Embryophyte stress signaling evolved in the algal progenitors of land plants

Plant evolution: landmarks on the path to terrestrial life

(2018) Jan de Vries et al.   NEW PHYTOLOGIST

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

(2018) Daniel Lang et al.   PLANT JOURNAL

The Carboxy Terminus of YCF1 Contains a Motif Conserved throughout >500 Myr of Streptophyte Evolution

(2017) Jan de Vries et al.   Genome Biology and Evolution

The monoplastidic bottleneck in algae and plant evolution

(2017) Jan de Vries et al.   JOURNAL OF CELL SCIENCE

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

The plant perceptron connects environment to development

(2017) Ben Scheres et al.   NATURE

Enhanced Desiccation Tolerance in Mature Cultures of the Streptophytic Green Alga Zygnema circumcarinatum Revealed by Transcriptomics

(2017) Martin Rippin et al.   PLANT AND CELL PHYSIOLOGY

How Embryophytic is the Biosynthesis of Phenylpropanoids and their Derivatives in Streptophyte Algae?

(2017) Jan de Vries et al.   PLANT AND CELL PHYSIOLOGY

Fern Stomatal Responses to ABA and CO 2 Depend on Species and Growth Conditions

(2017) Hanna Hõrak et al.   PLANT PHYSIOLOGY

Seedlings Lacking the PTM Protein Do Not Show a genomes uncoupled (gun) Mutant Phenotype

(2017) Mike T. Page et al.   PLANT PHYSIOLOGY

A chloroplast retrograde signal, 3’-phosphoadenosine 5’-phosphate, acts as a secondary messenger in abscisic acid signaling in stomatal closure and germination

(2017) Wannarat Pornsiriwong et al.   eLife

Regulatory Shifts in Plastid Transcription Play a Key Role in Morphological Conversions of Plastids during Plant Development

(2017) Monique Liebers et al.   Frontiers in Plant Science

LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell

(2017) Jana Sperschneider et al.   Scientific Reports

Learning the Languages of the Chloroplast: Retrograde Signaling and Beyond

(2016) Kai Xun Chan et al.   Annual Review of Plant Biology

Retrograde signaling: Organelles go networking

(2016) Tatjana Kleine et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

SLAH1, a homologue of the slow type anion channel SLAC1, modulates shoot Cl−accumulation and salt tolerance inArabidopsis thaliana

(2016) Jiaen Qiu et al.   JOURNAL OF EXPERIMENTAL BOTANY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Reactive oxygen species, abiotic stress and stress combination

(2016) Feroza K. Choudhury et al.   PLANT JOURNAL

Superoxide and Singlet Oxygen Produced within the Thylakoid Membranes Both Cause Photosystem I Photoinhibition

(2016) Daisuke Takagi et al.   PLANT PHYSIOLOGY

Transcriptome Profiling of the Green Alga Spirogyra pratensis (Charophyta) Suggests an Ancestral Role for Ethylene in Cell Wall Metabolism, Photosynthesis, and Abiotic Stress Responses

(2016) Bram Van de Poel et al.   PLANT PHYSIOLOGY

Redox- and Reactive Oxygen Species-Dependent Signaling into and out of the Photosynthesizing Chloroplast

(2016) Karl-Josef Dietz et al.   PLANT PHYSIOLOGY

Abscisic acid controlled sex before transpiration in vascular plants

(2016) Scott A. M. McAdam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phytochrome B integrates light and temperature signals in Arabidopsis

(2016) Martina Legris et al.   SCIENCE

Streptophyte Terrestrialization in Light of Plastid Evolution

(2016) Jan de Vries et al.   TRENDS IN PLANT SCIENCE

Phytochrome B and REVEILLE1/2-mediated signalling controls seed dormancy and germination in Arabidopsis

(2016) Zhimin Jiang et al.   Nature Communications

Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network

(2016) Guiomar Martín et al.   Nature Communications

Chloroplast RNA polymerases: Role in chloroplast biogenesis

(2015) Thomas Börner et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The Evolutionary Origin of a Terrestrial Flora

(2015) Charles Francis Delwiche et al.   CURRENT BIOLOGY

Stomatal Guard Cells Co-opted an Ancient ABA-Dependent Desiccation Survival System to Regulate Stomatal Closure

(2015) Christof Lind et al.   CURRENT BIOLOGY

Plastid RNA polymerases: orchestration of enzymes with different evolutionary origins controls chloroplast biogenesis during the plant life cycle

(2015) Thomas Pfannschmidt et al.   JOURNAL OF EXPERIMENTAL BOTANY

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Insights into the Origin and Evolution of the Plant Hormone Signaling Machinery

(2015) Chunyang Wang et al.   PLANT PHYSIOLOGY

Algal ancestor of land plants was preadapted for symbiosis

(2015) Pierre-Marc Delaux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell wall remodeling under abiotic stress

