Chapter 1 : The Fungal Tree of Life: From Molecular Systematics to Genome-Scale Phylogenies

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In 1996 the genome of was published and marked the beginning of a new era in fungal biology ( ). Since then, rapid advancements in both sequencing technologies and computational biology have resulted in the sequencing of genomes for more than 800 species (e.g., http://genome.jgi.doe.gov/fungi/). These genomes represent a windfall of data that are informing evolutionary studies of fungi and the search for biological solutions to alternative fuels, bioremediation, carbon sequestration, and sustainable agriculture and forestry ( ). Indeed, the marriage between genomics and phylogenetics occurred early, both in the use of phylogenetic techniques to study genome evolution and in the use of genome-scale data to infer evolutionary relationships. In this article we will review the impact of genomic-scale phylogenies, along with standard molecular phylogenies, on our understanding of the evolution of the fungal tree of life and the classification that communicates it.

Citation: Spatafora J, Aime M, Grigoriev I, Martin F, Stajich J, Blackwell M. 2017. The Fungal Tree of Life: From Molecular Systematics to Genome-Scale Phylogenies, p 3-34. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0053-2016
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Figure 1

Fungal tree of life. Cladogram of the kingdom Fungi based on published multi-gene and genome-scale phylogenies ( ). Polytomies represent regions of the tree currently unresolved by molecular and genomic data.

Citation: Spatafora J, Aime M, Grigoriev I, Martin F, Stajich J, Blackwell M. 2017. The Fungal Tree of Life: From Molecular Systematics to Genome-Scale Phylogenies, p 3-34. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0053-2016
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Figure 2

Examples of zoosporic fungal diversity. (Cryptomycota) parasitizing hyphae of (Blastocladiomycota). Chytridiomycota: (Chytridiomycetes) monocentric, operculate zoosporangium with rhizoids; sp. (Chytridiomycetes) monocentric, operculate zoosporangium with rhizoids; (Monoblepharidomycetes) mature zygote or oospore, empty and mature antheridia and antherozoids or male gametes emerging from antheridium (by Marilyn M. N. Mollicone); sp. (Neocallimastigomycetes) monocentric thallus with rhizoids (by Gary Easton); () zoospores (photo by D’Ann Rochon); sp. (Neocallimastigomycetes) multiflagellate zoospores (photo by Gary Easton).

Citation: Spatafora J, Aime M, Grigoriev I, Martin F, Stajich J, Blackwell M. 2017. The Fungal Tree of Life: From Molecular Systematics to Genome-Scale Phylogenies, p 3-34. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0053-2016
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Figure 3

Examples of zygomycete fungal diversity. Zoopagomycota: adult fly infected by a species of Entomophthorales; conidium; conidia; thallus with trichospores (photo by R.W. Lichtwardt); sporangium; sporangium; sporangium; sporangium. Mucoromycota: spore (photo from American Society for the Advancement of Science); sporocarp (photo by D. Redeker); arbuscule (photo by K. Wex); sporangium; sporangium; sporangium; sporangium; sporangium; zygosporangium; zygosporangium; sporocarp, zygospore (inset).

Citation: Spatafora J, Aime M, Grigoriev I, Martin F, Stajich J, Blackwell M. 2017. The Fungal Tree of Life: From Molecular Systematics to Genome-Scale Phylogenies, p 3-34. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0053-2016
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Figure 4

Examples of Ascomycota diversity. Apothecia (yellow) of , Orbiliomycetes (J. H. Petersen/MycoKey). Apothecia of , Pezizomycetes (J. H. Petertsen/MycoKey). Thallus of with apothecia, Lecanoromycetes (B. McCune, Oregon State University). Thallus of , Lichinomycetes (B. McCune, Oregon State University). Bitunicate asci of , Dothideomycetes (S. Huhndorf, Field Museum). Thallus of with apothecia, Arthoniomycetes (B. McCune, Oregon State University). Thallus of , Laboulbeniomycetes (A. Weir, SUNY-ESF). Perithecia of , Sordariomycetes (N. B. Raju, Stanford University). Earth-tongue apothecia of , Leotiomycetes (Z. Wang, Iowa State University). Cleistothecia of , Eurotiomycetes (D. Geiser, Penn State University). Operculate ascus of (J. H. Petersen/MycoKey). Ascostroma of , Dothideomycetes (T. Volk, University of Wisconsin at La Crosse). Unitunicate asci (N. B. Raju, Stanford University). Prototunicate ascus of (D. Geiser, Penn State University).

Citation: Spatafora J, Aime M, Grigoriev I, Martin F, Stajich J, Blackwell M. 2017. The Fungal Tree of Life: From Molecular Systematics to Genome-Scale Phylogenies, p 3-34. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0053-2016
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Figure 5

Examples of Basidiomycota diversity. Pucciniomycotina: uredinia of ; fruiting body of ; aecia of ; yeast state of . Ustilaginomycotina: smut galls of ; gall of ; culture of sp. Agaricomycotina: culture of ; stinkhorn fruiting body of (photo by Nu Nguyen). coral fruiting body of ; crust fruiting body of ; club fruiting body of ; polypore, conk fruiting body of ; gilled mushroom fruiting body of ; pored mushroom fruiting body of ; puffball fruiting body of .

Citation: Spatafora J, Aime M, Grigoriev I, Martin F, Stajich J, Blackwell M. 2017. The Fungal Tree of Life: From Molecular Systematics to Genome-Scale Phylogenies, p 3-34. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0053-2016
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