANT SCIENCE

Recurrent water deficit causes epigenetic and hormonal changes in citrus plants

(2017) Diana Matos Neves et al.   Scientific Reports

Plant Transgenerational Epigenetics

(2016) Leandro Quadrana et al.   Annual Review of Genetics

Differential methylation analysis for BS-seq data under general experimental design

(2016) Yongseok Park et al.   BIOINFORMATICS

DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity

(2016) Steven R. Eichten et al.   GENOME RESEARCH

Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA-Seq transcriptome

(2016) Alexander Watson-Lazowski et al.   GLOBAL CHANGE BIOLOGY

CO 2 Sensing and CO 2 Regulation of Stomatal Conductance: Advances and Open Questions

(2016) Cawas B. Engineer et al.   TRENDS IN PLANT SCIENCE

DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses

(2016) Thomas Wicker et al.   Nature Communications

Adaptation to elevated CO2 in different biodiversity contexts

(2016) Elizabeth J. Kleynhans et al.   Nature Communications

Whole genome DNA methylation: beyond genes silencing

(2016) Roberto Tirado-Magallanes et al.   Oncotarget

Elevated-CO2 Response of Stomata and Its Dependence on Environmental Factors

(2016) Zhenzhu Xu et al.   Frontiers in Plant Science

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

(2016) P. A. Crisp et al.   Science Advances

Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism

(2016) Hui Xia et al.   PLoS One

GOplot: an R package for visually combining expression data with functional analysis: Fig. 1.

(2015) Wencke Walter et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Low temperature-induced DNA hypermethylation attenuates expression of RhAG, an AGAMOUS homolog, and increases petal number in rose (Rosa hybrida)

(2015) Nan Ma et al.   BMC PLANT BIOLOGY

Elevated CO 2 -Induced Responses in Stomata Require ABA and ABA Signaling

(2015) Caspar Chater et al.   CURRENT BIOLOGY

The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome

(2015) Tanya Z. Berardini et al.   GENESIS

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

(2015) Manu J Dubin et al.   eLife

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

(2015) Rohini Garg et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

(2014) Edith Heard et al.   CELL

Contemporary evolution of an invasive grass in response to elevated atmospheric CO2at a Mojave Desert FACE site

(2014) Judah D. Grossman et al.   ECOLOGY LETTERS

Complex phylogeny and gene expression patterns of members of the NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family (NPF) in wheat

(2014) Peter Buchner et al.   JOURNAL OF EXPERIMENTAL BOTANY

Increasing CO2 threatens human nutrition

(2014) Samuel S. Myers et al.   NATURE

Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

(2014) S. R. Eichten et al.   PLANT PHYSIOLOGY

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

OrganellarGenomeDRAW—a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets

(2013) Marc Lohse et al.   NUCLEIC ACIDS RESEARCH

Response to multi-generational selection under elevated [CO2] in two temperature regimes suggests enhanced carbon assimilation and increased reproductive output inBrassica napusL.

(2013) Georg Frenck et al.   Ecology and Evolution

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Variable Changes in Genome Size Associated with Different Polyploid Events in Plantago (Plantaginaceae)

(2012) C. Wong et al.   JOURNAL OF HEREDITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Stomatal control as a driver of plant evolution

(2011) M. Haworth et al.   JOURNAL OF EXPERIMENTAL BOTANY

Phenotypic and genetic differences in a perennial herb across a natural gradient of CO2 concentration

(2011) Ito Nakamura et al.   OECOLOGIA

DNA cytosine methylation in plant development

(2010) Meishan Zhang et al.   Journal of Genetics and Genomics

Identification of a Novel Abscisic Acid-Regulated Farnesol Dehydrogenase from Arabidopsis

(2010) J. Bhandari et al.   PLANT PHYSIOLOGY

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Stress-induced DNA methylation changes and their heritability in asexual dandelions

(2009) Koen J. F. Verhoeven et al.   NEW PHYTOLOGIST

Maximum leaf conductance driven by CO2 effects on stomatal size and density over geologic time

(2009) P. J. Franks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS