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C. E. and J. , was supported by a Pasteur-Roux fellowship from Institut Pasteur. D.D. was the recipient of a PhD fellowship from Institut National de la Recherche Agronomique. E.P. was the recipient of a post-doctoral fellowship from the Wellcome Trust (WT088858MA). M.M.- H. and T.G. were supported by a grant from the Spanish Ministry of Economy and Competitiveness, the Genoscope (projet #15 AP2008/2009 SNP C. albicans) and the Swiss National Science Foundation BFU2015?67107 cofunded by the European Regional Development Fund (ERDF). were supported by a grant from the French and Korean Ministries for Foreign Affairs (PHC STAR 2011 25841YA). R.C.M. was supported by project MitoFun, funded by the European Research Council under the European Union's Seventh Framework Programme (FPERC Grant Agreement No. 614562 and by a Wolfson Research Merit Award from the Royal Society. R.C, 2007.

M. and K. V. , were funded by the Surgical Reconstruction and Microbiology Research Centre, which is supported by the National Institute of Health Research, UK. G.S. was supported by the NIH grants R01-HG003468 and RO1-DE015873. C.E. and T.G. are members of the CNRS GDRI 0814 iGenolevures consortium. High-throughput sequencing has been performed on the Genomics Platform, member of France Génomique consortium (ANR10-INBS-09-08) We thank Bernard Dujon and Tatiana Giraud for providing insights on an earlier version of this manuscript