Little Evidence of Antagonistic Selection in the Evolutionary Strata of Fungal Mating-Type Chromosomes (Microbotryum lychnidis-dioicae)

Abstract

Recombination suppression on sex chromosomes often extends in a stepwise manner, generating evolutionary strata of differentiation between sex chromosomes. Sexual antagonism is a widely accepted explanation for evolutionary strata, postulating that sets of genes beneficial in only one sex are successively linked to the sex-determining locus. The anther-smut fungus Microbotryum lychnidis-dioicae has mating-type chromosomes with evolutionary strata, only some of which link mating-type genes. Male and female roles are non-existent in this fungus, but mating-type antagonistic selection can also generate evolutionary strata, although the life cycle of the fungus suggests it should be restricted to few traits. Here, we tested the hypothesis that mating-type antagonism may have triggered recombination suppression beyond mating-type genes in M. lychnidis-dioicae by searching for footprints of antagonistic selection in evolutionary strata not linking mating-type loci. We found that these evolutionary strata (i) were not enriched in genes upregulated in the haploid phase, where cells are of alternative mating types, (ii) carried no gene differentially expressed between mating types, and (iii) carried no genes displaying footprints of specialization in terms of protein sequences (d_N/d_S) between mating types after recommended filtering. Without filtering, eleven genes showed signs of positive selection in the strata not linking mating-type genes, which constituted an enrichment compared to autosomes, but their functions were not obviously involved in antagonistic selection. Thus, we found no strong evidence that antagonistic selection has contributed to extending recombination suppression beyond mating-type genes. Alternative hypotheses should therefore be explored to improve our understanding of the sex-related chromosome evolution.

Keywords: Genetics of Sex; antagonistic selection; evolutionary strata; expression; fungi; haploid selection; mating-type chromosomes; sex chromosomes; sexual antagonism.

Figure 1

Schematic representation of the evolutionary strata on the mating-type chromosome of Microbotryum lychnidis-dioicae. The per-gene synonymous divergence between alleles (y-axis) represents relative timing of the suppression of recombination steps plotted along the ancestral gene order (x-axis). The PR and HD gene clusters (open black circles) show the most ancient divergences. They control pre- and post-mating compatibility, respectively, and encompass several ancestrally linked mating-type genes. The sequence of suppression of recombination begins around each of the mating-type loci, generating the blue and purple evolutionary strata. Recombination suppression then spread distally to the PR locus, creating the orange stratum. The event that linked the two mating-type loci and their surrounding strata generated the black stratum. The suppression of recombination then spread further outwards distal to the PR locus, creating the red and then the green strata. The pseudo-autosomal regions, which are still recombining, are shown in gray. Only the evolutionary strata shown in black (open or closed black circles) involve linking mating-type genes.

Figure 2

Life cycle of the anther-smut fungus Microbotryum lychnidis-dioicae. Diploid (2N) teliospores are produced in anthers of diseased plants, being heterozygous at all mating-type genes. The teliospores are dispersed to healthy plants by pollinators, wind or splashing. Once on a new plant, teliospores undergo meiosis. In the nectar of flowers, haploid sporidia (N) multiply clonally without mating until the flower wilts, after which flowers fall in male plants. On vegetative tissues where teliospores fall from flowers or by splashing, quick intra-tetrad mating occurs, preventing any haploid phase, producing dikaryotic infectious hyphae (N+N) penetrating the plant. In dikaryotic hyphae, there is exactly one nucleus of each mating type in each cell, preventing competition between mating types for replication and transmission. The flowers produced from infected meristems will produced diseased flowers. Pictures from López-Villavicencio et al. (2007) and Schäfer et al. (2010) © Canadian Science Publishing or its licensors.

Figure 3

Differential expression in Microbotryum lychnidis-dioicae. Proportions of genes upregulated in at least one haploid stage (in red, 1N upregulated), upregulated at the dikaryotic stage (in green, N+N upregulated) or showing no differential expression (in blue). Expression level was considered significantly different at the 0.001 threshold. Different thresholds for significance did not change the patterns notably (Suppl. Figure S1). Genes are separated according to their genomic compartment: autosomes, pseudoautosomal regions (PARs) of the mating-type chromosome, non-recombining region (NRR) of the mating-type chromosome, and into the black vs. color evolutionary strata.

Figure 4

Strength of haploid upregulation in the different genomic compartments in Microbotryum lychnidis-dioicae. Violin plots of the differential expression levels (beta values, calculated in a similar way as the usual log₂ fold-change) of the haploid compared to the dikaryotic phase for the various genomic compartments (autosomes, black stratum, color strata and PARs), with haploids grown in: A ‘rich’ or B ‘water’ media (dikaryotic expression was measured in planta). In panel B, no genes were found upregulated in water in color strata or PARs.

Figure 5

Strength of differential expression between mating-types in Microbotryum lychnidis-dioicae. Violin plot of differential expression (beta values, calculated in a similar way as the usual log₂ fold-change) between the a₁ and a₂ mating types at haploid stages in Microbotryum lychnidis-dioicae, for genes found upregulated in at least one haploid stage compared to the dikaryotic stage and for the other genes (either upregulated in the dikaryon or without differential expression), in the black stratum (A and C) or the color strata (B and D), on rich medium (A and B) or water (C and D).

Figure 6

Per-gene non-synonymous over synonymous (d_N/d_S) differences between a₁-a₂ associated mating types along the mating-type chromosomes in Microbotryum lychnidis-dioicae. Genes are located according to the ancestral-like gene order (i.e., gene order from M. lagerheimii) and evolutionary strata are indicated by their colors. Ancestral location of centromeres (before chromosomal fusion) are indicated in yellow; d_N/d_S values could not be computed for most of the genes in pseudo-autosomal regions (in gray), as most had null d_S values.