Chapter 1 : The Evolution of : The Ascomycetes

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This chapter provides a summary of the structure and evolution of mating-type locus () in a range of species representing the major subphyla and sister groups. Whereas the gene content and gene order at the locus vary considerably across the ascomycetous yeasts, the position of is surprisingly well conserved. Analysis of mating in provided a paradigm for one's understanding of sexual pathways in ascomycetes, and indeed in many other fungi. The analysis of homothallic and heterothallic isolates led to the description of the mating loci, the discovery of the cassette-based system, and the identification and characterization of mating-type switching. Switching occurs through unidirectional transposition, triggered by the action of the Ho endonuclease. is a filamentous yeast that has historically been used to generate large quantities of riboflavin. The Ho endonuclease is most closely related to the VDE intein. It also encodes protein-splicing and endonuclease domains, but it contains an additional zinc finger domain at the C terminus required for mating type switching. Mating appeared to be an extremely inefficient process, until an association was made with phenotypic switching. The structure of the MAT loci in heterothallic and species is somewhat simpler, as each idiomorph contains only one gene, either (alpha-box protein) or MAT-2 (HMG domain). The ongoing genome-sequencing projects will provide an invaluable resource for further investigation, particularly to address the origin of these additional genes and the evolution of mating within the clade.

Citation: Butler G. 2007. The Evolution of : The Ascomycetes, p 3-18. In Heitman J, Kronstad J, Taylor J, Casselton L (ed), Sex in Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555815837.ch1
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Figure 1.1

Phylogenetic relationships among the Ascomycota. A phylogenomic supertree was constructed using 4,805 gene families from fully sequenced genomes from 42 fungal species. The details will be published elsewhere (D. A. Fitzpatrick, unpublished data). was used as an outgroup. The divergence between the Basidiomycota and Ascomycota is shown, and the subphyla and classes discussed in the text are indicated. WGD; clade that has undergone a whole-genome duplication; CTG; clade in which CTG is translated as serine.

Citation: Butler G. 2007. The Evolution of : The Ascomycetes, p 3-18. In Heitman J, Kronstad J, Taylor J, Casselton L (ed), Sex in Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555815837.ch1
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Image of Figure 1.2
Figure 1.2

Organization of the loci and silent cassettes in the lineage. The figure is redrawn from reference . The two possible idiomorphs at the locus are shown between horizontal lines for all species except , where only was identified. The “Y” boxes encode a or alpha information and are specific to the idiomorphs. W, X, Y, and Z are shared sequence elements. It is not possible to determine the sizes of these regions in . Telomeres are indicated with arrowheads. The curly lines indicate when the cassettes are found on the same chromosome.

Citation: Butler G. 2007. The Evolution of : The Ascomycetes, p 3-18. In Heitman J, Kronstad J, Taylor J, Casselton L (ed), Sex in Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555815837.ch1
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Figure 1.3

Evolution of MAT and HO in the Saccharomycotina. The phylogenetic tree is schematic and is based on reference and Fig. 1.1 . The figure is redrawn from reference , with additional information for from reference and for and from references and . The genome does contain a sequence with similarity to , but it is unlikely to be an ortholog. Blanks indicate missing data.

Citation: Butler G. 2007. The Evolution of : The Ascomycetes, p 3-18. In Heitman J, Kronstad J, Taylor J, Casselton L (ed), Sex in Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555815837.ch1
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Image of Figure 1.4
Figure 1.4

Organization of the loci in the clade. The order of the genes surrounding the α and idiomorphs in is shown in the top two lines. The gene names are taken from the Candida Genome Database (http://www.candidagenome.org), or gene number designations are from Assembly 19. The structures of α idiomorphs from and are similar to the α idiomorph and are not shown. The gene order for is taken from reference , and for the other species it is extrapolated from ongoing genome-sequencing projects at the Wellcome Trust Sanger Centre (http://www.sanger.ac.uk/Projects/Fungi/) and the Broad Institute (http://www.broad.mit.edu/annotation/fgi/). α-specific genes are unfilled boxes and -specific genes are black. Orthologous genes are connected by gray lines; not all relationships are shown. Inversions in gene order are indicated by arrows. Wavy lines indicate regions of the chromosome where genes have been omitted. The “X” structures indicate the location of the pseudogene in and the expected location of in and of α2 in . The bottom line shows the gene order surrounding the , and region on chromosome E of , which is separate from the locus. There is no gap between the and orthologs. Abbreviations: Ca, ; Cp, ; Cd, ; Cgu, ; Cl, ; Dh, .

Citation: Butler G. 2007. The Evolution of : The Ascomycetes, p 3-18. In Heitman J, Kronstad J, Taylor J, Casselton L (ed), Sex in Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555815837.ch1
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Figure 1.5

Organization and evolution of the loci in the Pezizomycotina. Alpha-box genes are shown in black, and HMG-domain genes are either gray with a black border (equivalent to in the Saccharomycotina) or solid light gray ( orthologs). Orthologs of from the Sordariomycetes are shown as solid dark gray. (a) The gene names recommended in reference are used for the Sordariomycetes with the equivalent names from shown underneath. There is an ortholog of beside both idiomorphs in , and this is indicated by its being drawn at both loci. (b) The structure and proposed evolution in species are taken from reference . The fused genes in the homothallic species and most likely arose from crossing over between the alpha-box and HMG-domain genes in a heterothallic ancestor. Recombination between adjacent genes may have given rise to the locus in . The origin of the unlinked loci in is not known. (c) Galagan et al. ( ) suggest that both homothallic and putative heterothallic isolates of arose from a homothallic ancestor. In and the alpha-box and HMG-domain genes are offset from each other, suggesting that they arose through gene loss. In , like , the two genes are found in the same genome but are unlinked; *some species have not been shown to reproduce sexually, but the organization of the locus suggests that they are heterothallic or have only recently lost the ability to mate.

Citation: Butler G. 2007. The Evolution of : The Ascomycetes, p 3-18. In Heitman J, Kronstad J, Taylor J, Casselton L (ed), Sex in Fungi. ASM Press, Washington, DC. doi: 10.1128/9781555815837.ch1
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