, KANJI consortia Post-doctoral Fellowship

C. Ku-leuven and . Grant,

C. France-génomique,

, French Government's Investissement d'Avenir program (Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases, Funding for open access charge: Institutional

T. Jones, N. A. Federspiel, H. Chibana, J. Dungan, S. Kalman et al., The diploid genome sequence of Candida albicans, Proc. Natl. Acad. Sci. U.S.A, vol.101, pp.7329-7334, 2004.

D. Muzzey, K. Schwartz, J. S. Weissman, and G. Sherlock, Assembly of a phased diploid Candida albicans genome facilitates allele-specific measurements and provides a simple model for repeat and indel structure, Genome Biol, vol.14, p.97, 2013.

C. Enfert, S. Goyard, S. Rodriguez-arnaveilhe, L. Frangeul, L. Jones et al., CandidaDB: a genome database for Candida albicans pathogenomics, Nucleic Acids Res, vol.33, pp.353-357, 2005.

B. R. Braun, M. Van-het-hoog, C. Enfert, M. Martchenko, J. Dungan et al., A human-curated annotation of the Candida albicans Genome, PLoS Genet, vol.1, pp.36-57, 2005.

M. S. Skrzypek, J. Binkley, G. Binkley, S. R. Miyasato, M. Simison et al., The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data, Nucleic Acids Res, vol.45, pp.592-596, 2017.

T. Roemer, B. Jiang, J. Davison, T. Ketela, K. Veillette et al., Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery, Mol. Microbiol, vol.50, pp.167-181, 2003.

D. Xu, B. Jiang, T. Ketela, S. Lemieux, K. Veillette et al., , 2007.

, Genome-wide fitness test and mechanism-of-action studies of inhibitory compounds in Candida albicans, PLoS Pathog, vol.3, p.92

O. R. Homann, J. Dea, S. M. Noble, and A. D. Johnson, A phenotypic profile of the Candida albicans regulatory network, PLos Genet, vol.5, p.1000783, 2009.

S. M. Noble, S. French, L. A. Kohn, V. Chen, and A. D. Johnson, Systematic screens of a Candida albicans homozygous deletion library decouple morphogenetic switching and pathogenicity, Nat. Genet, vol.42, pp.590-598, 2010.

C. J. Nobile, V. M. Bruno, M. L. Richard, D. A. Davis, and A. P. Mitchell, Genetic control of chlamydospore formation in Candida albicans, Microbiology, vol.149, pp.3629-3637, 2003.

N. Sahni, S. Yi, K. J. Daniels, G. Huang, T. Srikantha et al., Tec1 mediates the pheromone response of the white phenotype of Candida albicans: insights into the evolution of new signal transduction pathways, PLoS Biol, vol.8, p.1000363, 2010.

M. Chauvel, A. Nesseir, V. Cabral, S. Znaidi, S. Goyard et al., A versatile overexpression strategy in the pathogenic yeast Candida albicans: identification of regulators of morphogenesis and fitness, PLoS One, vol.7, p.45912, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-01523618

R. Schillig and J. Morschhauser, Analysis of a fungus-specific transcription factor family, the Candida albicans zinc cluster proteins, by artificial activation, Mol. Microbiol, vol.89, pp.1003-1017, 2013.

J. F. Rual, D. E. Hill, and M. Vidal, ORFeome projects: gateway between genomics and omics, Curr. Opin. Chem. Biol, vol.8, pp.20-25, 2004.

S. Ghaemmaghami, W. K. Huh, K. Bower, R. W. Howson, A. Belle et al., Global analysis of protein expression in yeast, Nature, vol.425, pp.737-741, 2003.

J. Reboul, P. Vaglio, J. F. Rual, P. Lamesch, M. Martinez et al., C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression, Nat. Genet, vol.34, pp.35-41, 2003.
URL : https://hal.archives-ouvertes.fr/hal-01599842

D. M. Gelperin, M. A. White, M. L. Wilkinson, Y. Kon, L. A. Kung et al., Biochemical and genetic analysis of the yeast proteome with a movable ORF collection, Genes Dev, vol.19, pp.2816-2826, 2005.

A. Matsuyama and M. Yoshida, Systematic cloning of an ORFeome using the Gateway system, Methods Mol. Biol, vol.577, pp.11-24, 2009.

S. V. Rajagopala, N. Yamamoto, A. E. Zweifel, T. Nakamichi, H. K. Huang et al., , p.12, 2010.

, ORFeome: a resource for comparative molecular microbiology, BMC Genomics, vol.11, p.470

W. Gong, Y. P. Shen, L. G. Ma, Y. Pan, Y. L. Du et al., Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes, Plant Physiol, vol.135, pp.773-782, 2004.

