Basidioascus undulatus: genome, origins, and sexuality

Abstract

Basidioascus undulatus is a soil basidiomycete belonging to the order Geminibasidiales. The taxonomic status of the order was unclear as originally it was only tentatively classified in the class Wallemiomycetes. The fungi in Geminibasidiales have an ambiguously defined sexual cycle. In this study, we sequenced the genome of B. undulatus to gain insights into its sexuality and evolutionary origins. The assembled genome draft was approximately 32 Mb in size, had a median nucleotide coverage of 24X, and contained 6123 predicted genes. Previous morphological descriptions of B. undulatus relied on interpretation of putative sexual structures. In this study, nuclear staining and confocal microscopy showed meiosis occurring in basidia and genome analysis confirmed the existence of genes involved in meiosis and mating. Using 35 protein-coding genes extracted from genomic information, phylogenomic and molecular dating analyses confirmed that B. undulatus indeed belongs to a lineage distantly related to Wallemia while retaining a basal position in Agaricomycotina. These results, combined with differences in septal pore morphology, led us to move the order Geminibasidiales out of the Wallemiomycetes and into the new class Geminibasidiomycetes cl. nov. Finally, the concept of Agaricomycotina is emended to include both Wallemiomycetes and Geminibasidiomycetes.

Keywords: Agaricomycotina; Basidiomycota; Geminibasidiomycetes; Wallemiomycetes; septal pore ultastructure.

Fig. 1.

Basidioascus undulatus (DAOM 241956) sexual and asexual structures stained with DAPI (A–J) and SYTO 9 (K–L) and imaged with confocal microscopy. A. Dikaryotic basidium (2 nuclei). B. Karyogamy. C. Anaphase I. D. Telophase I and collapsed basal lateral projection. E. Telophase II (4 nuclei). F. Ejected basidium (4 nuclei). G–H. Maturation of a basidiospore on a basidium and the migration of a nucleus through the sterigma and into the basidiospore. I. Collapsing basidium with the three remaining nuclei. J. A totally collapsed basidium and probably one nucleus inside the mature basidiospore. K–L. Single nuclei inside arthroconidia. Bar = 5 μm.

Fig. 2.

Transmission electron micrographs showing septal pore morphology. A–B. Basidioascus undulatus (DAOM 241956 ex-type). C–D. Geminibasidium donsium (DAOM 241966 ex-type). E–F. Wallemia sebi (CBS 633.66). Bar = 20 μm.

Fig. 3.

Phylogenetic trees resulting from phylogenomic analysis and molecular dating. A. Consensus topology and branch lengths from analyses of concatenated amino acid sequences from 35 single copy genes with a total of 10129 data columns. Gapped and poorly aligned sites were removed. Analyses were performed with the CAT-GTR model. Posterior probabilities are shown at the nodes of the tree. Scale bar indicates expected changes per site. B. Chronogram resulting from a lognormal relaxed molecular clock analysis with the birth-death prior. The mean divergence time with standard error are shown at each node. Circled nodes were pre-calibrated before the analysis. The paleontological periods, in million years ago (Mya), are shown as a scale at the bottom. Rhizophagus irregularis (Glomeromycota) was used as the outgroup.

Fig. 3.

Phylogenetic trees resulting from phylogenomic analysis and molecular dating. A. Consensus topology and branch lengths from analyses of concatenated amino acid sequences from 35 single copy genes with a total of 10129 data columns. Gapped and poorly aligned sites were removed. Analyses were performed with the CAT-GTR model. Posterior probabilities are shown at the nodes of the tree. Scale bar indicates expected changes per site. B. Chronogram resulting from a lognormal relaxed molecular clock analysis with the birth-death prior. The mean divergence time with standard error are shown at each node. Circled nodes were pre-calibrated before the analysis. The paleontological periods, in million years ago (Mya), are shown as a scale at the bottom. Rhizophagus irregularis (Glomeromycota) was used as the outgroup.