Brachypodium: 20 years as a grass biology model system; the way forward?

Comparative Analysis of Transcriptome and sRNAs Expression Patterns in the Brachypodium distachyon—Magnaporthe oryzae Pathosystems

(2021) Silvia Zanini et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Sequence, Chromatin and Evolution of Satellite DNA

(2021) Jitendra Thakur et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Spatial analysis of the root system coupled to microbial community inoculation shed light on rhizosphere bacterial community assembly

(2021) Shaodong Wei et al.   BIOLOGY AND FERTILITY OF SOILS

Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation

(2021) Guanqing Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Microfabrication of a Chamber for High-Resolution, In Situ Imaging of the Whole Root for Plant–Microbe Interactions

(2021) Lauren K. Jabusch et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Homolog of the Arabidopsis TIME FOR COFFEE Gene Is Involved in Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon

(2021) Rafael Della Coletta et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport

(2021) Rachel Hestrin et al.   NEW PHYTOLOGIST

Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulence

(2021) Bernhard Timo Werner et al.   PLoS One

Gradual evolution of allopolyploidy in Arabidopsis suecica

(2021) Robin Burns et al.   Nature Ecology & Evolution

The Metabolic Response of Brachypodium Roots to the Interaction with Beneficial Bacteria Is Affected by the Plant Nutritional Status

(2021) Martino Schillaci et al.   Metabolites

Migration without interbreeding: Evolutionary history of a highly selfing Mediterranean grass inferred from whole genomes

(2021) Christoph Stritt et al.   MOLECULAR ECOLOGY

Differential Gene Expression of Brachypodium distachyon Roots Colonized by Gluconacetobacter diazotrophicus and the Role of BdCESA8 in the Colonization

(2021) Xuan Yang et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Tracking the ancestry of known and ‘ghost’ homeologous subgenomes in model grass Brachypodium polyploids

(2021) Rubén Sancho et al.   PLANT JOURNAL

Diversity in nonlinear responses to soil moisture shapes evolutionary constraints in Brachypodium

(2021) J Grey Monroe et al.   G3-Genes Genomes Genetics

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

(2021) Maria Angeles Decena et al.   Plants-Basel

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

(2020) Kirk J‐M. MacKinnon et al.   NEW PHYTOLOGIST

Mechanical stimulation in Brachypodium distachyon : Implications for fitness, productivity, and cell wall properties

(2020) Agnieszka Gladala‐Kostarz et al.   PLANT CELL AND ENVIRONMENT

The current revolution in transposable element biology enabled by long reads

(2020) Saima Shahid et al.   CURRENT OPINION IN PLANT BIOLOGY

Plant and animal chromatin three-dimensional organization: similar structures but different functions

(2020) Pengfei Dong et al.   JOURNAL OF EXPERIMENTAL BOTANY

A CRISPR/Cas9-Based Mutagenesis Protocol for Brachypodium distachyon and Its Allopolyploid Relative, Brachypodium hybridum

(2020) Karolina Hus et al.   Frontiers in Plant Science

Expression and evolution of the phospholipase C gene family in Brachypodium distachyon

(2020) Xianguo Wang et al.   Genes & Genomics

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

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

Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon

(2020) Michele Wyler et al.   Genome Biology and Evolution

Genetic and Methylome Variation in Turkish Brachypodium Distachyon Accessions Differentiate Two Geographically Distinct Subpopulations

(2020) Aleksandra Skalska et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Advances on genomics, biology, ecology and evolution of Brachypodium, a bridging model grass system for cereals and biofuel grasses

(2020) Pilar Catalán et al.   NEW PHYTOLOGIST

BdWRKY38 is required for the incompatible interaction of Brachypodium distachyon with the necrotrophic fungus Rhizoctonia solani

(2020) Yusuke Kouzai et al.   PLANT JOURNAL

Constitutive overexpression of RAM1 leads to an increase in arbuscule density in Brachypodium distachyon

