Microsporidia are eukaryotic intracellular parasites that evolved from fungi. However, they are highly derived and specialized, and lack several typical eukaryotic features, such as canonical mitochondria, flagella and peroxisomes. They also exhibit seemingly “primitive” traits, probably due to their extreme sequence divergence and reductive evolution, which long obscured their true phylogenetic affinity. Gene content and genomic architecture in Microsporidia are known from E. cuniculi, the only species whose complete genome has been sequenced. A genomic sequence survey of A. locustae, a second and distantly related species, carried out in our laboratory provided valuable data for many studies that improved our knowledge on the biology and evolution of Microsporidia. We present here the latest results of our survey, emphasizing comparative analyses between A. locustae and E. cuniculi in order to explore the dynamics of genome evolution and compaction in this intriguing group of parasites. We found that, in spite of their extreme rates of sequence evolution, microsporidian genome structure evolves slowly compared to other eukaryotic groups and we propose that it is a consequence of
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