The evolution of multi-gene families and metabolic pathways in the evening primroses (Oenothera: Onagraceae): a comparative transcriptomics approachEunice Kariñho-Betancourt, Dave Carlson, Jesse Hollister, Axel Fischer, Stephan Greiner & Marc Johnson
The plant genus Oenothera has played an important role in the study of genome evolution and plant defense and reproduction. Here, we built on the 1kp transcriptomic dataset and developed a molecular resource of 63 transcriptomes and present a large-scale comparative study across 29 Oenothera species. We produced 2.3 million transcripts and 25.4 Mb of total length assembly per individual. We used this transcriptome resource to examine genome-wide evolutionary patterns and functional diversification by searching...
Expression atlas of Selaginella moellendorffii provides insights into the evolution of vasculature, secondary metabolism and rootsCamilla Ferrari, Devendra Shivhare, Bjoern Oest Hansen, Asher Pasha, Eddi Esteban, Nicholas J. Provart, Friedrich Kragler, Alisdair Fernie, Takayuki Tohge & Marek Mutwil
Selaginella moellendorffii is a representative of the lycophyte lineage and is studied to understand the evolution of land plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, only few studies investigated about the gene expression and transcriptional coordination of Selaginella genes, precluding us from understanding the evolution of transcriptional programs behind these traits. We present a gene expression atlas comprising all major organs, tissue types, and the diurnal gene expression profiles...
Data from: The Arabidopsis kinome: phylogeny and evolutionary insights into functional diversificationMonika Zulawski, Gunnar Schulze, Rostyslav Braginets, Stefanie Hartmann & Waltraud X. Schulze
Background: Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase...
Data from: Evolutionary metabolomics reveals domestication-associated changes in tetraploid wheat kernelsRomina Beleggia, Domenico Rau, Giovanni Laidò, Cristiano Platani, Franca Nigro, Mariagiovanna Fragasso, Pasquale De Vita, Federico Scossa, Alisdair R. Fernie, Zoran Nikoloski & Roberto Papa
Domestication and breeding have influenced the genetic structure of plant populations due to selection for adaptation from natural habitats to agro-ecosystems. Here, we investigate the effects of selection on the contents of 51 primary kernel metabolites and their relationships in three Triticum turgidum L. subspecies (i.e., wild emmer, emmer, durum wheat) that represent the major steps of tetraploid wheat domestication. We present a methodological pipeline to identify the signature of selection for molecular phenotypic traits...
Data from: Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifsKlaas J. Van Wijk, Giulia Friso, Dirk Walther & Waltraud X. Schulze
Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry–based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of...
Ammonium (NH4+) is essential to generate the nitrogenous building blocks of life. It gets assimilated via the canonical biosynthetic routes to glutamate and is further distributed throughout metabolism via a network of transaminases. To study the flexibility of this network, we constructed an Escherichia coli glutamate auxotrophic strain. This strain allowed us to systematically study which amino acids serve as amine source and found that several amino acids complement the auxotrophy, either by producing glutamate...
Max Planck Institute for Molecular Plant Physiology4
University of Hohenheim2
Max Planck Institute of Molecular Plant Physiology2
University of Sassari1
Nanyang Technological University1
Agricultural Research Council1
University of Potsdam1
University of Toronto1
Nara Institute of Science and Technology1