(2020) Lena Maria Müller et al.   PLANT PHYSIOLOGY

Identification of effector candidate genes of Rhizoctonia solani AG-1 IA expressed during infection in Brachypodium distachyon

(2020) Sobhy S. H. Abdelsalam et al.   Scientific Reports

An efficient Oligo‐FISH painting system for revealing chromosome rearrangements and polyploidization in Triticeae

(2020) Guangrong Li et al.   PLANT JOURNAL

Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships

(2019) Patrice S. Albert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent roles of FT-like 9 in flowering transition under different day lengths in Brachypodium distachyon

(2019) Zhengrui Qin et al.   Nature Communications

Transcriptional and Metabolomic Analyses Indicate that Cell Wall Properties are Associated with Drought Tolerance in Brachypodium distachyon

(2019) Ingo Lenk et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Durum wheat genome highlights past domestication signatures and future improvement targets

(2019) Marco Maccaferri et al.   NATURE GENETICS

Tracing the origin and evolution history of methylation-related genes in plants

(2019) Liuling Pei et al.   BMC PLANT BIOLOGY

Detecting Brachypodium distachyon Chromosomes Bd4 and Bd5 in MH- and X-Ray-Induced Micronuclei Using mcFISH

(2019) Arita Kus et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Brachypodium histone deacetylase BdHD1 positively regulates ABA and drought stress responses

(2019) Jingpu Song et al.   PLANT SCIENCE

The Rabl configuration limits topological entanglement of chromosomes in budding yeast

(2019) Maxime Pouokam et al.   Scientific Reports

Resource allocation to growth or luxury consumption drives mycorrhizal responses

(2019) Rohan C. Riley et al.   ECOLOGY LETTERS

Dual‐color oligo‐FISH can reveal chromosomal variations and evolution in Oryza species

(2019) Xiaoyu Liu et al.   PLANT JOURNAL

Form, development and function of grass stomata

(2019) Tiago D.G. Nunes et al.   PLANT JOURNAL

Comparatively Barcoded Chromosomes of Brachypodium Perennials Tell the Story of Their Karyotype Structure and Evolution

(2019) Joanna Lusinska et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Progressive refinement of the karyotyping of Brachypodium genomes

(2019) Robert Hasterok et al.   NEW PHYTOLOGIST

Diversity, dynamics and effects of long terminal repeat retrotransposons in the model grass Brachypodium distachyon

(2019) Christoph Stritt et al.   NEW PHYTOLOGIST

Brachypodium distachyon MAP20 functions in metaxylem pit development and contributes to drought recovery

(2019) Tetyana Smertenko et al.   NEW PHYTOLOGIST

Brachypodium and plant viruses: entwined tools for discovery

(2019) Karen‐Beth G. Scholthof   NEW PHYTOLOGIST

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

Chromosome identification and reconstruction of evolutionary rearrangements in Brachypodium distachyon, B. stacei and B. hybridum

(2018) Joanna Lusinska et al.   ANNALS OF BOTANY

OUP accepted manuscript

(2018)   ANNALS OF BOTANY

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

A glycosyl transferase family 43 protein involved in xylan biosynthesis is associated with straw digestibility in Brachypodium distachyon

(2018) Caragh Whitehead et al.   NEW PHYTOLOGIST

Suppression of a single BAHD gene in Setaria viridis causes large, stable decreases in cell wall feruloylation and increases biomass digestibility

(2018) Wagner R. de Souza et al.   NEW PHYTOLOGIST

Brachypodium: A monocot grass model system for plant biology

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

An ortholog of CURLY LEAF/ENHANCER OF ZESTE like-1 is required for proper flowering in Brachypodium distachyon

(2018) Aaron Lomax et al.   PLANT JOURNAL

Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus

(2018) Yinjia Li et al.   PLANT JOURNAL

In the grass species Brachypodium distachyon , the production of mixed-linkage (1,3;1,4)-β-glucan (MLG) occurs in the Golgi apparatus

