Abstract
Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely that of the black truffle, Tuber melanosporum, a mycorrhizal species with unusual subterranean fruiting bodies. To help close the sequence gap among basal filamentous ascomycetes, and to allow conclusions about the evolution of fungal development, we sequenced the genome and assayed transcriptomes during development of Pyronema confluens, a saprobic Pezizomycete with a typical apothecium as fruiting body. With a size of 50 Mb and ∼13,400 protein-coding genes, the genome is more characteristic of higher filamentous ascomycetes than the large, repeat-rich truffle genome; however, some typical features are different in the P. confluens lineage, e.g. the genomic environment of the mating type genes that is conserved in higher filamentous ascomycetes, but only partly conserved in P. confluens. On the other hand, P. confluens has a full complement of fungal photoreceptors, and expression studies indicate that light perception might be similar to distantly related ascomycetes and, thus, represent a basic feature of filamentous ascomycetes. Analysis of spliced RNA-seq sequence reads allowed the detection of natural antisense transcripts for 281 genes. The P. confluens genome contains an unusually high number of predicted orphan genes, many of which are upregulated during sexual development, consistent with the idea of rapid evolution of sex-associated genes. Comparative transcriptomics identified the transcription factor gene pro44 that is upregulated during development in P. confluens and the Sordariomycete Sordaria macrospora. The P. confluens pro44 gene (PCON_06721) was used to complement the S. macrospora pro44 deletion mutant, showing functional conservation of this developmental regulator.
Highlights
Fungi (Eumycota) are a group of eukaryotes that are present in almost all habitats; they do play a great role in nature, and influence human life in many ways [1]
We argue that the use of different mycelia sharing the common denominator of ‘‘no fruiting bodies’’ would allow us to focus on genes that are differentially expressed during fruiting body morphogenesis by comparing the three different conditions
Overall genomic synteny with T. melanosporum is low, but regions of microsynteny between P. confluens and truffle are more numerous than between P. confluens and other ascomycetes, indicating that the two Pezizomycetes are more closely related to each other than to other ascomycete groups; the level of synteny still suggests a wide evolutionary range within the Pezizomycetes. This is consistent with phylogenetic analyses based on rDNA sequences that placed Pyronema and Tuber in subgroups C and B, respectively, of the Pezizomycetes [146,147]
Summary
Fungi (Eumycota) are a group of eukaryotes that are present in almost all habitats; they do play a great role in nature, and influence human life in many ways [1]. In a previous study with metazoans, genes could be grouped in two classes with high and low expression levels, respectively, independent of species, tissue type, or type of experiment [46] In fungi, this has been addressed only in the filamentous ascomycete Sordaria macrospora where the situation is different, because there were up to three expression peaks depending on the conditions analyzed [24]. A recent EST analysis of Neurospora intermedia and comparison with other Neurospora species indicated that sex-associated genes, i.e. those genes that are preferentially expressed during sexual development, are rapidly evolving in fungi, too [70] We approached this question from a different angle by analyzing gene expression levels for P. confluens genes with different degrees of evolutionary conservation to find out if genes with different lineage-specificities are preferentially expressed under any of the conditions that we investigated (Figure 6, Table S8). This indicates that this transcription factor gene is one of the core regulators of sexual development across filamentous ascomycetes
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
