Project description:We used microarrays to discern patterns of gene expression in response to global climate change factors on leaf tissue of an annual dicot, Geranium dissectum, growing in a natural grassland. Keywords: multifactorial global change treatments
Project description:We used microarrays to discern patterns of gene expression in response to global climate change factors on leaf tissue of an annual dicot, Geranium dissectum, growing in a natural grassland. Keywords: multifactorial global change treatments There are 5-8 biological replicates for each of the sixteen treatments - a total of 100 samples. The four global change factors at two levels are ambient or elevated CO2, ambient temperature or ambient + 1 degree C warming, natural rainfall (601.2 mm/yr) or natural rainfall supplemented with 50% of every storm added immediately following each storm with a 3 week season extension, ambient growth nitrogen or ambient supplemented with 7 g N m-2 y-1, supplied as Ca(NO3)2. There were 16 treatments applied in a nested design in the field.We hybridized the Geranium samples using cross-species hybridization to Arabidopsis cDNA arrays which had an Arabisopsis genomic DNA common reference in the Cy3 channel.
Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.
