Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics

(2014) Saemundur Sveinsson et al.   ANNALS OF BOTANY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

(2014) Brad R Ruhfel et al.   BMC EVOLUTIONARY BIOLOGY

Shared origins of a key enzyme during the evolution of C4 and CAM metabolism

(2014) Pascal-Antoine Christin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recurrent Loss of Sex Is Associated with Accumulation of Deleterious Mutations in Oenothera

(2014) Jesse D. Hollister et al.   MOLECULAR BIOLOGY AND EVOLUTION

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

(2014) F.-W. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Land plant origins and coalescence confusion

(2014) Mark S. Springer et al.   TRENDS IN PLANT SCIENCE

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

(2014) Pierre-Marc Delaux et al.   PLoS Genetics

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

Parasitic plants have increased rates of molecular evolution across all three genomes

(2013) Lindell Bromham et al.   BMC EVOLUTIONARY BIOLOGY

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

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

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos 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

Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants

(2013) R. De Smet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biosynthesis of betalains: yellow and violet plant pigments

(2013) Fernando Gandía-Herrero et al.   TRENDS IN PLANT SCIENCE

Taller plants have lower rates of molecular evolution

(2013) Robert Lanfear et al.   Nature Communications

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

(2012) Emmanuel Buschiazzo et al.   BMC EVOLUTIONARY BIOLOGY

Angiosperm Responses to a Low-CO2 World: CAM and C4 Photosynthesis as Parallel Evolutionary Trajectories

(2012) Erika J. Edwards et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Inference of Genome Duplications from Age Distributions Revisited

(2012) Kevin Vanneste et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

The beet R locus encodes a new cytochrome P450 required for red betalain production

(2012) Gregory J Hatlestad et al.   NATURE GENETICS

PGDD: a database of gene and genome duplication in plants

(2012) Tae-Ho Lee et al.   NUCLEIC ACIDS RESEARCH

Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

(2012) Marc T. J. Johnson et al.   PLoS One

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A broader model for C4 photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.)

(2012) G. Kadereit et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates

(2011) Brandon Gaut et al.   Annual Review of Ecology Evolution and Systematics

Transcriptomes of the Parasitic Plant Family Orobanchaceae Reveal Surprising Conservation of Chlorophyll Synthesis

(2011) Norman J. Wickett et al.   CURRENT BIOLOGY

The C4 plant lineages of planet Earth

(2011) R. F. Sage et al.   JOURNAL OF EXPERIMENTAL BOTANY

Ancestral polyploidy in seed plants and angiosperms

(2011) Yuannian Jiao et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Complex pigment evolution in the Caryophyllales

(2011) Samuel F. Brockington et al.   NEW PHYTOLOGIST

Phytozome: a comparative platform for green plant genomics

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

Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris)

(2011) Juliane C. Dohm et al.   PLANT JOURNAL

Contemporaneous and recent radiations of the world's major succulent plant lineages

(2011) M. Arakaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

The age and diversification of the angiosperms re-revisited

(2010) Charles D. Bell et al.   AMERICAN JOURNAL OF BOTANY

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

Genome-wide investigation reveals high evolutionary rates in annual model plants

(2010) Jia-Xing Yue et al.   BMC PLANT BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

(2010) M. J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary speed limited by water in arid Australia

(2010) X. Goldie et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Caryophyllalesphylogenetics: disentanglingPhytolaccaceaeandMolluginaceaeand description ofMicroteaceaeas a new isolated family

(2010) Bastian Schäferhoff et al.   Willdenowia

FrameDP: sensitive peptide detection on noisy matured sequences

(2009) J. Gouzy et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Phylogeny of the Caryophyllales Sensu Lato: Revisiting Hypotheses on Pollination Biology and Perianth Differentiation in the Core Caryophyllales

(2009) Samuel F. Brockington et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

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

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Evolution of Genome size in Hawaiian Endemic Genus Schiedea (Caryophyllaceae)

(2009) Maxim V. Kapralov et al.   Tropical Plant Biology

Phyutility: a phyloinformatics tool for trees, alignments and molecular data

(2008) S. A. Smith et al.   BIOINFORMATICS

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

(2008) M. S. Barker et al.   MOLECULAR BIOLOGY AND EVOLUTION

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE