Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species

Genetic Enablers Underlying the Clustered Evolutionary Origins of C4 Photosynthesis in Angiosperms

(2015) Pascal-Antoine Christin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice

(2015) Junhui Zhou et al.   PLANT JOURNAL

C 4 Photosynthesis in the Rice Paddy: Insights from the Noxious Weed Echinochloa glabrescens

(2015) Sarah Covshoff et al.   PLANT PHYSIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger 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

The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize

(2014) Thomas E. Hughes et al.   GENOME RESEARCH

Towards an integrative model of C4 photosynthetic subtypes: insights from comparative transcriptome analysis of NAD-ME, NADP-ME, and PEP-CK C4 species

(2014) Andrea Bräutigam et al.   JOURNAL OF EXPERIMENTAL BOTANY

Differential SPL gene expression patterns reveal candidate genes underlying flowering time and architectural differences in Mimulus and Arabidopsis

(2014) Stacy A. Jorgensen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Integrated Syntenic and Phylogenomic Analyses Reveal an Ancient Genome Duplication in Monocots

(2014) Yuannian Jiao et al.   PLANT CELL

Evolution of the Phosphoenolpyruvate Carboxylase Protein Kinase Family in C3 and C4 Flaveria spp.

(2014) S. H. Aldous et al.   PLANT PHYSIOLOGY

Evolutionary Convergence of Cell-Specific Gene Expression in Independent Lineages of C4 Grasses

(2014) C. R. John et al.   PLANT PHYSIOLOGY

Deep Evolutionary Comparison of Gene Expression Identifies Parallel Recruitment of Trans-Factors in Two Independent Origins of C4 Photosynthesis

(2014) Sylvain Aubry et al.   PLoS Genetics

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

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

From Endoplasmic Reticulum to Mitochondria: Absence of the Arabidopsis ATP Antiporter Endoplasmic Reticulum Adenylate Transporter1 Perturbs Photorespiration

(2013) C. Hoffmann et al.   PLANT CELL

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4Kranz anatomy

(2013) Peng Wang et al.   PLANT JOURNAL

Function Relaxation Followed by Diversifying Selection after Whole-Genome Duplication in Flowering Plants

(2013) H. Guo et al.   PLANT PHYSIOLOGY

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Leaf rolling allows quantification of mRNA abundance in mesophyll cells of sorghum

(2012) Sarah Covshoff et al.   JOURNAL OF EXPERIMENTAL BOTANY

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

PGDD: a database of gene and genome duplication in plants

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

The fate of duplicated genes in a polyploid plant genome

(2012) Anne Roulin et al.   PLANT JOURNAL

Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis

(2012) Y.-M. Chang et al.   PLANT PHYSIOLOGY

Molecular evolution of genes recruited into C4 photosynthesis

(2012) Ben P. Williams et al.   TRENDS IN PLANT SCIENCE

BRAD, the genetics and genomics database for Brassica plants

(2011) Feng Cheng et al.   BMC PLANT BIOLOGY

Organ and Cell Type–Specific Complementary Expression Patterns and Regulatory Neofunctionalization between Duplicated Genes in Arabidopsis thaliana

(2011) Shao-Lun Liu et al.   Genome Biology and Evolution

Exploiting the engine of C4 photosynthesis

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

The C4 plant lineages of planet Earth

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

New grass phylogeny resolves deep evolutionary relationships and discovers C4 origins

(2011)   NEW PHYTOLOGIST

Phytozome: a comparative platform for green plant genomics

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

C4Cycles: Past, Present, and Future Research on C4Photosynthesis

(2011) Jane A. Langdale   PLANT CELL

Systems Analysis of a Maize Leaf Developmental Gradient Redefines the Current C4 Model and Provides Candidates for Regulation

(2011) T. R. Pick et al.   PLANT CELL

Evolution of C4Photosynthesis in the GenusFlaveria: How Many and Which Genes Does It Take to Make C4?

(2011) Udo Gowik et al.   PLANT CELL

Independent and Parallel Recruitment of Preexisting Mechanisms Underlying C4 Photosynthesis

(2011) N. J. Brown et al.   SCIENCE

The developmental dynamics of the maize leaf transcriptome

(2010) Pinghua Li et al.   NATURE GENETICS

Structural and Metabolic Transitions of C4 Leaf Development and Differentiation Defined by Microscopy and Quantitative Proteomics in Maize

(2010) W. Majeran et al.   PLANT CELL

GORDITA (AGL63) is a young paralog of the Arabidopsis thaliana Bsister MADS box gene ABS (TT16) that has undergone neofunctionalization

(2010) Robert Erdmann et al.   PLANT JOURNAL

An mRNA Blueprint for C4 Photosynthesis Derived from Comparative Transcriptomics of Closely Related C3 and C4 Species

(2010) A. Brautigam et al.   PLANT PHYSIOLOGY

The Path from C3 to C4 Photosynthesis

(2010) U. Gowik et al.   PLANT PHYSIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Following Tetraploidy in Maize, a Short Deletion Mechanism Removed Genes Preferentially from One of the Two Homeologs

(2010) Margaret R. Woodhouse et al.   PLOS BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

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

Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

(2009) H. Tang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

(2008) M. Freeling et al.   GENOME RESEARCH

The age of the grasses and clusters of origins of C4photosynthesis

(2008) ALBERTO VICENTINI et al.   GLOBAL CHANGE BIOLOGY

Identification and Characterization of Shared Duplications between Rice and Wheat Provide New Insight into Grass Genome Evolution

(2008) J. Salse et al.   PLANT CELL

Oligocene CO2 Decline Promoted C4 Photosynthesis in Grasses

(2007) Pascal-Antoine Christin et al.   CURRENT BIOLOGY