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

Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution

(2020) Michael A. Hardigan et al.   Frontiers in Plant Science

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

(2020) Z. Jeffrey Chen et al.   NATURE GENETICS

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

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

Tracing the diploid ancestry of the cultivated octoploid strawberry

(2020) Chao Feng et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Homoeologous Exchanges, Segmental Allopolyploidy, and Polyploid Genome Evolution

(2020) Annaliese S. Mason et al.   Frontiers in Genetics

Origin and evolution of the octoploid strawberry genome

(2019) Patrick P. Edger et al.   NATURE GENETICS

Durum wheat genome highlights past domestication signatures and future improvement targets

(2019) Marco Maccaferri et al.   NATURE GENETICS

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

Revisiting the origin of octoploid strawberry

(2019) Aaron Liston et al.   NATURE GENETICS

Reply to: Revisiting the origin of octoploid strawberry

(2019) Patrick P. Edger et al.   NATURE GENETICS

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

(2018) Joanna Lusinska et al.   ANNALS OF BOTANY

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

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

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

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy 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

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events

(2017) W. C. Thomas Gregg et al.   SYSTEMATIC BIOLOGY

Polyploidy: Pitfalls and paths to a paradigm

(2016) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Ancient WGD events as drivers of key innovations in angiosperms

(2016) Pamela S Soltis et al.   CURRENT OPINION IN PLANT BIOLOGY

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism

(2016) Polina Yu Novikova et al.   NATURE GENETICS

Natural Variation in Brachypodium Links Vernalization and Flowering Time Loci as Major Flowering Determinants

(2016) Jan Bettgenhaeuser et al.   PLANT PHYSIOLOGY

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

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

Assignment of Homoeologs to Parental Genomes in Allopolyploids for Species Tree Inference, with an Example from Fumaria (Papaveraceae)

(2015) Yann J. K. Bertrand et al.   SYSTEMATIC BIOLOGY

The Root of Flowering Plants and Total Evidence

(2015) V. V. Goremykin et al.   SYSTEMATIC BIOLOGY

Species-Level Phylogeny and Polyploid Relationships inHordeum(Poaceae) Inferred by Next-Generation Sequencing andIn SilicoCloning of Multiple Nuclear Loci

(2015) Jonathan Brassac et al.   SYSTEMATIC BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reconstructing the Evolution of Brachypodium Genomes Using Comparative Chromosome Painting

(2014) Alexander Betekhtin et al.   PLoS One

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

From Gene Trees to a Dated Allopolyploid Network: Insights from the Angiosperm Genus Viola (Violaceae)

(2014) Thomas Marcussen et al.   SYSTEMATIC BIOLOGY

Update on the genomics and basic biology of Brachypodium

(2014) Pilar Catalan et al.   TRENDS IN PLANT SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex

(2014) Aureliano Bombarely et al.   PeerJ

The timetable for allopolyploidy in flowering plants

(2013) Donald A. Levin   ANNALS OF BOTANY

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Evolution and taxonomic split of the model grass Brachypodium distachyon

(2012) Pilar Catalán et al.   ANNALS OF BOTANY

A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae)

(2012) Diana López-Alvarez et al.   PLoS One

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Phytozome: a comparative platform for green plant genomics

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

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

THE EVOLUTIONARY SIGNIFICANCE OF NATURAL AND ARTIFICIAL POLYPLOIDS IN THE FAMILY GRAMINEAE

(2010) G. LEDYARD STEBBINS   HEREDITAS

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

An Integrated Physical, Genetic and Cytogenetic Map of Brachypodium distachyon, a Model System for Grass Research

(2010) Melanie Febrer et al.   PLoS One

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Dating the origins of polyploidy events

(2009) Jeff J. Doyle et al.   NEW PHYTOLOGIST