M. L. Berbee, T. Y. James, and C. Strullu-derrien, Early diverging fungi: diversity and impact at the dawn of terrestrial life, Annu. Rev. Microbiol, vol.71, pp.41-59, 2017.

I. V. Grigoriev, Fueling the future with fungal genomics, Mycology, vol.2, pp.192-209, 2011.

D. S. Hibbett, Progress in molecular and morphological taxon discovery in fungi and options for formal classification of environmental sequences, Fungal Biol. Rev, vol.25, pp.38-47, 2011.

T. Shirouzu, K. Uno, K. Hosaka, and T. Hosoya, Early-diverging wooddecaying fungi detected using three complementary sampling methods, Mol. Phylogenet. Evol, vol.98, pp.11-20, 2016.
DOI : 10.1016/j.ympev.2016.01.015
URL : https://doi.org/10.1016/j.ympev.2016.01.015

L. Tedersoo, M. Bahram, R. Puusepp, R. H. Nilsson, and T. Y. James, Novel soil-inhabiting clades fill gaps in the fungal tree of life, vol.5, p.42, 2017.

H. Grossart, C. Wurzbacher, T. Y. James, and M. Kagami, Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi, Fungal Ecol, vol.19, pp.28-38, 2016.

M. D. Jones, Discovery of novel intermediate forms redefines the fungal tree of life, Nature, vol.474, pp.200-203, 2011.

K. R. Freeman, Evidence that chytrids dominate fungal communities in high-elevation soils, Proc. Natl Acad. Sci. USA, vol.106, pp.18315-18320, 2009.
DOI : 10.1073/pnas.0907303106
URL : http://www.pnas.org/content/106/43/18315.full.pdf

M. Jobard, S. Rasconi, L. Solinhac, H. Cauchie, and T. Sime-ngando, Molecular and morphological diversity of fungi and the associated functions in three European nearby lakes, Environ. Microbiol, vol.14, pp.2480-2494, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00819272

Y. Chang, Phylogenomic analyses indicate that early fungi evolved digesting cell walls of algal ancestors of land plants, Genome Biol. Evol, vol.7, pp.1590-1601, 2015.

P. C. Blainey, The future is now: single-cell genomics of bacteria and archaea, FEMS Microbiol. Rev, vol.37, pp.407-427, 2013.

C. Gawad, W. Koh, and S. R. Quake, Single-cell genome sequencing: current state of the science, Nat. Rev. Genet, vol.17, pp.175-188, 2016.

T. Woyke, D. F. Doud, and F. Schulz, The trajectory of microbial single-cell sequencing, Nat. Methods, vol.14, pp.1045-1054, 2017.

C. Rinke, Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics, Nat. Protoc, vol.9, pp.1038-1048, 2014.

C. Rinke, Insights into the phylogeny and coding potential of microbial dark matter, Nature, vol.499, pp.431-437, 2013.

H. S. Yoon, Single-cell genomics reveals organismal interactions in uncultivated marine protists, Science, vol.332, pp.714-717, 2011.

R. S. Roy, Single cell genome analysis of an uncultured heterotrophic stramenopile, Sci. Rep, vol.4, p.4780, 2014.

D. López-escardó, Evaluation of single-cell genomics to address evolutionary questions using three SAGs of the choanoflagellate Monosiga brevicollis, Sci. Rep, vol.7, p.11025, 2017.

J. F. Strassert, Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates, ISME J, vol.12, pp.304-308, 2018.

K. Lin, Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus, PLoS Genet, vol.10, p.1004078, 2014.

F. Lan, B. Demaree, N. Ahmed, and A. R. Abate, Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding, Nat. Biotechnol, vol.35, pp.640-646, 2017.

J. W. Spatafora, A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data, Mycologia, vol.108, pp.1028-1046, 2016.

P. Jeffries and T. W. Young, Interfungal Parasitic Relationships (CAB International, 1994.

P. C. Blainey, A. C. Mosier, A. Potanina, C. A. Francis, and S. R. Quake, Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis, PLoS ONE, vol.6, p.16626, 2011.

