The genome sequence of the model ascomycete fungus Podospora anserina

Abstract

Background: The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development.

Results: We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown.

Conclusion: The features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.

Figure 1

The major stages of the life cycle of P. anserina as illustrated by light microphotography, with a corresponding schematic representation shown above. (a) The cycle starts with the germination of an ascospore, after the transit in the digestive tract of an herbivore in the wild. (b) Then, a mycelium, which usually carries two different and sexually compatible nuclei (pseudo-homothallism), called mat+ and mat-, develops and invades the substratum. (c) On this mycelium, male (top; microconidia) and female (bottom; ascogonium) gametes of both mating types differentiate after three days. In the absence of fertilization, ascogonium can develop into protoperithecium by recruiting hyphae proliferating from nearby cells. (d) This structure, in which an envelope protects the ascogonial cell, awaits fertilization. (e,f) This occurs only between mat+ and mat- sexually compatible gametes (heterothallism) and triggers the development completed in four days of a complex fructification (e) or perithecium, in which the dikaryotic mat+/mat- fertilized ascogonium gives rise to dikaryotic ascogenous hyphae (f). (g) These eventually undergo meiosis and differentiate into ascii, mostly with four binucleate mat+/mat- ascospores (pseudo-homothallism), but sometime with three large binucleate ascospores and two smaller uninucleate ones (bottom asci is five-spored). Unlike those issued from large binucleate ascospores, mycelia issued from these smaller ascospores are self-sterile because their nuclei carry only one mating type. (h) When ripe, ascospores are expelled from perithecia and land on nearby vegetation awaiting ingestion by an herbivore. Scale bar: 10 μm in (a-d,f,h); 200 μm in (e,g).

Figure 2

Orthologue conservation in some Pezizomycotina. (a) Venn diagram of orthologous gene conservation in four ascomycete fungi. The diagram was constructed with orthologous genes identified by the best reciprocal hit method with a cut-off e-value lower than 10^-3 and a BLAST alignment length greater than 60% of the query CDS. (b) Phylogenetic tree of the four fungal species. The average percentage of identity ± standard deviation between orthologous proteins of P. anserina and the three other fungi are indicated on the right.

Figure 3

Genome-wide comparison of orthogolous genes of N. crassa (x-axis) and P. anserina (y-axis). Each dot corresponds to a couple of orthologous genes. The lines delimit the chromosomes. The scale is based on the number of orthologous genes per chromosome.

Figure 4

Size distribution of synteny block between P. anserina and N. crassa. Block size is given on the x-axis and frequency on the y-axis. Black bars indicate the actual value, and the red line shows the theoretical curve expected in the case of the random break model. The two distribution functions are not statistically different (Kolmogorov-Smirnov test, p >> 5%).

Figure 5

Repartition of transposons (top in red) and segmental duplications (bottom in blue) in the P. anserina genome. Chromosome numbering and orientation is that of the genetic map [85]. The double arrows indicate the putative centromere positions. Two regions have been expanded to show the interspacing of segmental duplications (in blue) with transposons (other colors); numbering refers to the nucleotide position with respect to the beginning of the scaffolds.

Figure 6

Gene gain and loss in fungal genomes. (a-c) Unrooted phylogenetic trees of putative alkaline phosphatase D precusors (a), putative HC-toxin efflux carrier proteins related to ToXA from Cochliobolus carbonum (b), and putative chitinases related to the killer toxin of Kluyveromyces lactis (c). The putative CDSs were aligned with ProbCons 1.10 [101] and manually edited to eliminate poorly conserved regions, resulting in alignment over 565, 544, 505 amino acids, respectively. Phylogenetic trees were constructed with Phyml 2.4.4 [102] under the WAG model of amino acid substitution. The proportion of variable sites and the gamma distribution parameters of four categories of substitution rate were estimated by phyml. For each tree, we performed 100 boostrap replicates. The recently duplicated P. anserina paralogues are highlighted in red and the divergent duplication of chitinases in green. Trees with similar topologies and statistical support (1,000 boostrap replicates) were recovered with the neighbor joining method. Especially, recent duplication of Pa_4_1520/Pa_6_8120, Pa_2_7900/Pa_6_8600 and Pa_4_5560/Pa_5_1570 as well as the distinction of the two subfamilies of chitinases were recovered with 100% confidence. AN, A. nidulans; MGG, M. grisea; NC, N. crassa; Pa, P. anserina.

Figure 7

Carbohydrate utilization in P. anserina. Cultures were incubated for one week with 1% of the indicated compounds as carbon source.