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Chapter 28 : Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution

Authors: Robert T. Todd1, Anja Forche2, Anna Selmecki3
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Affiliations: 1: Creighton University, Department of Medical Microbiology and Immunology, Omaha, NE 68178; 2: Bowdoin College, Brunswick, ME 04011-8451; 3: Creighton University, Department of Medical Microbiology and Immunology, Omaha, NE 68178
Content Type: Monograph
Publication Year: 2017

Category: Microbial Genetics and Molecular Biology; Environmental Microbiology

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Abstract:

Cellular ploidy is the number of complete sets of chromosomes in a cell. Many eukaryotic species have two (diploid) or more than two (polyploid) sets of chromosomes ( ). These diploid and polyploid states are often the result of ancient whole-genome duplication (WGD) or hybridization events that occurred throughout the evolution of plants, animals, and fungi ( ). Ploidy changes also occur during the development of many organisms and can vary within different tissues of the same organism and between individuals of the same species. For example, ploidy changes occur during the sexual cycle of eukaryotes, from haploid gametes to diploid somatic cells. Additionally, some cells continue to increase in ploidy during development, resulting in somatic tissues that have a mixture of diploid and polyploid cells, including human hepatocytes and megakaryocytes ( ). These ongoing, developmentally programmed changes in ploidy are important for viability and are beneficial to many organisms ( ), but the mechanisms controlling ploidy and the physiological significance of each ploidy level are not well characterized.

Citation: Todd R, Forche A, Selmecki A. 2017. Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution, p 599-618. 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-0051-2016
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Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution
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Citation: Todd R, Forche A, Selmecki A. 2017. Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution, p 599-618. 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-0051-2016
/content/10.1128/9781555819583.chap28.fig28-1
Figure 1

Methods for detection of ploidy and aneuploidy. Ploidy is determined with flow cytometry. Total genome fluorescence, measured using a fluorescent nucleotide label (e.g., propidium iodide or Sytox Green). Cells are first fixed (in ethanol) and RNA is removed with RNase, then genomic DNA is fluorescently labeled and analyzed on a flow cytometer. Cells are passed through a laser, and the number of cells are plotted as a function of fluorescence intensity. Cells in a population typically have two fluorescent peaks, representing cells in either G1 or G2 phases of the cell cycle. Flow cytometry plots for yeast with the following ploidy levels are shown: haploid (1N), diploid (2N), triploid (3N), tetraploid (4N), and a near-tetraploid aneuploid. Chromosome copy number is determined with WGS and microarray aCGH. The axis represents a log fold change of sequence reads relative to the reference sequence and chromosome number increases from left to right starting with chromosome I and ending with chromosome XVI ( axis). Chromosome copy number plots for with the following ploidy levels indicate euploid genome for haploid (1N), diploid (2N), triploid (3N), and tetraploid (4N). However, the near-tetraploid isolate (bottom panel) is aneuploid for ChrXII (pentasomic) and ChrXIV (trisomic) and contains a segmental aneuploidy of ChrIV. Figures generated from data obtained in reference . Allele frequencies obtained from WGS data also can be used to determine the ploidy of a strain. The axis shows the heterozygous allele frequencies ranging from zero to one, plotted as a function of chromosome number starting with chromosome I and ending with chromosome XVI ( axis). Allele frequency plot of the example haploid strain with single nucleotide polymorphisms (SNPs) at allele frequencies at 1.0; a diploid strain with SNPs at allele frequencies of 0.5 and 1.0; a triploid strain with SNPs at allele frequencies of 0.33 and 0.66; and a tetraploid strain with SNPs at allele frequencies at 0.25, 0.5, 0.75, and 1.0. Images obtained from reference . A diploid strain that is trisomic (three copies of a chromosome) for chromosome XII (left panel). Interestingly, the allele frequency plot has SNPs at allele frequencies of 0.5 and 1.0 for all chromosomes except ChrXII, which is at allele frequencies of 0.33 and 0.66, supporting that this chromosome is aneuploid (right panel).