J. A. Dodsworth, Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage, Nat. Commun, vol.4, p.1854, 2013.

G. Parra, K. Bradnam, and I. Korf, CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, Bioinformatics, vol.23, pp.1061-1067, 2007.

R. Emerson, Current trends of experimental research on the aquatic Phycomycetes, Annu. Rev. Microbiol, vol.4, pp.169-200, 1950.

E. A. Morehouse, Multilocus sequence typing suggests the chytrid pathogen of amphibians is a recently emerged clone, Mol. Ecol, vol.12, pp.395-403, 2003.

A. Pelin, M. Selman, S. Aris-brosou, L. Farinelli, and N. Corradi, Genome analyses suggest the presence of polyploidy and recent human-driven expansions in eight global populations of the honeybee pathogen Nosema ceranae, Environ. Microbiol, vol.17, pp.4443-4458, 2015.

M. B. Rogers, Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

, Genome Res, vol.21, pp.2129-2142, 2011.

J. Ropars, Evidence for the sexual origin of heterokaryosis in arbuscular mycorrhizal fungi, Nat. Microbiol, vol.1, p.16033, 2016.

M. A. Lodato, Somatic mutation in single human neurons tracks developmental and transcriptional history, Science, vol.350, pp.94-98, 2015.

A. Omsland, T. Hackstadt, and R. A. Heinzen, Bringing culture to the uncultured: Coxiella burnetii and lessons for obligate intracellular bacterial pathogens, PLoS Pathog, vol.9, p.1003540, 2013.

L. Stevens, M. D. Winther, and . Spermine, spermidine and putrescine in fungal development, Adv. Microb. Physiol, vol.19, pp.63-148, 1979.

L. Valdés-santiago, J. A. Cervantes-chávez, C. G. León-ramírez, and J. Ruiz-herrera, Polyamine metabolism in fungi with emphasis on phytopathogenic species, J. Amino Acids, vol.2012, p.837932, 2012.

J. F. Jiménez-bremont, J. Ruiz-herrera, and A. Dominguez, Disruption of gene YlODC reveals absolute requirement of polyamines for mycelial development in Yarrowia lipolytica, FEMS Yeast Res, vol.1, pp.195-204, 2001.

L. Valdés-santiago, J. A. Cervantes-chávez, and J. Ruiz-herrera, Ustilago maydis spermidine synthase is encoded by a chimeric gene, required for morphogenesis, and indispensable for survival in the host, FEMS Yeast Res, vol.9, pp.923-935, 2009.

J. Paietta, The Mycota (A Comprehensive Treatise on Fungi as Experimental Systems for, Biochemistry and Molecular Biology, vol.3, pp.369-383, 2004.

J. Maruyama and K. Kitamoto, Expanding functional repertoires of fungal peroxisomes: contribution to growth and survival processes, Front. Physiol, vol.4, p.177, 2013.

V. Lombard, H. Golaconda-ramulu, E. Drula, P. M. Coutinho, and B. Henrissat, The carbohydrate-active enzymes database (CAZy) in 2013, Nucleic Acids Res, vol.42, pp.490-495, 2014.

N. D. Rawlings, A. J. Barrett, and R. Finn, Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors, Nucleic Acids Res, vol.44, pp.343-350, 2016.

R. J. Siezen and J. A. Leunissen, Subtilases: the superfamily of subtilisin-like serine proteases, Protein Sci, vol.6, pp.501-523, 1997.

G. Hu and R. J. Leger, A phylogenomic approach to reconstructing the diversification of serine proteases in fungi, J. Evol. Biol, vol.17, pp.1204-1214, 2004.

A. Muszewska, J. W. Taylor, P. Szczesny, and M. Grynberg, Independent subtilases expansions in fungi associated with animals, Mol. Biol. Evol, vol.28, pp.3395-3404, 2011.

J. Li, F. Gu, R. Wu, J. Yang, and K. Zhang, Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi, Sci. Rep, vol.7, p.45456, 2017.

F. Brouta, Purification and characterization of a 43.5 kDa keratinolytic metalloprotease from Microsporum canis, Med. Mycol, vol.39, pp.269-275, 2001.