(2018) Sang-Jin Kim et al.   PLANT JOURNAL

Revised Phylogeny of theCellulose SynthaseGene Superfamily: Insights into Cell Wall Evolution

(2018) Alan Little et al.   PLANT PHYSIOLOGY

De novo generation of helper virus-satellite chimera RNAs results in disease attenuation and satellite sequence acquisition in a host-dependent manner

(2018) J.D. Pyle et al.   VIROLOGY

A mosaic monoploid reference sequence for the highly complex genome of sugarcane

(2018) Olivier Garsmeur et al.   Nature Communications

3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering

(2018) Jinlei Han et al.   Molecular Cytogenetics

Genomic Dissection of Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon

(2018) Rafael Della Coletta et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Genome sequence of the progenitor of wheat A subgenome Triticum urartu

(2018) Hong-Qing Ling et al.   NATURE

Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

(2018) Yann Bourgeois et al.   PLANT JOURNAL

SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae

(2018) Pubudu P. Handakumbura et al.   PLANT JOURNAL

A Trihelix Family Transcription Factor is Associated with Key Genes in Mixed-linkage Glucan Accumulation

(2018) Mingzhu Fan et al.   PLANT PHYSIOLOGY

Components of Brachypodium distachyon resistance to nonadapted wheat stripe rust pathogens are simply inherited

(2018) Brian Gilbert et al.   PLoS Genetics

Cloning and characterization of the homoeologous genes for the Rec8-like meiotic cohesin in polyploid wheat

(2018) Guojia Ma et al.   BMC PLANT BIOLOGY

Global Diversity of the Brachypodium Species Complex as a Resource for Genome-Wide Association Studies Demonstrated for Agronomic Traits in Response to Climate

(2018) Pip B. Wilson et al.   GENETICS

Multi-lab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

(2018) Joelle Sasse et al.   NEW PHYTOLOGIST

The genomic landscape of molecular responses to natural drought stress in Panicum hallii

(2018) John T. Lovell et al.   Nature Communications

Identification, Molecular Cloning, and Functional Characterization of a Wheat UDP-Glucosyltransferase Involved in Resistance to Fusarium Head Blight and to Mycotoxin Accumulation

(2018) Miriam Gatti et al.   Frontiers in Plant Science

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

(2017) Christoph Stritt et al.   Genome Biology and Evolution

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

(2017) Ming-Cheng Luo et al.   NATURE

Salicylic acid-dependent immunity contributes to resistance against Rhizoctonia solani , a necrotrophic fungal agent of sheath blight, in rice and Brachypodium distachyon

(2017) Yusuke Kouzai et al.   NEW PHYTOLOGIST

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

(2017) Rubén Sancho et al.   NEW PHYTOLOGIST

The interplay between aridity and competition determines colonization ability, exclusion and ecological segregation in the heteroploid Brachypodium distachyon species complex

(2017) Pedro J. Rey et al.   NEW PHYTOLOGIST

Live-cell CRISPR imaging in plants reveals dynamic telomere movements

(2017) Steven Dreissig et al.   PLANT JOURNAL

Genome-wide survey of heat shock factors and heat shock protein 70s and their regulatory network under abiotic stresses in Brachypodium distachyon

(2017) Feng Wen et al.   PLoS One

Establishment of a vernalization requirement inBrachypodium distachyonrequiresREPRESSOR OF VERNALIZATION1

(2017) Daniel P. Woods et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform

(2017) Sangrong Sun et al.   Frontiers in Plant Science

Integrated proteomic analysis of Brachypodium distachyon roots and leaves reveals a synergistic network in the response to drought stress and recovery