10.1128/9781555819583/fig28-1_thmb.gif
10.1128/9781555819583/fig28-1.gif
Image of Figure 1
Figure 1

Methods for detection of ploidy and aneuploidy. Ploidy is determined with flow cytometry. Total genome fluorescence, measured using a fluorescent nucleotide label (e.g., propidium iodide or Sytox Green). Cells are first fixed (in ethanol) and RNA is removed with RNase, then genomic DNA is fluorescently labeled and analyzed on a flow cytometer. Cells are passed through a laser, and the number of cells are plotted as a function of fluorescence intensity. Cells in a population typically have two fluorescent peaks, representing cells in either G1 or G2 phases of the cell cycle. Flow cytometry plots for yeast with the following ploidy levels are shown: haploid (1N), diploid (2N), triploid (3N), tetraploid (4N), and a near-tetraploid aneuploid. Chromosome copy number is determined with WGS and microarray aCGH. The axis represents a log fold change of sequence reads relative to the reference sequence and chromosome number increases from left to right starting with chromosome I and ending with chromosome XVI ( axis). Chromosome copy number plots for with the following ploidy levels indicate euploid genome for haploid (1N), diploid (2N), triploid (3N), and tetraploid (4N). However, the near-tetraploid isolate (bottom panel) is aneuploid for ChrXII (pentasomic) and ChrXIV (trisomic) and contains a segmental aneuploidy of ChrIV. Figures generated from data obtained in reference . Allele frequencies obtained from WGS data also can be used to determine the ploidy of a strain. The axis shows the heterozygous allele frequencies ranging from zero to one, plotted as a function of chromosome number starting with chromosome I and ending with chromosome XVI ( axis). Allele frequency plot of the example haploid strain with single nucleotide polymorphisms (SNPs) at allele frequencies at 1.0; a diploid strain with SNPs at allele frequencies of 0.5 and 1.0; a triploid strain with SNPs at allele frequencies of 0.33 and 0.66; and a tetraploid strain with SNPs at allele frequencies at 0.25, 0.5, 0.75, and 1.0. Images obtained from reference . A diploid strain that is trisomic (three copies of a chromosome) for chromosome XII (left panel). Interestingly, the allele frequency plot has SNPs at allele frequencies of 0.5 and 1.0 for all chromosomes except ChrXII, which is at allele frequencies of 0.33 and 0.66, supporting that this chromosome is aneuploid (right panel).

Citation: Todd R, Forche A, Selmecki A. 2017. Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution, p 599-618. 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-0051-2016
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Figure 2

Many polyploid-evolved clones are highly aneuploid. Chromosome copy number was determined by WGS and plotted for the parental diploid (2N) and tetraploid (4N) strains and different tetraploid evolved clones after 250 generations in raffinose medium. Adaptation resulted in clones with increased chromosome copies, approximately trisomic copies of every chromosome (∼3N), or highly aneuploid genomes. Figures generated from data obtained from the supplementary data Table 1 in reference .

10.1128/9781555819583/fig28-2_thmb.gif
10.1128/9781555819583/fig28-2.gif
Image of Figure 2
Figure 2

Many polyploid-evolved clones are highly aneuploid. Chromosome copy number was determined by WGS and plotted for the parental diploid (2N) and tetraploid (4N) strains and different tetraploid evolved clones after 250 generations in raffinose medium. Adaptation resulted in clones with increased chromosome copies, approximately trisomic copies of every chromosome (∼3N), or highly aneuploid genomes. Figures generated from data obtained from the supplementary data Table 1 in reference .

Citation: Todd R, Forche A, Selmecki A. 2017. Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution, p 599-618. 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-0051-2016
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Tables

Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution
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Citation: Todd R, Forche A, Selmecki A. 2017. Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution, p 599-618. 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-0051-2016
/content/10.1128/9781555819583.chap28.tab28-1
Table 1

Summary of experimental evolution studies in fungi and the ploidy and aneuploidy associated with different environmental stresses. Ploidy levels of haploid (1N), diploid (2N), triploid (3N), and tetraploid (4N) are euploid states, while aneuploidy is indicated if known.

Generic image for table
Table 1

Summary of experimental evolution studies in fungi and the ploidy and aneuploidy associated with different environmental stresses. Ploidy levels of haploid (1N), diploid (2N), triploid (3N), and tetraploid (4N) are euploid states, while aneuploidy is indicated if known.

Citation: Todd R, Forche A, Selmecki A. 2017. Ploidy Variation in Fungi: Polyploidy, Aneuploidy, and Genome Evolution, p 599-618. 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-0051-2016

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