Comparative Genomics, Evolution, and Drought-Induced Expression of Dehydrin Genes in Model Brachypodium Grasses

RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars ‘TAM 111’ and ‘TAM 112’

(2021) Chenggen Chu et al.   Scientific Reports

Comparative transcriptome profiling of a resistant vs susceptible bread wheat (Triticum aestivum L.) cultivar in response to water deficit and cold stress

(2021) Dmitrii K. Konstantinov et al.   PeerJ

Sensitivity and Responses of Chloroplasts to Heat Stress in Plants

(2020) Shanshan Hu et al.   Frontiers in Plant Science

Gradual polyploid genome evolution revealed by pan-genomic analysis of Brachypodium hybridum and its diploid progenitors

(2020) Sean P. Gordon et al.   Nature Communications

Genome Wide Identification and Comparative Analysis of the Serpin Gene Family in Brachypodium and Barley

(2020) Shazia Rehman et al.   Plants-Basel

Evolution of the modular, disordered stress proteins known as dehydrins

(2019) Andrew C. Riley et al.   PLoS One

BES/BZR Transcription Factor TaBZR2 Positively Regulates Drought Responses by Activation of TaGST1

(2019) Xiao-Yu Cui et al.   PLANT PHYSIOLOGY

Over-expression of the Brachypodium ASR gene, BdASR4, enhances drought tolerance in Brachypodium distachyon

(2019) Jin Seok Yoon et al.   PLANT CELL REPORTS

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures

(2019) Jiyao Wang et al.   BIOINFORMATICS

Variation in functional responses to water stress and differentiation between natural allopolyploid populations in the Brachypodium distachyon species complex

(2018) Luisa M Martínez et al.   ANNALS OF BOTANY

Revisiting the Role of Plant Transcription Factors in the Battle against Abiotic Stress

(2018) Sardar-Ali Khan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

(2018) Steven Weaver et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing the origins and the biogeography of species’ genomes in the highly reticulate allopolyploid-rich model grass genus Brachypodium using minimum evolution, coalescence and maximum likelihood approaches

(2018) Antonio Díaz-Pérez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RSAT 2018: regulatory sequence analysis tools 20th anniversary

(2018) Nga Thi Thuy Nguyen et al.   NUCLEIC ACIDS RESEARCH

Brachypodium: A monocot grass model system for plant biology

(2018) Karen-Beth G. Scholthof et al.   PLANT CELL

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Characterization of Dehydrin protein, CdDHN4-L and CdDHN4-S, and their differential protective roles against abiotic stress in vitro

(2018) Aimin Lv et al.   BMC PLANT BIOLOGY

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets

(2018) Sergio Gálvez et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Structural and Functional Dynamics of Dehydrins: A Plant Protector Protein under Abiotic Stress

(2018) Zhengyang Yu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes

(2017) Rubén Sancho et al.   NEW PHYTOLOGIST

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

Hiding in plain sight: the F segment and other conserved features of seed plant SKn dehydrins

(2017) G. Richard Strimbeck   PLANTA

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

(2017) Sean P. Gordon et al.   Nature Communications

Multifunctional Roles of Plant Dehydrins in Response to Environmental Stresses

(2017) Yang Liu et al.   Frontiers in Plant Science

Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

(2017) Ahmad A. Malik et al.   Frontiers in Plant Science

Genome-wide analysis of rice dehydrin gene family: Its evolutionary conservedness and expression pattern in response to PEG induced dehydration stress

(2017) Giti Verma et al.   PLoS One

Emerging Roles of RNA-Binding Proteins in Plant Growth, Development, and Stress Responses

(2016)   MOLECULES AND CELLS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Interactive effects of water limitation and elevated temperature on the physiology, development and fitness of diverse accessions of Brachypodium distachyon

(2016) David L. Des Marais et al.   NEW PHYTOLOGIST

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

(2016) Jana Trifinopoulos et al.   NUCLEIC ACIDS RESEARCH

Linking Dynamic Phenotyping with Metabolite Analysis to Study Natural Variation in Drought Responses of Brachypodium distachyon