E. B. Rosenblum, J. E. Stajich, N. Maddox, and M. B. Eisen, Global gene expression profiles for life stages of the deadly amphibian pathogen Batrachochytrium dendrobatidis, Proc. Natl Acad. Sci. USA, vol.105, pp.17034-17039, 2008.

J. Flach, P. E. Pilet, and P. Jollès, What's new in chitinase research?, Experientia, vol.48, pp.701-716, 1992.

L. Duo-chuan, Review of fungal chitinases, Mycopathologia, vol.161, pp.345-360, 2006.

J. Latgé, The cell wall: a carbohydrate armour for the fungal cell, Mol. Microbiol, vol.66, pp.279-290, 2007.

G. R. Hemsworth, B. Henrissat, G. J. Davies, and P. H. Walton, Discovery and characterization of a new family of lytic polysaccharide monooxygenases, Nat. Chem. Biol, vol.10, pp.122-126, 2014.

B. Henrissat, Classification of chitinases modules, EXS, vol.87, pp.137-156, 1999.

K. E. Bushley and B. G. Turgeon, Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships, BMC Evol. Biol, vol.10, p.26, 2010.

C. R. Howell, R. D. Stipanovic, and R. D. Lumsden, Antibiotic production by strains of Gliocladium virens and its relation to the biocontrol of cotton seedling diseases, Biocontrol Sci. Technol, vol.3, pp.435-441, 1993.

H. A. Wösten, Hydrophobins: multipurpose proteins, Annu. Rev. Microbiol, vol.55, pp.625-646, 2001.

O. M. De-vries, M. Peter-fekkes, H. A. Wösten, and J. G. Wessels, Insoluble hydrophobin complexes in the walls of Schizophyllum commune and other filamentous fungi, Arch. Microbiol, vol.159, pp.330-335, 1993.

L. S. Olive, Caulochytrium protostelioides sp. nov., a new chytrid with aerial spporangia, Am. J. Bot, vol.67, pp.568-574, 1980.
DOI : 10.2307/3792789

R. K. Benjamin and . Merosporangium, Mycologia, vol.58, pp.1-42, 1966.

M. M. White, Phylogeny of the Zygomycota based on nuclear ribosomal sequence data, Mycologia, vol.98, pp.872-884, 2006.

T. Y. James, A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota), Mycologia, vol.98, pp.860-871, 2006.

D. J. Barr, An outline for the reclassification of the Chytridiales, and for a new order, the Spizellomycetales, Can. J. Bot, vol.58, pp.2380-2394, 1980.

I. J. Tsai, D. Bensasson, A. Burt, and V. Koufopanou, Population genomics of the wild yeast Saccharomyces paradoxus: quantifying the life cycle, Proc. Natl Acad. Sci. USA, vol.105, pp.4957-4962, 2008.

K. Saikkonen, C. A. Young, M. Helander, and C. L. Schardl, Endophytic Epichloë species and their grass hosts: from evolution to applications, Plant Mol. Biol, vol.90, pp.665-675, 2016.

L. M. Schloegel, Novel, panzootic and hybrid genotypes of amphibian chytridiomycosis associated with the bullfrog trade, Mol. Ecol, vol.21, pp.5162-5177, 2012.

E. B. Rosenblum, Complex history of the amphibian-killing chytrid fungus revealed with genome resequencing data, Proc. Natl Acad. Sci. USA, vol.110, pp.9385-9390, 2013.

C. A. Quandt, The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism, vol.6, p.29594, 2017.

J. J. Ellis, On growing Syncephalis in pure culture, Mycologia, vol.58, pp.465-469, 1966.

K. L. Lazarus, G. L. Benny, H. Ho, and M. E. Smith, Phylogenetic systematics of Syncephalis (Zoopagales, Zoopagomycotina), a genus of ubiquitous mycoparasites, Mycologia, vol.109, pp.333-349, 2017.

C. G. Staggs, W. M. Sealey, B. J. Mccabe, A. M. Teague, and D. M. Mock, Determination of the biotin content of select foods using accurate and sensitive HPLC/avidin binding, J. Food. Compost. Anal, vol.17, pp.767-776, 2004.

