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Cells are the vehicles that allows genetic code to proliferate in the world, taking on various forms – as illustrated by the tree of life. The cell features are determined by the manufacturing of proteins, a process that has its blueprints encoded as genes in the genome. It is crucial for all cells to have the right amount of protein, regardless of context (part of a multicellular organism or self-sustained). The protein landscape (amount and type) vary depending on the environment. Cells of the multicellular organism should maintain the protein balance to provide its’ intended function in the organism tissue. The cells of multicellular organisms are faced with an imbalance due to sex-related chromosomal imbalances and other genome effects that change the number of gene copies. Restoration from the imbalance is done by dosage compensation systems. Cells that are isolated from the organism and grown inside the lab are common in research, known as cell lines. Cancer cells are similar to cell lines and have lost their original function in the organism in favor of a self-sustained lifestyle. The new environment (context) for these isolated cells impose a challenge; the cells must reorganize their genomes (holding the blueprints for proteins) to obtain autonomy.

In this thesis, the genome evolution of isolated cells, cell lines, has been studied using Drosophila melanogaster (the fruit fly). Compared to normal cells of the host organism, cell line genomes are highly mutated and rearranged. With the emergence of novel sequencing technologies that can read long fragments of the genome, this complexity of cell line genomes can be captured. On the topic of novel sequencing technologies, new software implementations are presented and the future of software for long reads and complex genomes is discussed. The main focus of this thesis is to describe how an established and commonly used cell line has reorganized its’ genome to sustain a culture environment. Important information about the genome structure is provided to the research community. The thesis also describes the genome reorganization in new cell lines, covering the early adaptations to cell autonomy. Together, these investigations are of high relevance to human cancer research. This thesis has also studied the fundamentals for regulation of protein balance in organismal cells. Specifically, a recognition sequence to the X chromosome of the protein Painting of Fourth. This protein is related to dosage compensation and primarily enhance transcription from the 4 thchromosome in Drosophila melanogaster, but has been observed tooccasionally bind to the X chromosome.