Aspects of the bioinformatic analysis and annotation of the genome of Rhodopirellula baltica

This thesis focuses on the bioinformatic analysis and annotation of the genome of the marine planctomycete Rhodopirellula baltica. A comprehensive bioinformatic pipeline was set up and established that comprises gene prediction, annotation and visualization tools. Considerable effort was put into the manual annotation process.The annotation of the genome of Rhodopirellula baltica revealed that this organism is specialized on the aerobic degradation of complex carbohydrates. Its genome harbors 110 sulfatases, which are likely excreted to get access to the carbon skeletons of sulfated heteropolysaccharides like chondroitin sulfate or carrageen.Phylogenetic analysis of numerous marker genes from the genome support a relationship with the Chlamydia or at least an affiliation with the Chlamydia-Spirochaetes superclade. This is in agreement with earlier 16S rRNA-based analysis and contradicts the recently proposed deepest branching position of the Planctomycetes within the bacterial domain. The presence of many genes for peptidoglycan biosynthesis indicates that the proteinaceous cell envelopes of planctomycetes are secondary adaptions rather than a relict from a time preceding peptidoglycan cell walls. This is also consistent with findings that suggest that the Planctomycetes originated from organisms with Gram negative-type cell envelopes (e.g. genes for lipid A biosynthesis) and that the outer ribosome-free compartments of Planctomycetes descended from a former periplasmic space.Two spin-off projects from the annotation of the Rhodopirellula baltica genome have lead to independent software developments. The first is MORFind, a flexible and extensible meta-tool for the in silico prediction of protein-coding genes. The second is a method for the probability-based assignment of genomic fragments originating from metagenome projects that is based on skewed tetranucleotide distributions. A dedicated program named TETRA has been developed for this purpose.