R. Riley, Comparative genomics of biotechnologically important yeasts, Proc. Natl Acad. Sci. USA, vol.113, pp.9882-9887, 2016.

N. A. Moran and G. M. Bennett, The tiniest tiny genomes, Annu. Rev. Microbiol, vol.68, pp.195-215, 2014.

I. S. Druzhinina, Trichoderma: the genomics of opportunistic success, Nat. Rev. Microbiol, vol.9, pp.749-759, 2011.

P. K. Mukherjee, B. A. Horwitz, and C. M. Kenerley, Secondary metabolism in Trichoderma-a genomic perspective, Microbiology, vol.158, pp.35-45, 2012.

T. Y. James, Shared signatures of parasitism and phylogenomics unite Cryptomycota and Microsporidia, Curr. Biol, vol.23, pp.1548-1553, 2013.

G. L. Benny, H. Ho, K. Lazarus, and M. E. Smith, Five new species of the obligate mycoparasite Syncephalis (Zoopagales, Zoopagomycotina) from soil, Mycologia, vol.108, pp.1114-1129, 2016.

F. Lutzoni, Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits, Am. J. Bot, vol.91, pp.1446-1480, 2004.

A. Bankevich, SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing, J. Comput. Biol, vol.19, pp.455-477, 2012.

I. V. Grigoriev, MycoCosm portal: gearing up for 1000 fungal genomes, Nucleic Acids Res, vol.42, pp.699-704, 2014.

F. A. Simão, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, pp.3210-3212, 2015.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.

E. Garrison and G. Marth, Haplotype-based variant detection from short-read sequencing, p.3907, 2012.

A. Lex, N. Gehlenborg, H. Strobelt, R. Vuillemot, and H. Pfister, UpSet: visualization of intersecting sets, IEEE Trans. Vis. Comput. Graph, vol.20, 1983.

T. Frickey and A. Lupas, CLANS: a Java application for visualizing protein families based on pairwise similarity, Bioinformatics, vol.20, pp.3702-3704, 2004.

A. Stamatakis, Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM cell, J. VLSI Signal Process. Syst. Signal Image Video Technol, vol.48, pp.271-286, 2007.

I. Letunic and P. Bork, Interactive Tree of Life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-245, 2016.

S. R. Eddy, Accelerated profile HMM searches, PLoS Comput. Biol, vol.7, p.1002195, 2011.

R. C. Edgar, R. M. Drive, and M. Valley, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004.

S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, Basic Local Alignment Search Tool, J. Mol. Biol, vol.215, pp.403-410, 1990.
DOI : 10.1006/jmbi.1990.9999

A. J. Enright, S. Van-dongen, and C. A. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Res, vol.30, pp.1575-1584, 2002.
DOI : 10.1093/nar/30.7.1575
URL : https://academic.oup.com/nar/article-pdf/30/7/1575/7039591/gkf245.pdf

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol, vol.30, pp.772-780, 2013.
DOI : 10.1093/molbev/mst010
URL : https://academic.oup.com/mbe/article-pdf/30/4/772/6420419/mst010.pdf

J. Castresana, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol. Biol. Evol, vol.17, pp.540-552, 2000.

E. Paradis, J. Claude, and K. Strimmer, APE: analyses of phylogenetics and evolution in R language, Bioinformatics, vol.20, pp.289-290, 2004.
URL : https://hal.archives-ouvertes.fr/ird-01887318

C. Claudel-renard, C. Chevalet, T. Faraut, and D. Kahn, Enzyme-specific profiles for genome annotation: PRIAM, Nucleic Acids Res, vol.31, pp.6633-6639, 2003.
DOI : 10.1093/nar/gkg847
URL : https://hal.archives-ouvertes.fr/hal-00427393

T. Yamada, I. Letunic, S. Okuda, M. Kanehisa, and P. Bork, 0: interactive pathway explorer, Nucleic Acids Res, vol.39, pp.412-415, 2011.
DOI : 10.1093/nar/gkr313
URL : https://academic.oup.com/nar/article-pdf/39/suppl_2/W412/18782997/gkr313.pdf