B. A. Underwood, R. Vanderhaeghen, R. Whitford, C. D. Town, and P. Hilson, Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations, Plant Biotechnol. J, vol.4, pp.317-324, 2006.

I. M. Grant, D. Balcha, T. Hao, Y. Shen, P. Trivedi et al., The Xenopus ORFeome: a resource that enables functional genomics, Dev. Biol, vol.408, pp.345-357, 2015.

J. Bischof, M. Bjorklund, E. Furger, C. Schertel, J. Taipale et al., A versatile platform for creating a comprehensive UAS-ORFeome library in Drosophila, Development, vol.140, pp.2434-2442, 2013.

A. Dricot, J. F. Rual, P. Lamesch, N. Bertin, D. Dupuy et al., Generation of the Brucella melitensis ORFeome version 1.1, Genome Res, vol.14, pp.2201-2206, 2004.

J. C. Aguiar, J. Labaer, P. L. Blair, V. Y. Shamailova, M. Koundinya et al., High-throughput generation of P. falciparum functional molecules by recombinational cloning, Genome Res, vol.14, pp.2076-2082, 2004.

R. Hauser, A. Ceol, S. V. Rajagopala, R. Mosca, G. Siszler et al., A second-generation protein-protein interaction network of Helicobacter pylori, Mol. Cell. Proteomic, vol.13, pp.1318-1329, 2014.

C. J. Maier, R. H. Maier, D. P. Virok, M. Maass, H. Hintner et al., Construction of a highly flexible and comprehensive gene collection representing the ORFeome of the human pathogen Chlamydia pneumoniae, BMC Genomics, p.632, 2012.

C. J. Brandner, R. H. Maier, D. S. Henderson, H. Hintner, J. W. Bauer et al., The ORFeome of Staphylococcus aureus v 1.1, BMC Genomics, vol.9, p.321, 2008.

A. Von-brunn, C. Teepe, J. C. Simpson, R. Pepperkok, C. C. Friedel et al., Analysis of intraviral protein-protein interactions of the SARS coronavirus ORFeome, PLoS One, vol.2, p.459, 2007.

P. Lamesch, N. Li, S. Milstein, C. Fan, T. Hao et al., ) hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes, Genomics, vol.89, pp.307-315, 2007.

A. J. Walhout, G. F. Temple, M. A. Brasch, J. L. Hartley, M. A. Lorson et al., GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes, Methods Enzymol, vol.328, pp.575-592, 2000.

V. Cabral, S. Znaidi, L. A. Walker, H. Martin-yken, E. Dague et al., Targeted changes of the cell wall proteome influence Candida albicans ability to form single-and multi-strain biofilms, PLoS Pathog, vol.10, p.1004542, 2014.

B. Stynen, P. Van-dijck, and H. Tournu, A CUG codon adapted two-hybrid system for the pathogenic fungus Candida albicans, Nucleic Acids Res, vol.38, p.184, 2010.

D. Hanahan, Studies on transformation of Escherichia coli with plasmids, J. Mol. Biol, vol.166, pp.557-580, 1983.

V. Cabral, M. Chauvel, A. Firon, M. Legrand, A. Nesseir et al., Modular gene over-expression strategies for Candida albicans, Methods Mol. Biol, vol.845, pp.227-244, 2012.

, Nucleic Acids Research, vol.46, issue.14, p.6949, 2018.

S. Gola, R. Martin, A. Walther, A. Dunkler, and J. Wendland, New modules for PCR-based gene targeting in Candida albicans: rapid and efficient gene targeting using 100 bp of flanking homology region, Yeast, vol.20, pp.1339-1347, 2003.

T. T. Liu, S. Znaidi, K. S. Barker, L. Xu, R. Homayouni et al., , 2007.

, Genome-wide expression and location analyses of the Candida albicans Tac1p regulon, Eukaryot. Cell, vol.6, pp.2122-2138

B. Enjalbert, A. Rachini, G. Vediyappan, D. Pietrella, R. Spaccapelo et al., A multifunctional, synthetic Gaussia princeps luciferase reporter for live imaging of Candida albicans infections, Infect. Immun, vol.77, pp.4847-4858, 2009.
URL : https://hal.archives-ouvertes.fr/pasteur-01525033

O. Reuss, A. Vik, R. Kolter, and J. Morschhauser, The SAT1 flipper, an optimized tool for gene disruption in Candida albicans, 2004.