(2016) Lorraine H. C. Fisher et al.   Frontiers in Plant Science

Natural variation, differentiation, and genetic trade-offs of ecophysiological traits in response to water limitation inBrachypodium distachyonand its descendent allotetraploidB. hybridum(Poaceae)

(2015) Antonio J. Manzaneda et al.   EVOLUTION

Plant hormones in salt stress tolerance

(2015) Hojin Ryu et al.   JOURNAL OF PLANT BIOLOGY

Gene-Wide Identification of Episodic Selection

(2015) Ben Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Physiology and transcriptomics of water-deficit stress responses in wheat cultivars TAM 111 and TAM 112

(2014) Srirama Krishna Reddy et al.   JOURNAL OF PLANT PHYSIOLOGY

The crucial role of Φ- and K-segments in the in vitro functionality of Vitis vinifera dehydrin DHN1a

(2014) Raquel Rosales et al.   PHYTOCHEMISTRY

Novel dehydrins lacking complete K-segments in Pinaceae. The exception rather than the rule

(2014) Pedro Perdiguero et al.   Frontiers in Plant Science

Wheat and barley dehydrins under cold, drought, and salinity – what can LEA-II proteins tell us about plant stress response?

(2014) Klára Kosová et al.   Frontiers in Plant Science

Disorder and function: a review of the dehydrin protein family

(2014) Steffen P. Graether et al.   Frontiers in Plant Science

Expression analysis of dehydrin multigene family across tolerant and susceptible barley (Hordeum vulgare L.) genotypes in response to terminal drought stress

(2013) Amin Karami et al.   ACTA PHYSIOLOGIAE PLANTARUM

A KS-type dehydrin and its related domains reduce Cu-promoted radical generation and the histidine residues contribute to the radical-reducing activities

(2013) Masakazu Hara et al.   JOURNAL OF EXPERIMENTAL BOTANY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Environmental and physiological determinants of carbon isotope discrimination in terrestrial plants

(2013) Lucas A. Cernusak et al.   NEW PHYTOLOGIST

The Importance of Size and Disorder in the Cryoprotective Effects of Dehydrins

(2013) S. L. Hughes et al.   PLANT PHYSIOLOGY

Classification and expression diversification of wheat dehydrin genes

(2013) Yuezhi Wang et al.   PLANT SCIENCE

Brachypodium sylvaticum, a Model for Perennial Grasses: Transformation and Inbred Line Development

(2013) Michael A. Steinwand et al.   PLoS One

MYB transcription factor genes as regulators for plant responses: an overview

(2013) Supriya Ambawat et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

Evolution and taxonomic split of the model grass Brachypodium distachyon

(2012) Pilar Catalán et al.   ANNALS OF BOTANY

The K-Segments of the Wheat Dehydrin DHN-5 are Essential for the Protection of Lactate Dehydrogenase and β-Glucosidase Activities In Vitro

(2012) Marwa Drira et al.   MOLECULAR BIOTECHNOLOGY

Template-based protein structure modeling using the RaptorX web server

(2012) Morten Källberg et al.   Nature Protocols

LEA Gene Introns: is the Intron of Dehydrin Genes a Characteristic of the Serine-Segment?

(2012) Juan Francisco Jiménez-Bremont et al.   PLANT MOLECULAR BIOLOGY REPORTER

Detecting Individual Sites Subject to Episodic Diversifying Selection

(2012) Ben Murrell et al.   PLoS Genetics

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Overexpression of a maize dehydrin gene, ZmDHN2b, in tobacco enhances tolerance to low temperature

(2011) Xin Xing et al.   PLANT GROWTH REGULATION

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Dehydrin gene expression provides an indicator of low temperature and drought stress: transcriptome-based analysis of Barley (Hordeum vulgare L.)

(2008) Livia Tommasini et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Phylogenetic Signal, Evolutionary Process, and Rate

(2008) Liam J. Revell et al.   SYSTEMATIC BIOLOGY