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In humans, Encephalitozoon cuniculi is responsible for various pathologies, affecting the nervous system as well as the respiratory and digestive tracts. This organism has a very compact genome (the smallest eukaryotic genome known to date) of 2.9 Mbases. The genome is organized into 11 chromosomes. Sequencing of the complete genome is underway using a shotgun approach on a plasmidic library as well as BAC end sequencing. The results may lead to new treatments for microsporidial infections, as well as insights into the positioning of the microsporidae in the eukaryotic classification scheme. Sequencing of the Encephalitozoon cuniculi genome is a collaborative project between Genoscope and the team led by Pr. Christian Vivares (Laboratoire de Protistologie Moléculaire et Cellulaire des Parasites Opportunistes, Université Blaise Pascal, Aubière, France).