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Chapter 29 : Fungal Genomes and Insights into the Evolution of the Kingdom

Author: Jason E. Stajich1
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Affiliations: 1: Department of Plant Pathology and Microbiology and Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
Content Type: Monograph
Publication Year: 2017

Category: Microbial Genetics and Molecular Biology; Environmental Microbiology

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Abstract:

Studies of fungal evolution require an understanding of the phylogenetic relationships and relative evolutionary divergence of organisms. The first approaches to organizing fungi into related groups relied on morphological characteristics ( ). These approaches provided a broad framework to organize fungal organisms for taxonomic classification based on recognizable morphological characteristics such as spore shape, asexual and sexual structures, and in mushroom-forming fungi, the shape and presence/absence of gills, veil attachments, and spore color. In zoosporic chytrid fungi the characteristics seen by scanning electron microscopy of zoospores reveal that the ultrastructure of the kinetosomes and flagellum are all diagnostic for the classification of many lineages ( ). However, the microscopic nature of many fungi and especially of yeast-forming fungi with limited visible differences, and the prevalence of convergent evolution to homoplasies or similar characteristics across a tree, has made taxonomic classification of groups of fungi difficult or easily misled. The invention and application of DNA sequencing ( ) and PCR ( ) and the development of primers to amplify fungal rRNA enabled a new era of molecular phylogenetic studies in fungi ( ). These approaches provided invaluable information that was used to resolve the major fungal lineages ( ) and the delineation of species ( ). Using DNA approaches to study the entire fungal tree of life provided new insight into the order of branching of major groups and the timing of morphological changes such as the loss of the flagellum found in zoosporic fungi ( ).

Citation: Stajich J. 2017. Fungal Genomes and Insights into the Evolution of the Kingdom, p 619-633. 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-0055-2016
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Fungal Genomes and Insights into the Evolution of the Kingdom
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Citation: Stajich J. 2017. Fungal Genomes and Insights into the Evolution of the Kingdom, p 619-633. 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-0055-2016
/content/10.1128/9781555819583.chap29.fig29-1
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. ( ). Phyla are presented in bold and subphyla in regular type. The Chytridiomycetes and Monoblepharidomycetes represent lineages for which a subphylum is not yet named.

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10.1128/9781555819583/fig29-1.gif
Image of Figure 1
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. ( ). Phyla are presented in bold and subphyla in regular type. The Chytridiomycetes and Monoblepharidomycetes represent lineages for which a subphylum is not yet named.

Citation: Stajich J. 2017. Fungal Genomes and Insights into the Evolution of the Kingdom, p 619-633. 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-0055-2016
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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).

10.1128/9781555819583/fig29-2_thmb.gif
10.1128/9781555819583/fig29-2.gif
Image of Figure 2
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).

Citation: Stajich J. 2017. Fungal Genomes and Insights into the Evolution of the Kingdom, p 619-633. 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-0055-2016
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