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Open Access Highly Accessed Research article

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

Marco A Coelho, Paula Gonçalves and José P Sampaio*

Author Affiliations

Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal

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BMC Evolutionary Biology 2011, 11:249  doi:10.1186/1471-2148-11-249

Published: 31 August 2011

Additional files

Additional file 1:

List of species/strains used in this study and relevant information pertaining to them. GenBank accessions numbers are given for each genomic region analysed in this study. Sequences retrieved from the CBS culture collection database ('CBS seq.') or from genome projects ('JGI genome') are indicated. Mating behaviour as originally determined by classical mating tests ('old') and as reassigned in this study based on the molecular data ('new') is indicated when needed: A1, A2, As and Sf stand for mating type A1, A2, asexual and self-fertile strains, respectively. The "molecular mating type" as identified by PCR detection of the pheromone receptor alleles STE3.A1 and STE3.A2 is depicted by yellow and blue circles, respectively. White circles indicate strains for which PCR detection gave negative results and 'n.d.' stands for 'not determined'. Strains highlighted in boldface were used in Figure 1 and those indicated by thick-lined blue or yellow circles were used in Figure 3. Sequences accession number of the HD1/HD2 alleles used in Figures 4b and 4c are also highlighted in boldface. Abbreviations: Rhodosporidium (R.), Rhodotorula (Rh.), Sporidiobolus (S.), Sporobolomyces (Sp.), Type strain (T), Lectotype (LT), Authentic strain (AUT). Species not yet formally described are shadowed in light yellow and those for which no molecular mating type was determined are shadowed in gray.

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Additional file 2:

Synteny of the genomic regions flanking the alternate PR in MAT A1 and MAT A2 strains of several red yeasts species. (a) Simplified illustration of the tree represented in Figure 1, indicating the phylogenetic placement of the species where gene organization in the vicinity of the pheromone receptor genes was determined. Clades A, B and C are the same as in Figure 1 and 2. (b) The mating behaviour (A1, A2, As and Sf stands for mating type A1, A2, asexual and self-fertile, respectively), the molecular mating type (STE3.A1, yellow circles; STE3.A2, dark blue circles; STE3.A1 and STE3.A2, half-coloured circles) and the obtained genomic regions flanking the pheromone receptor alleles (STE3.A1 and STE3.A2) are shown for each strain. Orthologues are shown in the same colour. In Rhodosporidium lusitaniae, the intervening region between the STE3.A2 and the RibL6 genes (faint line) was not sequenced. Abbreviations of generic names are as in Figure 1 and the remaining features are represented as in Figure 3.

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Additional file 3:

Pheromone precursors of different red yeast species. (a) The organization of the genomic region encompassing the MAT A1 pheromone precursor genes in Sporobolomyces sp. IAM 13481 is shown on top. Coding regions of the pheromone precursor genes (RHA1, RHA2 and RHA3) are depicted by gray arrows, indicating the direction of transcription. (b) Alignment of the Rha2 pheromone precursor of different MAT A1 red yeast species/strains (Ss, Sporidiobolus salmonicolor; Sj, Sporidiobolus johnsonii; Sp, Sporobolomyces sp. IAM 13481; Rt, Rhodosporidium toruloides). Amino acids differing from the S. salmonicolor strain CBS 483 are shown in red. Sequence repeats proposed to represent the peptide moiety of the mature pheromone are shadowed and those resembling the CAAX motif are underlined. (c) Phylogenetic tree showing the relationships between RHA2 genes from the indicated red yeast species, based on the alignment of their coding sequences. Groups are the same as in (b). Sequences of strains depicted in boldface are shown in (b). The tree was inferred using Maximum Parsimony. Bootstrap values from 1000 replicates are shown in the tree nodes.

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Additional file 4:

Supplementary Table S1. Likelihood ratio statistics and parameter estimates for the dataset of clade A (S. salmonicolor and S. johnsonii) as inferred under seven models of ω over codons. Supplementary Table S2. Likelihood ratio statistics and parameter estimates for the dataset of clade B (R. babjevae, Rh. glutinis and Rh. graminis) as inferred under seven models of ω over codons. Supplementary Methods. Model characteristics and parameters for CODEML ctl file.

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Additional file 5:

List of primers and specific PCR conditions used to amplify the indicated regions.

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Additional file 6:

Supplementary Files 1. Files used to construct the phylogenetic tree represented in Figure 1 (alignment file: "Fig1Align.fas"; Tree files: "Fig1TreeNewick.nwk ", "Fig1TreeNexus.nex", and "Fig1TreeRootNexus.nex"). Supplementary Files 2. Files used to construct the phylogenetic trees represented in Figure 2 (alignment file for Ste3a1: "Fig2A1Align.fas"; Tree files: "Fig2A1TreeNewick.nwk", "Fig2A1TreeNexus.nex", "Fig2A1TreeRootNexus.nex"; alignment file for Ste3a2: "Fig2A2Align.fas"; Tree files: "Fig2A2TreeNewick.nwk", "Fig2A2TreeNexus.nex", "Fig2A2TreeRootNexus.nex"). Supplementary Files 3. Files used to construct the phylogenetic tree represented in Figure 4 (alignment file: "Fig4Align.fas"; Tree files: "Fig4TreeNewick.nwk", "Fig4TreeRootNexus.nex"). Nexus files can be viewed by Mesquite software http://mesquiteproject.org/mesquite/download/download.html webcite).

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