1 Genomics of Preaxostyla Flagellates Illuminates Evolutionary Transitions and the Path 1 Towards Mitochondrial Loss 2 Lukáš V. F. Novák* 1,2 , Sebastian C. Treitli* 1 , Jan Pyrih 1 , Paweł Hałakuc 3 , Shweta V. Pipaliya 4,5 , 3 Vojtěch Vacek 1 , Ondřej Brzoň 1 , Petr Soukal 1 , Laura Eme 2 , Joel B. Dacks 4,6 , Anna Karnkowska 3 , 4 Marek Eliáš 7 & Vladimír Hampl 1$ 5 6 1 Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech 7 Republic. 8 2 Ecology, Systematics, and Evolution Unit, Université Paris-Saclay, CNRS, Orsay, France. 9 3 Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, 10 University of Warsaw, Poland. 11 4 Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, 12 Canada. 13 5 School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland; 14 Swiss Institute of Bioinformatics, Lausanne, Switzerland. 15 6 Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 16 Czechia. 17 7 University of Ostrava, Faculty of Science, Department of Biology and Ecology, Ostrava, Czech 18 Republic. 19 20 . CC-BY-ND 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made The copyright holder for this preprint this version posted December 13, 2022. ; https://doi.org/10.1101/2022.11.24.517819 doi: bioRxiv preprint