De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4 Species of Tribe Salsoleae (Chenopodiaceae)

KaliversusSalsola: the instructive story of a questionable nomenclatural resurrection

(2017) Sergei L. Mosyakin et al.   ISRAEL JOURNAL OF PLANT SCIENCES

Shared characteristics underpinning C4leaf maturation derived from analysis of multiple C3and C4species ofFlaveria

(2017) Britta M.C. Kümpers et al.   JOURNAL OF EXPERIMENTAL BOTANY

C3 -C4 intermediates may be of hybrid origin - a reminder

(2017) Gudrun Kadereit et al.   NEW PHYTOLOGIST

Comprehensive evaluation ofde novotranscriptome assembly programs and their effects on differential gene expression analysis

(2016) Sufang Wang et al.   BIOINFORMATICS

Understanding metabolite transport and metabolism in C4 plants through RNA-seq

(2016) Urte Schlüter et al.   CURRENT OPINION IN PLANT BIOLOGY

Glycine decarboxylase in C3, C4 and C3–C4 intermediate species

(2016) Stefanie Schulze et al.   CURRENT OPINION IN PLANT BIOLOGY

Convergent Evolution and the Origin of Complex Phenotypes in the Age of Systems Biology

(2016) Jacob D. Washburn et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Photorespiration connects C3and C4photosynthesis

(2016) Andrea Bräutigam et al.   JOURNAL OF EXPERIMENTAL BOTANY

Photosynthesis in C3–C4intermediateMoricandiaspecies

(2016) Urte Schlüter et al.   JOURNAL OF EXPERIMENTAL BOTANY

C3cotyledons are followed by C4leaves: intra-individual transcriptome analysis ofSalsola soda(Chenopodiaceae)

(2016) Maximilian Lauterbach et al.   JOURNAL OF EXPERIMENTAL BOTANY

A portrait of the C4photosynthetic family on the 50th anniversary of its discovery: species number, evolutionary lineages, and Hall of Fame

(2016) Rowan F. Sage   JOURNAL OF EXPERIMENTAL BOTANY

Molecular phylogeny and forms of photosynthesis in tribe Salsoleae (Chenopodiaceae)

(2016) Christina Schüssler et al.   JOURNAL OF EXPERIMENTAL BOTANY

The Road to C4Photosynthesis: Evolution of a Complex Trait via Intermediary States

(2016) Urte Schlüter et al.   PLANT AND CELL PHYSIOLOGY

Taxonomic novelties from Irano-Turanian region and NE Iran: Oreosalsola, a new segregate from Salsola s.l., two new species in Anabasis and Salvia, and two new combinations in Caroxylon and Seseli

(2016) HOSSEIN AKHANI et al.   Phytotaxa

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

(2016) Loren A. Honaas et al.   PLoS One

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Kranz and single-cell forms of C4plants in the subfamily Suaedoideae show kinetic C4convergence for PEPC and Rubisco with divergent amino acid substitutions

(2015) Josh J. Rosnow et al.   JOURNAL OF EXPERIMENTAL BOTANY

An assessment of the capacity for phosphoenolpyruvate carboxykinase to contribute to C4 photosynthesis

(2015) Nuria K. Koteyeva et al.   PLANT SCIENCE

AtPHT4;4 is a chloroplast-localized ascorbate transporter in Arabidopsis

(2015) Takaaki Miyaji et al.   Nature Communications

A taxonomic backbone for the global synthesis of species diversity in the angiosperm orderCaryophyllales

(2015) Patricia Hernández-Ledesma et al.   Willdenowia

Developmental Genetic Mechanisms of C4 Syndrome Based on Transcriptome Analysis of C3 Cotyledons and C4 Assimilating Shoots in Haloxylon ammodendron

(2015) Yuanyuan Li et al.   PLoS One

Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species

(2015) Zehong Ding et al.   PLoS One

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

The Draft Genome and Transcriptome of Amaranthus hypochondriacus: A C4 Dicot Producing High-Lysine Edible Pseudo-Cereal

(2014) Meeta Sunil et al.   DNA RESEARCH

When do different C4 leaf anatomies indicate independent C4 origins? Parallel evolution of C4 leaf types in Camphorosmeae (Chenopodiaceae)

(2014) Gudrun Kadereit et al.   JOURNAL OF EXPERIMENTAL BOTANY

Positive selection of Kranz and non-Kranz C4 phosphoenolpyruvate carboxylase amino acids in Suaedoideae (Chenopodiaceae)

(2014) Josh J. Rosnow et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Three distinct biochemical subtypes of C4 photosynthesis? A modelling analysis

(2014) Yu Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Comparative Transcriptome Atlases Reveal Altered Gene Expression Modules between Two Cleomaceae C3 and C4 Plant Species

(2014) C. Kulahoglu et al.   PLANT CELL

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

Predicting C4 Photosynthesis Evolution: Modular, Individually Adaptive Steps on a Mount Fuji Fitness Landscape

(2013) David Heckmann et al.   CELL

Structural and physiological analyses in Salsoleae (Chenopodiaceae) indicate multiple transitions among C3, intermediate, and C4 photosynthesis

(2013) Elena V. Voznesenskaya et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2013) Juliane C. Dohm et al.   NATURE

Environmental and physiological determinants of carbon isotope discrimination in terrestrial plants

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

Greater efficiency of photosynthetic carbon fixation due to single amino-acid substitution

(2013) Judith Katharina Paulus et al.   Nature Communications

Photorespiration and the Evolution of C4Photosynthesis

(2012) Rowan F. Sage et al.   Annual Review of Plant Biology

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The dicotyledonous NAD malic enzyme C4plant Cleome gynandra displays age-dependent plasticity of C4decarboxylation biochemistry

(2012) M. Sommer et al.   PLANT BIOLOGY

C4 eudicots are not younger than C4 monocots

(2011) Pascal-Antoine Christin et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evolution of the C4 photosynthetic mechanism: are there really three C4 acid decarboxylation types?

(2011) R. T. Furbank   JOURNAL OF EXPERIMENTAL BOTANY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

Molecular phylogeny of Atripliceae (Chenopodioideae, Chenopodiaceae): Implications for systematics, biogeography, flower and fruit evolution, and the origin of C4 photosynthesis

(2010) Gudrun Kadereit et al.   AMERICAN JOURNAL OF BOTANY

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

Photorespiration: players, partners and origin

(2010) Hermann Bauwe et al.   TRENDS IN PLANT SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Structural, biochemical, and physiological characterization of photosynthesis in two C4 subspecies of Tecticornia indica and the C3 species Tecticornia pergranulata (Chenopodiaceae)

(2008) Elena V. Voznesenskaya et al.   JOURNAL OF EXPERIMENTAL BOTANY

Mitochondria from leaf mesophyll cells of C4 plants are deficient in the H protein of glycine decarboxylase complex

(2007) Eugeniusz Parys et al.   JOURNAL OF PLANT PHYSIOLOGY