Development of a computational approach to accurately detect gene losses in genome sequences

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An important question in biology is what are the DNA changes that are involved in phenotypic differences between species. Case studies found that the loss of genes can be important for both the loss and gain of phenotypes during evolution. The goal of this project is the development of a bioinformatics method that uses comparative genomes to systematically detect genes that are lost in the genomes of a given species. Our main focus is to increase the specificity and thus reduce the false positive rate to an extent that no manual curation of gene loss candidates is necessary, which is key to apply this approach to many genomes. Our preliminary work clearly identified which filtering steps and sequence alignment approaches need to be implemented in order to achieve this high accuracy. Using this method, we will then detect gene losses in vertebrate species with short lifespans to uncover candidate genes that influence aging. Furthermore, we will use this method to create a catalog of gene losses in vertebrates, fruit flies and nematodes. This will form the basis to systematically study how gene loss had an impact on the evolution of phenotypic differences.