The prevalence of gene duplication and non-functionalization in plasmid evolution

This thesis investigates the prevalence of gene duplications and non-functionalization in plasmid genome evolution. It provides a comprehensive analysis of plasmid pseudogenes and their association to the loss of plasmid self-transmissibility, which represents as a possible route to domesticated plasmids as exemmplified in enterobacterial isolates. Furthermore, the thesis introduces SegMantX, a novel tool for detecting diverged segmental duplications and demonstrates its ability to detect DNA transfer and plasmid hybridization events. Overall, the thesis highlights that gene non-functionalization and amplification in plasmids is frequently due to mobile genetic elements such as transposons and insertion sequences.

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