Transcriptome reconstruction and exprssion profiling in plants

In this thesis, massive RNA sequencing (RNA-Seq) data have been used to investigate the transcriptome of complex eukaryotic organisms. The first of the studies presented here was performed on the Medicago truncatula plant species, starting from data obtained with early RNA-Seq sequencing protocols. In this first study, notwithstanding the limits of the original data, we have tried to improve the genic annotation for the species both with reference-based and de novo assembly methods. RNA-Seq data have been also used to perform a global gene expression analysis and investigate transcriptional modulation in some processes of biological interest. In the following studies, we have refined the approach in order to analyze the genic annotation of the Vitis vinifera species. In particular, we focused on the issue of the representativeness of the reference genome of the species, considering that this plant is characterized by high degrees of intraspecies variability. By exploiting the improvements in the quality of RNA-Seq data and our refined protocols, we have thus analyzed two different grape cultivars distinct from the reference, in order to detect and characterize genes still unknown that might be specific of these cultivars. RNA-Seq data have also been used to analyze the expression of these genes during berry development and determine whether they could have any influence on phenotypic variability.