Project description:eQTL mapping in a F1 diversity panel generated from 111 A.thaliana natural accessions 57 F1 lines without replicates, the 5th or 6th true leaf
Project description:This SuperSeries is composed of the following subset Series: GSE32550: A conserved transcriptional regulator governs fungal morphology in widely diverged species [expression data] GSE32557: A conserved transcriptional regulator governs fungal morphology in widely diverged species [ChIP-chip, Transcriptional regulation by Mit1 and orthologs] Refer to individual Series
Project description:Methylation is a common post-translational modification of lysine and arginine in eukaryotic proteins. To date, these methylomes are best characterised in model organisms and higher eukaryotes. Herein, we integrated bioinformatics, proteomics and high-content drug-screening to comprehensively explore protein methylation in the human gastrointestinal parasite and deep-branching eukaryote, Giardia duodenalis. We demonstrate Giardia and other Diplomonadida species lack arginine-methyltransferases and have remodelled RGG/RG motifs preferred by these enzymes. Further, Giardia had no detectable methylarginine in vitro, demonstrating the first eukaryote with no arginine methylome. In contrast, we performed detailed curation of 11 putative lysine-methyltransferases, including highly-diverged SET-domain proteins, and novel annotations demonstrating conserved eEF1a methyllysine. We identified >200 high-confidence methyllysine sites, highlighting methyllysine within coiled-coil features, and for Giardia cytoskeletal regulation. Lastly, using known methylation-inhibitors, we demonstrate inhibition of methylation plays a key role in replication and cyst formation in this parasite.
Project description:Metal tolerance is often a result of metal storage or distribution. Thus, with the goal of advancing the molecular understanding of such metal homeostatic mechanisms, natural variation of metal tolerance in Arabidopsis thaliana was investigated. Substantial variation exists in tolerance of excess copper (Cu), zinc (Zn) and cadmium (Cd). Two accessions, Col-0 and Bur-0, and a recombinant inbred line (RIL) population derived from these parents were chosen for further analysis of Cd and Zn tolerance variation, which is evident at different plant ages in various experimental systems and appears to be genetically linked. Three QTLs, explaining in total nearly 50 % of the variation in Cd tolerance, were mapped. The one obvious candidate gene in the mapped intervals, HMA3, is unlikely to contribute to the variation. In order to identify additional candidate genes the Cd responses of Col-0 and Bur-0 were compared at the transcriptome level. The sustained common Cd response of the two accessions was dominated by processes implicated in plant pathogen defense. Accession-specific differences suggested a more efficient activation of acclimative responses as underlying the higher Cd tolerance of Bur-0. The second hypothesis derived from the physiological characterization of the accessions is a reduced Cd accumulation in Bur-0. The microarray analysis was used to identify candidate genes for Cd-tolerance and -accumulation differences between the accessions Bur-0 and Col-0 as well as to analyse the expressional response of A.thaliana to Cd-stress.
Project description:We have sequenced messenger RNA isolated from seedling tissue for 19 accessions of Arabidopsis thaliana (with biological replication). The 19 accessions for which RNA-Seq reads were collected have served as the founders for the MAGIC lines, a high-resolution recombinant inbred line mapping resource. RNA sequencing data was used to examine differential gene expression among the accessions.
Project description:To identify the transcriptome divergence and sex roles underlying it in recently diverged Drosophia pseudoobscura group, we compare the global gene expression of 7-day-old whole body adults of pure species. 7-day-old virgin flies were assayed by species and sex. At least three isofemale inbred lines were used for each species (D. pseudoobscura; D. persimilis; D. pseudoobscura bogotana).All lines of each species were pooled in equal amounts.Two separate labeling reactions per sample were pooled and hybridized to the Agilent single color (Cyanine 3-CTP dye) arrays. Three different replicates were hybridized for each species and sex.
