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Identifier

000449902

Title

Analysing the genomic novelty in budding yeast

Alternative Title

Ανάλυση της γενωμικής καινοτομίας στους βλαστικούς μύκητες

Author

Τάσσιος, Αιμίλιος

Thesis advisor

Νικολάου, Χριστόφορος

Abstract

While for many years evolution was thought as a tinkerer, that creates novelty through mixing and matching basic building blocks that already existed, it has been fifteen years since the first series of studies that documented a case of de novo gene emergence. De novo gene emergence is a mechanism, which gives birth to new genes out of previously non coding genomic regions. Since the first studies, there have been multiple articles regarding this specific mechanism of gene birth in a plethora of different organisms such as plants, yeasts, primates and even humans. By definition, this particular mechanism has the potential to be the footing for new phenotypic traits and environmental adaptations. For example, in arctic cod an antifreeze protein that is vital for the survival of the fish in the low temperature waters is a product of a de novo gene. Whilst the large number of recorded de novo gene emergence cases, there is little knowledge on the whens, wheres and hows of the mechanism. This project constitutes the largest scale computational investigation of de novo gene emergence to date. Through exploiting a rich dataset published by Shen et al., that contains 332 Saccharomycotina genomes, 11 outgroup genomes and various phylogenetic data in conjunction with cutting-edge bioinformatic approaches , the taxinomically restricted genes (T.R.Gs) of this particular were isolated. Moreover, a subset of these T.R.Gs were characterized as de novo emerged through a thorough genomic comparison analysis. Besides the quantification of the phenomenon, an effort was made to explain the notion behind it, by investigating a wide variety of genomic and proteomic properties and how they might affect the evolutionary fate of the newly emerged genes. In a recently published work, it was showed that a tendency of intergenic sequences to form transmembrane domains more frequently than expected by chance, if theoretically translated, exists in S.cerevisiae. Using the dataset, an attempt to investigate, explain this observation on a subphylum level and link it to the de novo gene emergence mechanism was made.

Language

English

Subject

Genomics

Molecular evolution

Γονιδιωματική

Μοριακή εξέλιξη

Issue date

2022-07-29

Collection

School/Department--School of Medicine--Department of Medicine--Post-graduate theses

Type of Work--Post-graduate theses