Dokument

Summary:
The model organism Physcomitrium patens, formerly Physcomitrella patens is a moss in the Funariaceae family. Due to P. patens ability to generate easily transgenic plants via homologous recombination, the interest of scientists worldwide was attracted. P. patens was the world's first completely sequenced non-seed plant genome (V1). Constant improvements of the genome assembly and the associated gene annotations resulted in the current P. patens pseudo-chromosomal genome version (V3). This genome version is the basis of all analyses performed in this thesis. Since P. patens became a U.S. Department of Energy Joint Genome Institute (DOE JGI) plant flagship genome 1 and a member of the JGI Gene Atlas project 2, hundreds of P. patens RNA-seq samples were generated. During my time as a PhD student, I analysed the JGI Gene Atlas RNA-seq samples and several dozen other RNA-seq samples from different projects. These RNA-seq samples contained data from five different P. patens ecotypes/accessions (Gransden, Kaskaskia, Reute, Villersexel, and Wisconsin).To efficiently analyse this data, I developed a powerful RNA-seq pipeline to perform differentially expressed gene (DEG) calling. The performance of the RNA-seq pipeline was tested by comparing its results to commercial software solutions and multiple RNA-seq samples from different species. My newly generated gene expression results, together with previous published expression data from a variety of other projects, were stored at our novel online tool PEATmoss. Furthermore, my gene version lookup tables were implemented in a database structure. This, allows PEATmoss users to find gene models of different gene annotation versions and to use them in PEATmoss. With an updated version of my RNA-seq pipeline, I identified and analysed sequence variations in P. patens accessions. A clear clustering by individual accessions could be shown. I could demonstrate, that due to decades of vegetative propagation in laboratories, somatic mutations have accumulated in Gransden laboratory plants. In addition, we used restriction fragment length polymorphism (RFLP) to offer a simple method for quick identification of unknown P. patens plants. 1 https://jgi.doe.gov/our-science/science-programs/plant-genomics/plant-flagship-genomes/ 2 https://jgi.doe.gov/doe-jgi-plant-flagship-gene-atlas/

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