In this thesis, we extensively and systematically studied evolution patterns of newtraits in yeast genomes by bioinformatics methods. Mitochondria are essential forcellular energy production in most eukaryotic organisms. However, even whenglucose is abundant yeast species that underwent whole genome duplication (WGD)mostly conduct fermentation even under aerobic conditions and most can survive without a functional mitochondrial genome. In this study we show that evolutionary rate for the nuclear-encoded mitochondrial genes were greater in post-WGD speciesthan pre-WGD species. Furthermore, codon usage bias was relaxed for these genes in post-WGD yeast species. The codon usage pattern and the distribution of a particular transcription regulatory element suggest that the change to an efficient aerobic fermentation lifestyle in this lineage might have emerged after WGD between the divergence of Kluyveromyces polysporus and Saccharomyces castellii from their common ancestor. This new energy production strategy could have led to the relaxation of mitochondrial function in the relevant yeast species. Second, the emergence of multicellular organisms was one of the most profound developmental transitions in the history of life. The filamentous fungus Ashbya gossypii grows into multicellular mycelium which is distinct from its closely related unicellular yeast species. It has been proposed that genes functioning during cell cycle play central roles for such phenotypic differences. Because A. gossypii shares an almost identical set of cell cycle genes with the typical yeast Saccharomyces cerevisiae, the divergences might occur at the regulation level for orthologous genes. Here we show that cell cycle genes have significantly higher translation efficiency in A. gossypii than their orthologous genes in yeasts. Meanwhile, genes which have significantly higher translation efficiency in yeasts are enriched with metabolic functions. Because translation efficiency of a gene is closely related with its functional importance, the observed functional distributions of orthologous genes with different translation efficiency might account, at least partially, for the phenotypic differentiation between A. gossypii and the yeast species.
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