High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex

Abstract

The filamentous fungus Podospora anserina is a model organism used extensively in the study of molecular biology, senescence, prion biology, meiotic drive, mating-type chromosome evolution, and plant biomass degradation. It has recently been established that P. anserina is a member of a complex of 7 closely related species. In addition to P. anserina, high-quality genomic resources are available for 2 of these taxa. Here, we provide chromosome-level annotated assemblies of the 4 remaining species of the complex, as well as a comprehensive data set of annotated assemblies from a total of 28 Podospora genomes. We find that all 7 species have genomes of around 35 Mb arranged in 7 chromosomes that are mostly collinear and less than 2% divergent from each other at genic regions. We further attempt to resolve their phylogenetic relationships, finding significant levels of phylogenetic conflict as expected from a rapid and recent diversification.

Keywords: Podospora bellae-mahoneyi; Podospora pseudoanserina; Podospora pseudocomata; Podospora pseudopauciseta; Sordariales; chromosomal rearrangements; phylogenomics.

Fig. 1.

Circos plots comparing the reference assembly of P. anserina (strain S+, right side of each plot) to the best genome assembly of each of the other members of the species complex (left side). Light colors correspond to NUCmer alignments (larger than 5 kb) of the different chromosomes as defined in P. anserina (chr. 1: red; chr. 2: turquoise; chr. 3: yellow; chr. 4: blue; chr. 5: orange; chr. 6: olive green; chr 7: gray). Red solid links mark chromosome inversions or inverted translocations. The internal track in black is a histogram of repetitive element abundance calculated in sliding windows of 50 kb with steps of 10 kb. The stars and triangles mark shared structural variants (relative to P. anserina). The location of the insertion in chr. 5 discussed in the text is marked with a red square.

Fig. 2.

Phylogenetic relationships of the Podospora strains with genomic resources and their geographic distribution. a) Summary cladogram based on the phylogenomic analyses and the detected structural variants, with dotted branches illustrating an alternative topology. Fruiting body cartoons mark the country where the different strains were sampled. Phylogenetic relationships were inferred from a supermatrix ML analysis b) or a MSC analysis c) of nuclear genes, as well as a ML analysis of concatenated mitochondrial genes d). Rooting is tentative based on analyses with C. samala as an outgroup. Branch lengths of the phylograms are drawn to scale as indicated by the scale bar (nucleotide substitutions per site in b) and d) and coalescent units in c)). Different support metrics are shown next to their corresponding branches (within-species values are removed for clarity). The EQP-IC value of the conflicting branch is highlighted in bold. MSC, multispecies coalescent; UFBoot, ultrafast bootstrap; EQP-IC, extended quadripartition internode certainty; LPP, local posterior probability; NB, nonparametric bootstrap.