Evidence for maintenance of sex determinants but not of sexual stages in red yeasts, a group of early diverged basidiomycetes

Abstract

Background: The red yeasts are an early diverged group of basidiomycetes comprising sexual and asexual species. Sexuality is based on two compatible mating types and sexual identity is determined by MAT loci that encode homeodomain transcription factors, peptide pheromones and their receptors. The objective of the present study was to investigate the presence and integrity of MAT genes throughout the phylogenetic diversity of red yeasts belonging to the order Sporidiobolales.

Results: We surveyed 18 sexual heterothallic and self-fertile species and 16 asexual species. Functional pheromone receptor homologues (STE3.A1 and STE3.A2) were found in multiple isolates of most of the sexual and asexual species. For each of the two mating types, sequence comparisons with whole-genome data indicated that synteny tended to be conserved along the pheromone receptor region. For the homeodomain transcription factor, likelihood methods suggested that diversifying selection acting on the self/non-self recognition region promotes diversity in sexual species, while rapid evolution seems to be due to relaxed selection in asexual strains.

Conclusions: The majority of both sexual and asexual species of red yeasts have functional pheromone receptors and homeodomain homologues. This and the frequent existence of asexual strains within sexual species, makes the separation between sexual and asexual species imprecise. Events of loss of sexuality seem to be recent and frequent, but not uniformly distributed within the Sporidiobolales. Loss of sex could promote speciation by fostering the emergence of asexual lineages from an ancestral sexual stock, but does not seem to contribute to the generation of exclusively asexual lineages that persist for a long time.

Figure 1

Phylogeny of the Sporidiobolales. Molecular phylogeny based on a concatenated alignment of the ITS region (ITS1, 5.8S and ITS2) and the D1/D2 domain of the LSU rRNA. Mating types (MAT A1 and MAT A2), asexual and self-fertile strains are designated as A1, A2, As and Sf, respectively. Circles before each strain depict the type of PR gene: yellow, STE3.A1; blue, STE3.A2; white, not detected; half-coloured circles, simultaneous detection of STE3.A1 and STE3.A2. For each species, the type strain is highlighted in boldface. A, B and C are three statistically well-supported clades (see text for details). Abbreviations of generic names: Rhodosporidium (R.), Rhodotorula (Rh.), Sporidiobolus (S.) and Sporobolomyces (Sp.). Asterisks indicate instances where the original mating type designation was altered to match the molecular identity of the strains (see Additional File 1). Species not yet formally described are indicated by inverted commas. The tree was rooted with sequences of Microbotryum lychnidis-dioicae and Leucosporidium scottii (see methods). Branch lengths are given in number of substitutions per site. Bootstrap values (>50%) from 1000 replicates are shown.

Figure 2

Phylogeny of the pheromone receptors. Phylogeny based on the amino acid sequence of the MAT A1 and MAT A2 PR (Ste3.A1 and Ste3.A2, respectively) of several red yeast species. Groups A, B and C are the same as in Figure 1. Strains marked with asterisks have both PR. MAT A1 and MAT A2 PR sequences from Microbotryum lychnidis-dioicae were used as outgroups. Bootstrap values (>50%) from 1000 replicates are shown. See Figure 1 for additional details.

Figure 3

Synteny between MAT A1 and MAT A2 PR loci in different species. The structure of the MAT A1 and MAT A2 PR loci (~50 kb) is shown for Sporobolomyces sp. IAM 13481 and Rhodotorula graminis WP1 and compared with shorter homologous regions of S. salmonicolor and R. toruloides. MAT A1 and MAT A2-specific genes are depicted in yellow and dark blue arrows, respectively, showing the direction of transcription. Genes enclosed in box A are flanking the STE3.A1 gene in most members of Sporidiobolales and those in box B are usually flanking the STE3.A2 gene. Orthologous genes in boxes A and B have the same colour. Genes shared by Sporobolomyces sp. and Rh. graminis are shown in gray, while others are shown in white. Yellow lines or bars connect, respectively, genes or syntenic blocks that are in the same orientation, while pink lines or bars indicate inversions. Asterisks in the MAT region of Rh. graminis indicate three identical repeats of ~280 bp (the repeat located downstream of the RNAPOL gene is inverted in relation to the other two).

Figure 4

Diversity of HD1/HD2 alleles and evolution of HD1 in two different clades of red yeast species. (a) Phylogeny of the HD1/HD2 alleles in two groups of red yeasts. Abbreviations of generic names are as in Figure 1. Strains belonging to the same species are indicated by boxes of the same colour after strain numbers: Clade A - S. salmonicolor (green) and S. johnsonii (light green); clade B - Rh. glutinis (red), R. babjevae (pink) and Rh. graminis (light pink). R. diobovatum formed a more divergent group external to clade B. Sexual (MAT A1/A2), asexual and self-fertile strains are indicated as "A1/A2", "As" and "Sf", respectively, after strain numbers. Circles before each strain depict the type of pheromone receptor genes (yellow, STE3.A1; blue, STE3.A2). White stars in tree branches symbolize premature stop codons detected in the corresponding HD2 alleles. Branch lengths are given in number of substitutions per site. Bootstrap values (>50%) from 1000 replicates are shown. (b) Posterior probabilities of site classes for codons along the N-terminal and HD domains of the HD1 gene, obtained under model M8 (beta&ω) for the clade B dataset. The first six categories are collapsed into one, represented as ω < 0.26 (purifying selection) as well as the categories seven to ten that are represented as 0.26 < ω < 0.92. (c) Posterior probabilities obtained for the dataset of clade A under the model M8. The first 5 categories are collapsed into one (ω <0.26) as well as the categories six to ten (0.26 < ω < 0.93). Sites for which the posterior probability for the site class of positive selection (with ω > 1) exceeds 0.80 are inferred to be under diversifying selection and are indicated by asterisks (see Supplementary Tables S1 and S2 in Additional File 4 for details).