(2017) Yanwei Bian et al.   Scientific Reports

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

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

The arrangement ofBrachypodium distachyonchromosomes in interphase nuclei

(2016) Ewa Robaszkiewicz et al.   JOURNAL OF EXPERIMENTAL BOTANY

Double trouble: taxonomy and definitions of polyploidy

(2016) Jeff J. Doyle et al.   NEW PHYTOLOGIST

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

Differential growth responses of Brachypodium distachyon genotypes to inoculation with plant growth promoting rhizobacteria

(2016) Fernanda P. do Amaral et al.   PLANT MOLECULAR BIOLOGY

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

(2016) Daniel P. Woods et al.   PLANT PHYSIOLOGY

Grasses use an alternatively wired bHLH transcription factor network to establish stomatal identity

(2016) Michael T. Raissig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Structure in the Model Grass Is Highly Correlated with Flowering Differences across Broad Geographic Areas

(2016) Ludmila Tyler et al.   Plant Genome

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

Recreating Stable Brachypodium hybridum Allotetraploids by Uniting the Divergent Genomes of B. distachyon and B. stacei

(2016) Vinh Ha Dinh Thi et al.   PLoS One

Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat

(2016) Akitomo Kawasaki et al.   PLoS One

Environmental niche variation and evolutionary diversification of the Brachypodium distachyon grass complex species in their native circum-Mediterranean range

(2015) D. Lopez-Alvarez et al.   AMERICAN JOURNAL OF BOTANY

Spatial distribution of centromeres and telomeres at interphase varies amongBrachypodiumspecies

(2015) Dominika Idziak et al.   JOURNAL OF EXPERIMENTAL BOTANY

Effects ofPHENYLALANINE AMMONIA LYASE(PAL) knockdown on cell wall composition, biomass digestibility, and biotic and abiotic stress responses inBrachypodium

(2015) Cynthia L. Cass et al.   JOURNAL OF EXPERIMENTAL BOTANY

Determining the Subcellular Location of Synthesis and Assembly of the Cell Wall Polysaccharide (1,3; 1,4)-β-d-Glucan in Grasses

(2015) Sarah M. Wilson et al.   PLANT CELL

The cytoplasmic localization of the catalytic site of CSLF6 supports a channeling model for the biosynthesis of mixed-linkage glucan

(2015) Sang-Jin Kim et al.   PLANT JOURNAL

Absence of SUN1 and SUN2 proteins inArabidopsis thalianaleads to a delay in meiotic progression and defects in synapsis and recombination

(2015) Javier Varas et al.   PLANT JOURNAL

Impact of plant domestication on rhizosphere microbiome assembly and functions

(2015) Juan E. Pérez-Jaramillo et al.   PLANT MOLECULAR BIOLOGY

Functional testing of a PF02458 homologue of putative rice arabinoxylan feruloyl transferase genes in Brachypodium distachyon

(2015) Marcia M. de O. Buanafina et al.   PLANTA

Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead?

(2015) Aimée T. Classen et al.   Ecosphere

Cell wall composition and digestibility alterations in Brachypodium distachyon achieved through reduced expression of the UDP-arabinopyranose mutase

(2015) David M. Rancour et al.   Frontiers in Plant Science

Pushing the boundaries of resistance: insights from Brachypodium-rust interactions

(2015) Melania Figueroa et al.   Frontiers in Plant Science

Accelerated Growth Rate and Increased Drought Stress Resilience of the Model Grass Brachypodium distachyon Colonized by Bacillus subtilis B26

(2015) François Gagné-Bourque et al.   PLoS One

Comparative Cellular Analysis of Pathogenic Fungi with a Disease Incidence in Brachypodium distachyon and Miscanthus x giganteus

(2014) Christian Falter et al.   BioEnergy Research

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach

(2014) Matteo Dell’Acqua et al.   BMC GENOMICS

Brachypodium distachyonis a pathosystem model for the study of the wheat disease rhizoctonia root rot

(2014) K. Schneebeli et al.   PLANT PATHOLOGY

Range of cell-wall alterations enhance saccharification inBrachypodium distachyonmutants

(2014) Poppy E. Marriott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

Genome interplay in the grain transcriptome of hexaploid bread wheat

(2014) M. Pfeifer et al.   SCIENCE

Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

A dynamic meiotic SUN belt includes the zygotene-stage telomere bouquet and is disrupted in chromosome segregation mutants of maize (Zea mays L.)