, Gene, vol.341, pp.119-127

R. B. Wilson, D. Davis, and A. P. Mitchell, Rapid hypothesis testing with Candida albicans through gene disruption with short homology regions, J. Bacteriol, vol.181, pp.1868-1874, 1999.

A. Walther and J. Wendland, PCR-based gene targeting in Candida albicans, Nat. Protoc, vol.3, pp.1414-1421, 2008.

Y. N. Park and J. Morschhauser, Tetracycline-inducible gene expression and gene deletion in Candida albicans, Eukaryot. Cell, vol.4, pp.1328-1342, 2005.

G. Huang, H. Wang, S. Chou, X. Nie, J. Chen et al., Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.12813-12818, 2006.

H. Liu, J. Kohler, and G. R. Fink, Suppression of hyphal formation in Candida albicans by mutation of a STE12 homolog, Science, vol.266, pp.1723-1726, 1994.

R. J. Bennett and A. D. Johnson, Completion of a parasexual cycle in Candida albicans by induced chromosome loss in tetraploid strains, EMBO J, vol.22, pp.2505-2515, 2003.

M. Van-het-hoog, T. J. Rast, M. Martchenko, S. Grindle, D. Dignard et al., Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes, Genome Biol, vol.8, p.52, 2007.

W. A. Fonzi and M. Y. Irwin, Isogenic strain construction and gene mapping in Candida albicans, Genetics, vol.134, pp.717-728, 1993.

M. S. Skrzypek, J. Binkley, G. Binkley, S. R. Miyasato, M. Simison et al., Candida Genome Database, 2017.

S. Alberti, A. D. Gitler, and S. Lindquist, A suite of gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae, Yeast, vol.24, pp.913-919, 2007.

R. Hallez, J. J. Letesson, J. Vandenhaute, and X. De-bolle, Gateway-based destination vectors for functional analyses of bacterial ORFeomes: application to the Min system in Brucella abortus, Appl. Environ. Microbiol, vol.73, pp.1375-1379, 2007.

P. L. Carlisle, M. Banerjee, A. Lazzell, C. Monteagudo, J. L. Lopez-ribot et al., Expression levels of a filament-specific transcriptional regulator are sufficient to determine Candida albicans morphology and virulence, Proc. Natl. Acad. Sci. U.S.A, vol.106, pp.599-604, 2009.

U. Zeidler, T. Lettner, C. Lassnig, M. Muller, R. Lajko et al., UME6 is a crucial downstream target of other transcriptional regulators of true hyphal development in Candida albicans, FEMS Yeast Res, vol.9, pp.126-142, 2009.

R. J. Bennett, The parasexual lifestyle of Candida albicans, Curr. Opin. Microbiol, vol.28, pp.10-17, 2015.

M. G. Miller and A. D. Johnson, White-opaque switching in Candida albicans is controlled by mating-type locus homeodomain proteins and allows efficient mating, Cell, vol.110, pp.293-302, 2002.

S. M. Noble and A. D. Johnson, Strains and strategies for large-scale gene deletion studies of the diploid human fungal pathogen Candida albicans, Eukaryot. Cell, vol.4, pp.298-309, 2005.

R. E. Zordan, D. J. Galgoczy, and A. D. Johnson, Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.12807-12812, 2006.

R. Loll-krippleber, A. Feri, M. Nguyen, C. Maufrais, J. Yansouni et al., A FACS-optimized screen identifies regulators of genome stability in Candida albicans, Eukaryot. Cell, vol.14, pp.311-322, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01515479

Q. M. Mitrovich, B. B. Tuch, C. Guthrie, and A. D. Johnson, Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans, Genome Res, vol.17, pp.492-502, 2007.

M. A. Santos and M. F. Tuite, The CUG codon is decoded in vivo as serine and not leucine in Candida albicans, Nucleic Acids Res, vol.23, pp.1481-1486, 1995.

A. Coste, V. Turner, F. Ischer, J. Morschhauser, A. Forche et al., A mutation in Tac1p, a transcription factor regulating CDR1 and CDR2, is coupled with loss of heterozygosity at chromosome 5 to mediate antifungal resistance in Candida albicans, Genetics, vol.172, pp.2139-2156, 2006.

A. R. Holmes, S. Tsao, S. W. Ong, E. Lamping, K. Niimi et al., Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2, Mol. Microbiol, vol.62, pp.170-186, 2006.

D. Muzzey, G. Sherlock, and J. S. Weissman, Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans, Genome Res, vol.24, pp.963-973, 2014.