Project description:We investigated the ascomycete truffle Tuber melanosporum exploits DNA methylation and transcription to cope with the more than 45,000 repeated elements that are present in its genome. Whole-genome bisulfite sequencing and RNA-sequencing, were performed on different developmental stages of this symbiotic hypogeous fungus -fruitbody (FB), free-living mycelium (FLM), and ectomycorrhiza.
Project description:Illumina HiSeq technology was used to generate mRNA profiles from Tuber magnatum truffles, free-living mycelium and oak mycorrhizal root tips. Paired-end reads of 100 bp were generated and aligned to Tuber magnatum reference transcripts using CLC Genomics Workbench 9.
Project description:The Transcriptome of different tissues and developmental stages of Tuber melanosporum was analyzed. The array probes were designed from gene models taken from the French Genoscope - Centre National de Séquençage Tuber melanosporum genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and to use this transcriptional information to confirm, to correct or to reject gene models. Another goal was to identify tissue-specific gene expression, e.g. mycorrhiza up-regulated transcripts or fruiting body up-regulated transcripts for further detailed analyses.
Project description:Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economical importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still a lot to learn about this complex phenotype. Here, we used genotype by sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis for tuber bruising. In addition, we collected transcriptomics data to enrich the GWAS results, by performing a differential expression analysis between samples with high- and low-bruising susceptibility.
