| Summary: | Genomic sequence data from the three domains of life have revealed a remarkable diversity of genome architectures. The relative contributions of adaptive versus non-adaptive processes in shaping this diversity are poorly understood and hotly debated. This thesis investigates the evolution of genome architecture in the Chloroplastida (i.e., green algae and land plants), with a particular focus on the mitochondrial and plastid genomes of chlamydomonadalean algae (Chlorophyceae, Chlorophyta). Much of the work presented here describes unprecedented extremes in: i) genome compactness (i.e., the fraction of noncoding DNA in a genome), ii) genome conformation (e.g., circular vs. linear vs. linear fragmented genomes), iii) intron and repeat content; and iv) nucleotide-composition landscape (e.g., GC-rich vs. AT-rich genomes). These data are then combined with intra-population nucleotide diversity data to explore the degree to which non-adaptive forces, such as random genetic drift and mutation rate, have shaped the organelle and nuclear genomes of the Chloroplastida. The major conclusions from this dissertation are that chlamydomonadalean algae show a much greater variation in organelle genome architecture than previously thought — this group boasts some of the most unusual mitochondrial and plastid genomes from all eukaryotes — and that the majority of this variation can be explained in non-adaptive terms.
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