Evolution of organellar genome architecture in seed plants: The role of intracellular gene transfer, recombination and mutation

One of the fundamental goals of evolutionary genomics is to identify the forces that shape genome architecture. The mutational burden hypothesis presents a potential unifying explanation for the remarkable genomic diversity across the tree of life. However, a number of exceptional genome architectures that could not be explained by this hypothesis have undermined its robustness. The mitochondrial (mt) and plastid (pt) DNA of seed plants are great study systems for this purpose because they exhibit many contrasting evolutionary phenomena. For example, while mtDNA of seed plants generally has a very low level of sequence divergence, their genomic structures are quite fluid, gene order is rarely conserved, and genome sizes are highly variable. In contrast, ptDNA of seed plants has higher nucleotide substitution rates. However, the overall genome organization, size and content are usually quite conserved. RNA editing is also quite extensive in mitochondria but much less frequent in plastids. In this dissertation, I assembled and analyzed the organelle genomes of several seed plants. The completely sequenced organelle DNAs that were generated not only expanded the organelle genomic diversity to an unprecedented level, but also provided a chance to study the evolutionary forces that have shaped this incredible genomic diversity. I show that intracellular gene transfer, recombination and mutation play major roles in driving organelle genome evolution in seed plants