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Background  Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in  Saccharomyces cerevisiae  and  Schizosaccharomyces pombe ; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus  Podospora anserina  serves as a model for understanding the basic features of mating-type control. Its  mat+  and  mat−  mating types are determined by dissimilar allelic sequences. The  mat−  sequence contains three genes, designated  FMR1 ,  SMR1  and  SMR2 , while the  mat+  sequence contains one gene,  FPR1 .  FMR1  and  FPR1  are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation.    Methodology/Principal Findings  The transcriptomic profiles of the  mat+  and  mat−  strains revealed 157 differentially transcribed genes, and transcriptomic analysis of  fmr1 −   and  fpr1 −   mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in  mat+  and  mat−  strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species.    Conclusions/Significance  This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating.

Genome-Wide Gene Expression Profiling of Fertilization Competent Mycelium in Opposite Mating Types in the Heterothallic Fungus Podospora anserina