Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota

Abstract

Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.

Fig. 1. Maximum likelihood (ML) phylogeny of 1107 taxa in the fungal phylum Ascomycota.

The concatenation-based ML phylogeny (lnL = −269,043,834.145) was inferred from a set of 815 BUSCO amino acid genes (total of 562,376 sites) under a single LG + G4 substitution model using IQ-TREE multicore version 1.5.1. The number of species sampled in each subphylum is given in parentheses. Internal branch labels are acronyms for 12 major clades in the subphylum Saccharomycotina and nine classes in the subphylum Pezizomycotina. S. cerevisiae, Saccharomyces cerevisiae; H. vineae, Hanseniaspora vineae; D. hansenii, Debaryomyces hansenii; O. sinensis, Ophiocordyceps sinensis; P. hyperparasitica, Pseudovirgaria hyperparasitica; A. nidulans, Aspergillus nidulans. Images representing taxa were drawn by hand, taken from PhyloPic (http://phylopic.org), or modified from Google Images. The bar next to each species indicates the guanine-cytosine (GC) content. On average, lineages in the subphylum Saccharomycotina have significantly lower GC content (49.6% versus 40.6%; Wilcoxon rank-sum test; P = 3.07 × 10⁻¹⁰³) but higher evolutionary rate (1.80 substitutions per site versus 1.12 substitutions per site; Wilcoxon rank-sum test; P = 6.57 × 10⁻¹²⁶) compared with lineages in the subphylum Pezizomycotina. The complete phylogenetic relationships of 1107 taxa are given in fig. S2 and in the Figshare repository. For easy determination of the relationships among any subset of taxa, the phylogeny is also available through Treehouse (63).

Fig. 2. Distribution of phylogenetic signal for three historically contentious relationships within Ascomycota.

For each relationship/internal branch [(A) Which class(es) is the sister group to the rest of the Pezizomycotina? (B) What is the relationship among three classes Schizosaccharomycetes, Pneumocystidomycetes, and Taphrinomycetes in the subphylum Taphrinomycotina? (C) What is the relationship among three subphyla Pezizomycotina, Saccharomycotina, and Taphrinomycotina in the phylum Ascomycota?], we applied the framework presented by Shen et al. (35) to examine proportions of genes (left) and sites (right) supporting each of three competing hypotheses (topology 1 or T1 in red, topology 2 or T2 in green, and topology 3 or T3 in yellow). Note that both concatenation- and coalescent-based approaches supported T1 in our study. Dashed horizontal lines on one-third y axis value denote expectation of proportion of genes/sites under a polytomy scenario. The G-test was used to test whether the sets of three values are significantly different (***P ≤ 0.001). All values are given in tables S4 and S5. Input and output files associated with phylogenetic signal estimation are also deposited in the Figshare repository.

Fig. 3. Contrasting patterns for seven genomic properties between Pezizomycotina and Saccharomycotina.

As the subphylum Taphrinomycotina (no. of species = 14) has a much smaller number of species than the subphylum Saccharomycotina (no. of species = 332) and the subphylum Pezizomycotina (no. of species = 761) in our dataset, we focused our analyses on the comparisons of seven genome properties between Saccharomycotina and Pezizomycotina. (A) For each species in Pezizomycotina (colored in red, n = 761) and Saccharomycotina (colored in green, n = 332), we calculated evolutionary rate, GC content, genome size, number of protein-coding genes, number of DNA repair genes, number of tRNA genes, and d_N/d_S (see Materials and Methods for details). The Wilcoxon rank-sum test was used to test whether the sets of values in two subphyla are significantly different. (B) Pairwise standard Pearson’s correlation coefficient among pairs of the seven genomic properties was conducted using R 3.4.2 for Pezizomycotina (lower diagonal) and Saccharomycotina (upper diagonal), respectively. For each cell, the top value corresponds to the P value (NS, P > 0.05; *P ≤ 0.05; **P ≤ 0.01; ***P ≤ 0.001), whereas the bottom value corresponds to Pearson’s coefficient value. Orange cells denote instances where correlation trends in Pezizomycotina and Saccharomycotina are in opposite directions, whereas blue cells denote instances where the trends are in the same direction. The detailed values of all seven properties in Pezizomycotina and Saccharomycotina are given in table S7. The correlations among these seven properties are largely consistent before (i.e., standard Pearson’s correlations) and after (i.e., phylogenetically independent contrasts) accounting for correlations due to phylogeny (see table S8).

Fig. 4. Contrasting modes of genome evolution in Pezizomycotina and Saccharomycotina.

(A) For each of the seven genomic properties examined (see Materials and Methods for details), we reconstructed them as continuous traits on the species phylogeny (Fig. 1) and visualized their ancestral states with the R package phytools v0.6.44 (62). Heatmap bars denote ancestral state values from small (blue) to large (red). Three ancestral state values next to three red dots are shown for the ancestor of the subphyla Pezizomycotina and Saccharomycotina, the ancestor of the subphylum Pezizomycotina, and the ancestor of the subphylum Saccharomycotina, respectively. Sub., substitution. (B) Phylogeny key showing the placement of the 21 nodes representing the last common ancestors of the 12 major clades in the subphylum Saccharomycotina and of the nine classes in the subphylum Pezizomycotina; the 21 nodes are indicated by the red dots. The orders of branches in (A) are identical to those in (B).