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Fungal Genomes and Insights into the Evolution of the Kingdom

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  • Author: Jason E. Stajich1
  • Editors: Joseph Heitman2, Eva Holtgrewe Stukenbrock3
    Affiliations: 1: Department of Plant Pathology and Microbiology and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521; 2: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710; 3: Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany, and Max Planck Institute for Evolutionary Biology, Plön, Germany
  • Source: microbiolspec August 2017 vol. 5 no. 4 doi:10.1128/microbiolspec.FUNK-0055-2016
  • Received 19 May 2017 Accepted 19 June 2017 Published 18 August 2017
  • Jason E Stajich, jason.stajich@ucr.edu
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  • Abstract:

    The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute’s Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.

  • Citation: Stajich J. 2017. Fungal Genomes and Insights into the Evolution of the Kingdom. Microbiol Spectrum 5(4):FUNK-0055-2016. doi:10.1128/microbiolspec.FUNK-0055-2016.

Key Concept Ranking

Major Facilitator Superfamily
Scanning Electron Microscopy


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The kingdom Fungi comprises species that inhabit nearly all ecosystems. Fungi exist as both free-living and symbiotic unicellular and multicellular organisms with diverse morphologies. The genomes of fungi encode genes that enable them to thrive in diverse environments, invade plant and animal cells, and participate in nutrient cycling in terrestrial and aquatic ecosystems. The continuously expanding databases of fungal genome sequences have been generated by individual and large-scale efforts such as Génolevures, Broad Institute’s Fungal Genome Initiative, and the 1000 Fungal Genomes Project (http://1000.fungalgenomes.org). These efforts have produced a catalog of fungal genes and genomic organization. The genomic datasets can be utilized to better understand how fungi have adapted to their lifestyles and ecological niches. Large datasets of fungal genomic and transcriptomic data have enabled the use of novel methodologies and improved the study of fungal evolution from a molecular sequence perspective. Combined with microscopes, petri dishes, and woodland forays, genome sequencing supports bioinformatics and comparative genomics approaches as important tools in the study of the biology and evolution of fungi.

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Image of FIGURE 1

Phylogenetic relationships of the fungal phyla and subphyla. A phylogenetic tree from 434 conserved protein-coding genes resolves the relationships of most of the known lineages of fungi. This tree is a simplified version of that presented by Spatafora et al. ( 43 ). Phyla are presented in bold and subphyla in regular type. The Chytridiomycetes and Monoblepharidomycetes represent lineages for which a subphylum is not yet named.

Source: microbiolspec August 2017 vol. 5 no. 4 doi:10.1128/microbiolspec.FUNK-0055-2016
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Image of FIGURE 2

Scatter plot showing the relationship between genome size and gene count. Genome size varies among subphyla of fungi, with some of the smallest genomes in the Microsporidia and the largest currently sequenced genomes in the Agaricomycotina and Pezizomycotina. Primary data are gathered from genome information available at the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/) and Joint Genome Institute Mycocosm (https://jgi.doe.gov/fungi) and archived in the 1KFG genome_stats github project (https://github.com/1KFG/genome_stats).

Source: microbiolspec August 2017 vol. 5 no. 4 doi:10.1128/microbiolspec.FUNK-0055-2016
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