(2015) Raimund Tenhaken   Frontiers in Plant Science

Conservation of ethylene as a plant hormone over 450 million years of evolution

(2015) Chuanli Ju et al.   Nature Plants

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Meta-Analysis of Retrograde Signaling in Arabidopsis thaliana Reveals a Core Module of Genes Embedded in Complex Cellular Signaling Networks

(2014) Christine Gläßer et al.   Molecular Plant

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

An Uncharacterized Apocarotenoid-Derived Signal Generated in  -Carotene Desaturase Mutants Regulates Leaf Development and the Expression of Chloroplast and Nuclear Genes in Arabidopsis

(2014) A.-O. Avendano-Vazquez et al.   PLANT CELL

FourArabidopsis AREB/ABF transcription factors function predominantly in gene expression downstream of SnRK2 kinases in abscisic acid signalling in response to osmotic stress

(2014) TAKUYA YOSHIDA et al.   PLANT CELL AND ENVIRONMENT

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Klebsormidium flaccidum genome reveals primary factors for plant terrestrial adaptation

(2014) Koichi Hori et al.   Nature Communications

An ELIP-like gene in the freshwater green alga, Spirogyra varians (Zygnematales), is regulated by cold stress and CO2 influx

(2013) Jong Won Han et al.   JOURNAL OF APPLIED PHYCOLOGY

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

Biogenesis and homeostasis of chloroplasts and other plastids

(2013) Paul Jarvis et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Green Targeting Predictor and Ambiguous Targeting Predictor 2: the pitfalls of plant protein targeting prediction and of transient protein expression in heterologous systems

(2013) Janina Fuss et al.   NEW PHYTOLOGIST

H2O2-triggered Retrograde Signaling from Chloroplasts to Nucleus Plays Specific Role in Response to Stress

(2012) Takanori Maruta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PredAlgo: A New Subcellular Localization Prediction Tool Dedicated to Green Algae

(2012) Marianne Tardif et al.   MOLECULAR BIOLOGY AND EVOLUTION

Carotenoid oxidation products are stress signals that mediate gene responses to singlet oxygen in plants

(2012) F. Ramel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peroxiredoxins in Plants and Cyanobacteria

(2011) Karl-Josef Dietz   ANTIOXIDANTS & REDOX SIGNALING

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Evolution of Abscisic Acid Synthesis and Signaling Mechanisms

(2011) Felix Hauser et al.   CURRENT BIOLOGY

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

(2011) Philippe Lamesch et al.   NUCLEIC ACIDS RESEARCH

Evidence for a SAL1-PAP Chloroplast Retrograde Pathway That Functions in Drought and High Light Signaling inArabidopsis

(2011) Gonzalo M. Estavillo et al.   PLANT CELL

The Selaginella Genome Identifies Genetic Changes Associated with the Evolution of Vascular Plants

(2011) J. A. Banks et al.   SCIENCE

Fibrillin protein function: the tip of the iceberg?

(2011) Dharmendra K. Singh et al.   TRENDS IN PLANT SCIENCE

Abscisic Acid: Emergence of a Core Signaling Network

(2010) Sean R. Cutler et al.   Annual Review of Plant Biology

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

Molecular Basis of the Core Regulatory Network in ABA Responses: Sensing, Signaling and Transport

(2010) T. Umezawa et al.   PLANT AND CELL PHYSIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Streptophyte algae and the origin of embryophytes

(2009) Burkhard Becker et al.   ANNALS OF BOTANY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Two Novel GPCR-Type G Proteins Are Abscisic Acid Receptors in Arabidopsis

(2009) Sona Pandey et al.   CELL

Structural insights into the mechanism of abscisic acid signaling by PYL proteins

(2009) Ping Yin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PYR/PYL/RCAR family members are major in-vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis

(2009) Noriyuki Nishimura et al.   PLANT JOURNAL

Functional analyses of the ABI1-related protein phosphatase type 2C reveal evolutionarily conserved regulation of abscisic acid signaling between Arabidopsis and the moss Physcomitrella patens

(2009) Kenji Komatsu et al.   PLANT MOLECULAR BIOLOGY

Regulators of PP2C Phosphatase Activity Function as Abscisic Acid Sensors

(2009) Y. Ma et al.   SCIENCE

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

(2009) A. Z. Worden et al.   SCIENCE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana

(2008) Michaela Hundertmark et al.   BMC GENOMICS

Retrograde signaling and plant stress: plastid signals initiate cellular stress responses

(2008) Aurora Piñas Fernández et al.   CURRENT OPINION IN PLANT BIOLOGY

SLAC1 is required for plant guard cell S-type anion channel function in stomatal signalling

(2008) Triin Vahisalu et al.   NATURE

PPDB, the Plant Proteomics Database at Cornell

(2008) Qi Sun et al.   NUCLEIC ACIDS RESEARCH