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Abstract
The greatest diversity in eukaryotic genomes is observed in the deep branching protist phyla. The protist phylum Apicomplexa consists of at least 5,000 species of mostly obligate intracellular parasites, many of medical and veterinary importance. A number of apicomplexan genomes have been sequenced, providing us with a rich resource for comparative evolutionary studies. Apicomplexans have reductive genomes, yet, they show immense genome diversity and innovation. This diversity is captured in the parasites of the coccidian lineage. Sarcocystis neurona has the largest sequenced apicomplexan genome at >125 Mb, twice as large as the next largest genome from Toxoplasma gondii, the highly-successful zoonotic pathogen. We find that repeats are responsible for a large S. neurona genome, however the out-group parasite Eimeria while repetitive has a ~55 Mb genome. The in-group parasites, T. gondii, Neospora caninum and Hammondia hammondi are repeat-poor. Instead, they contain unprecedented levels of organellar DNA insertions; NUM/PTs. While repeats shape the genomes of the early-branching coccidians, our study suggests NUM/PTs to be the significant drivers of genome evolution in later-branching coccidians.