Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution.

Coprinopsis cinerea (also known as Coprinus cinereus) is a multicellular basidiomycete mushroom particularly suited to the study of meiosis due to its synchronous meiotic development and prolonged prophase. We examined the 15-hour meiotic transcriptional program of C. cinerea, encompassing time points prior to haploid nuclear fusion though tetrad formation, using a 70-mer oligonucleotide microarray. As with other organisms, a large proportion (∼20%) of genes are differentially regulated during this developmental process, with successive waves of transcription apparent in nine transcriptional clusters, including one enriched for meiotic functions. C. cinerea and the fungi Saccharomyces cerevisiae and Schizosaccharomyces pombe diverged ∼500-900 million years ago, permitting a comparison of transcriptional programs across a broad evolutionary time scale. Previous studies of S. cerevisiae and S. pombe compared genes that were induced upon entry into meiosis; inclusion of C. cinerea data indicates that meiotic genes are more conserved in their patterns of induction across species than genes not known to be meiotic. In addition, we found that meiotic genes are significantly more conserved in their transcript profiles than genes not known to be meiotic, which indicates a remarkable conservation of the meiotic process across evolutionarily distant organisms. Overall, meiotic function genes are more conserved in both induction and transcript profile than genes not known to be meiotic. However, of 50 meiotic function genes that were co-induced in all three species, 41 transcript profiles were well-correlated in at least two of the three species, but only a single gene (rad50) exhibited coordinated induction and well-correlated transcript profiles in all three species, indicating that co-induction does not necessarily predict correlated expression or vice versa. Differences may reflect differences in meiotic mechanisms or new roles for paralogs. Similarities in induction, transcript profiles, or both, should contribute to gene discovery for orthologs without currently characterized meiotic roles.

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.

Fungal sex genes-searching for the ancestors.

The sex-determining genes of fungi reside at one or two specialised regions of the chromosome known as the mating type (MAT) loci. The genes are sufficient to determine haploid cell identity, enable compatible mating partners to attract each other, and prepare cells for sexual reproduction after fertilisation. How conserved are these genes in different fungal groups? New work1 seeks an answer to this question by identifying the sex-determining regions of an early diverged fungus. These regions bear remarkable similarity to those described in other fungi, but the sex proteins they encode belong to only a single class of transcription factor, the high mobility group (HMG), indicating that these are likely to be ancestral to other proteins recruited for fungal sex.

The origin of multiple B mating specificities in Coprinus cinereus.

Mushrooms, such as Coprinus cinereus, possess large families of pheromones and G-protein-coupled receptors that are sequestered at the B mating-type locus and whose function is to confer vast numbers of different mating types. This ability results from complex patterns of cognate and noncognate pheromone/receptor pairings, which potentially offer a unique insight into the molecular interaction between receptor and ligand. In this study we have identified many more members of these families by molecular analysis of strains collected worldwide. There are three groups of genes at each B locus. We have identified two alleles of group 1, five alleles of group 2, and seven alleles of group 3, encoding in total 14 different receptors and 29 different pheromones. The specificity of many newly identified alleles was determined by transformation analysis. One striking finding was that receptors fall into groups based on sequence homology but these do not correspond to the groups defined by position, indicating that complex evolutionary processes gave rise to the B loci. While additional allelic versions may occur in nature, the number of B specificities possible by combination of the alleles that we describe is 70, close to previous estimates based on population analysis.

The art and design of genetic screens: filamentous fungi.

In the 1940s, screens for metabolic mutants of the filamentous fungus Neurospora crassa established the fundamental, one-to-one relationship between a gene and a specific protein, and also established fungi as important genetic organisms. Today, a wide range of filamentous species, which represents a billion years of evolutionary divergence, is used for experimental studies. The developmental complexity of these fungi sets them apart from unicellular yeasts, and allows the development of new screens that enable us to address biological questions that are relevant to all eukaryotes.

Mate recognition in fungi.

The ascomycete and basidiomycete fungi have contributed much to our understanding of eukaryotic cell biology. The study of mate recognition, in particular, has provided detailed understanding of cell signalling pathways and cell-specific gene transcription. Sexual dimorphism has little relevance to mating in these organisms, indeed specialised cells for mating are found only in filamentous ascomycetes and even here, a single individual produces both male and female structures. None the less, most species have genetic barriers to prevent selfing. The genes that determine self-incompatibility divide populations into different mating types, and only individuals with different mating types can engage in sexual reproduction. Ascomycetes have just two mating types, but basidiomycetes may have several thousands. Despite apparent differences in the biology and numbers of mating types in these fungi, it is becoming increasingly apparent that many components of their mating pathways are highly conserved.