(2014) Shaun P. Murphy et al.   Frontiers in Plant Science

Infection ofBrachypodium distachyonwith Selected Grass Rust Pathogens

(2013) Michael Ayliffe et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Functional Characterization of Two Clusters of Brachypodium distachyon UDP-Glycosyltransferases Encoding Putative Deoxynivalenol Detoxification Genes

(2013) Wolfgang Schweiger et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

p-Coumaroyl-CoA:monolignol transferase (PMT) acts specifically in the lignin biosynthetic pathway inBrachypodium distachyon

(2013) Deborah L. Petrik et al.   PLANT JOURNAL

Overexpression of a BAHD Acyltransferase, OsAt10, Alters Rice Cell Wall Hydroxycinnamic Acid Content and Saccharification

(2013) L. E. Bartley et al.   PLANT PHYSIOLOGY

Interaction of Photoperiod and Vernalization Determines Flowering Time of Brachypodium distachyon

(2013) T. S. Ream et al.   PLANT PHYSIOLOGY

Evolution and taxonomic split of the model grass Brachypodium distachyon

(2012) Pilar Catalán et al.   ANNALS OF BOTANY

Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality

(2012) Scott J Lee et al.   Biotechnology for Biofuels

Comparison of cytotoxic and genotoxic effects of plutonium-239 alpha particles and mobile phone GSM 900 radiation in the Allium cepa test

(2012) Dmitry S. Pesnya et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

A physical, genetic and functional sequence assembly of the barley genome

(2012)   NATURE

Reference genome sequence of the model plant Setaria

(2012) Jeffrey L Bennetzen et al.   NATURE BIOTECHNOLOGY

TIME FOR COFFEE Represses Accumulation of the MYC2 Transcription Factor to Provide Time-of-Day Regulation of Jasmonate Signaling inArabidopsis

(2012) Jieun Shin et al.   PLANT CELL

Diversity of morphology and function in arbuscular mycorrhizal symbioses in Brachypodium distachyon

(2012) Jeon J. Hong et al.   PLANTA

Fine Mapping of the Bsr1 Barley Stripe Mosaic Virus Resistance Gene in the Model Grass Brachypodium distachyon

(2012) Yu Cui et al.   PLoS One

Brachypodium distachyon: a new pathosystem to study Fusarium head blight and other Fusarium diseases of wheat

(2011) Antoine Peraldi et al.   BMC PLANT BIOLOGY

Assessment of the genotoxicity of quinolone and fluoroquinolones contaminated soil with the Vicia faba micronucleus test

(2011) A. Khadra et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Hemicelluloses

(2010) Henrik Vibe Scheller et al.   Annual Review of Plant Biology

FISH in analysis of gamma ray-induced micronuclei formation in barley

(2010) Jolanta Juchimiuk-Kwasniewska et al.   JOURNAL OF APPLIED GENETICS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Natural variation of drought response in Brachypodium distachyon

(2010) Na Luo et al.   PHYSIOLOGIA PLANTARUM

The Maize Mixed-Linkage (1->3),(1->4)- -D-Glucan Polysaccharide Is Synthesized at the Golgi Membrane

(2010) N. C. Carpita et al.   PLANT PHYSIOLOGY

Genetic and comparative genomics mapping reveals that a powdery mildew resistance gene Ml3D232 originating from wild emmer co-segregates with an NBS-LRR analog in common wheat (Triticum aestivum L.)

(2010) Hongtao Zhang et al.   THEORETICAL AND APPLIED GENETICS