Project description:We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
Project description:Spider silk proteins are synthesized in the silk-producing glands, where the spidroins are produced, stored and processed into a solid fiber from a crystalline liquid solution. Despite great interest in the spider silk properties, that make this material suitable for biomedical and biotechnological applications, the mechanism of formation and spinning of the silk fibers has not been fully elucidated; and no combination of proteomic and transcriptomic study has been carried out so far in the spider silk-producing glands. Nephila clavipes is an attractive orb-web spider to investigate the spinning process of silk production, given the properties of strength, elasticity and biocompatibility of their silk fibers. Thus, considering that the combination of proteomic and transcriptomic analysis may reveal an extensive repertoire of novel proteins involved in the silk spinning process, and in order to facilitate and enable proteomics in this non-model organism, the current study aims to construct a high quality reference mRNA-derived protein database that could be used to identify tissue specific expression patterns in spider silk glands. Next-generation sequencing has offered a powerful and cost-efficient technique for the generation of transcriptomic datasets in non-model species using diverse platforms such as the Illumina HiSeq, Roche 454, Pacific Biosystems, and Applied Biosystems SOLiD; In the current study, the Illumina HiSeq 2000 platform will be used to generate a N. clavipes spider silk glands transcriptome-based protein database. The transcriptome data generated in this study will provide a comprehensive and valuable genomic resource for future research of the group of spider silk-producing glands, in order to improve our understanding of the overall mechanism of action involved in production, secretion, storage, transport, protection and conformational changes of spidroins during the spinning process, and prey capture; and the results may be relevant for scientists in material Science, biology, biochemistry, and environmental scientists.
Project description:In this study, we profiled the transcriptional changes in a polyphagous spider mite, Tetranychus urticae, after adaptation to spatial and tempospatial stress. We show heritable down-regulation of genes encoding for core enzymes involved in the citric acid and gluconeogenesis/glycolyse pathways (glucose 6-phosphatase among others). Additionally, we observe heritable transcriptional changes in amino acid pathways (methionine, tyrosine and phenylalanine) and in laterally acquired genes from bacteria (cobalamin-independent methionine synthase). By similiar study results in other organisms, we argue that these heritable transcriptional changes (partially) underpin the changed life history traits observed in our experimental evolution set-up.
Project description:This study characterizes the transcriptomic alterations of Serpula lacrymans in contact with tree roots compared to the transcriptome of free-living mycelium.
Project description:Transcriptional profiling of Candida albicans comparing SDH2 deletion mutant cells with the wild-type cells in both Spider medium and Spider medium supplemented with 100mM glucose
