The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution.

Traeger, S., Altegoer, F., Freitag, M., Gabaldon, T., Kempken, Frank, Kumar, Abhishek, Marcet-Houben, M., Poggeler, S., Stajich, J. E. and Nowrousian, M. (2013) The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution. PLoS Genetics, 9 (9). DOI 10.1371/journal.pgen.1003820.

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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.

Document Type: Article
Additional Information: Times Cited: 0 Traeger, Stefanie Altegoer, Florian Freitag, Michael Gabaldon, Toni Kempken, Frank Kumar, Abhishek Marcet-Houben, Marina Poeggeler, Stefanie Stajich, Jason E. Nowrousian, Minou
Keywords: Fungal genomics Ascomycetes Sexual differentiation Gene expression Fungi Fungal genetics Protein domains Transcription factors
Research affiliation: Kiel University > Kiel Marine Science
OceanRep > The Future Ocean - Cluster of Excellence
Kiel University
Refereed: Yes
Open Access Journal?: Yes
DOI etc.: 10.1371/journal.pgen.1003820
ISSN: 1553-7404
Projects: Future Ocean
Date Deposited: 08 Jul 2014 09:56
Last Modified: 19 Aug 2019 11:17
URI: http://oceanrep.geomar.de/id/eprint/25226

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