The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi

Abstract

Changes in gene expression have been hypothesized to play an important role in the evolution of divergent morphologies. To test this hypothesis in a model system, we examined differences in fruiting body morphology of five filamentous fungi in the Sordariomycetes, culturing them in a common garden environment and profiling genome-wide gene expression at five developmental stages. We reconstructed ancestral gene expression phenotypes, identifying genes with the largest evolved increases in gene expression across development. Conducting knockouts and performing phenotypic analysis in two divergent species typically demonstrated altered fruiting body development in the species that had evolved increased expression. Our evolutionary approach to finding relevant genes proved far more efficient than other gene deletion studies targeting whole genomes or gene families. Combining gene expression measurements with knockout phenotypes facilitated the refinement of Bayesian networks of the genes underlying fruiting body development, regulation of which is one of the least understood processes of multicellular development.

Fig 1. Phylogeny of Fusarium and Neurospora species, with Blumeria graminis as an outgroup, illustrating convergent and divergent evolution in gene expression during morphological development.

The phylogeny was estimated from amino acid sequences of the largest (RPB1) and the second-largest (RPB2) subunits of DNA-dependent RNA polymerase, and the timing was calibrated based on results from Taylor and Berbee [38]. Ancestral expression estimates of lpe-1, stc1, and pna-2 genes for the most recent common ancestor (MRCA) of Fusarium and Neurospora (Inset A), for the MRCA of the Fusarium species (Inset B), and for the MRCA of the Neurospora species (Inset C) are depicted. Orthologous gene sets across taxa are represented by distinct colors. Stages (1–5) of development (not drawn to scale) are indicated in Insets A–C and illustrated in Inset D.

Fig 2. Flow chart for ortholog predictions, sequence data, phylogeny, and phenotyping.

Fig 3. Example of fold increases and decreases in expression between developmental stages (blue, based on (X_t+1-X_t) / min [X_t, X_t+1], where X is the expression level and t is the stage), the continuous ancestral state estimations of the fold increases and decreases between stages for nodes of interest (also blue), the corresponding estimates of stage-to-stage relative expression across stages normalized to the stage of lowest expression (red), and the raw (un-normalized) sequencing counts (black, in parentheses).

Numerical values depicted are for the orthologs of pna-2, for which estimated gene expression in the most recent common ancestor (MRCA) of the Neurospora species increases markedly between stages 4 and 5, whereas estimated gene expression in the ancestor of Fusarium drops markedly between stages 4 and 5. In this research, we found that a knockout of pna-2 exhibits a sexual development phenotype starting at stage 4 in both N. crassa and F. graminearum.

Fig 4. Distribution of phenotypes for knockout strains across stages of development in F. graminearum and N. crassa.

For each stage, numbers of genes exhibiting knockout mutant phenotypes are reported in the center (outside in black, F. graminearum; inside in orange, N. crassa). These numbers were compared to the distribution reported in three previous systematic studies—outside left (blue), analyzing function of the protein kinase genes [97]; outside right (red), functional analysis of transcription factor genes in F. graminearum [96]; and inside (tan), functional analysis of genes across the genome in N. crassa [87,88]—yielding significantly higher representation of phenotypes per knockout (*), significantly lower representation of phenotypes (†), or no statistically significant difference (NS). Revision of figure reproduced with permission from: Sex and Fruiting in Fusarium. F. Trail. In Fusarium: Genomics, Molecular and Cellular Biology, Chapter 2, D.W. Brown and R. H. Proctor, Eds., Caister Academic Press pp. 11–30 [36].

Fig 5. Gene interaction networks underlying early perithecial development in N. crassa (left, blue) and F. graminearum (right, green), represented by directed acyclic graphical models of selected genes (S7 Table), displayed in proximity to the cognate ancestor in the phylogeny of Neurospora and Fusarium species.

Genes within networks were suggested by assembling genes with common knockout phenotypes observed within each species. Networks were inferred from the expression level changes measured between all equivalent stages of development in the three most recent common ancestors of these Neurospora and Fusarium species. Arrows indicate an inferred causal dependency of the two genes they connect. Edges are depicted by dashed black arrows, unless they are present within all three putative ancestral nodes regardless of orientation, in which case they are depicted in blue within the Neurospora-specific network, or pink within the Fusarium-specific network.

Fig 6. Gene interaction networks underlying beak formation in N. crassa (left, orange), and ascospore release in F. graminearum (right, pink), represented by directed acyclic graphical model of selected genes (S7 Table), displayed in proximity to the cognate ancestor in the phylogeny of Neurospora and Fusarium species.

Genes within networks were suggested by assembling genes with common knockout phenotypes observed within each species. Networks were inferred from the expression level changes measured between all equivalent stages of development in the three most recent common ancestors of these Neurospora and Fusarium species. Arrows indicate an inferred causal dependency of the two genes they connect. Edges are depicted by dashed black arrows, unless the edge is present within all three putative ancestral nodes regardless of orientation, in which case they are depicted in blue within the Neurospora-specific network, or red within the Fusarium-specific network.