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

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,...

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Autores principales: Traeger, Stefanie, Altegoer, Florian, Freitag, Michael, Gabaldon, Toni, Kempken, Frank, Kumar, Abhishek, Marcet-Houben, Marina, Pöggeler, Stefanie, Stajich, Jason E., Nowrousian, Minou
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778014/
https://www.ncbi.nlm.nih.gov/pubmed/24068976
http://dx.doi.org/10.1371/journal.pgen.1003820
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author Traeger, Stefanie
Altegoer, Florian
Freitag, Michael
Gabaldon, Toni
Kempken, Frank
Kumar, Abhishek
Marcet-Houben, Marina
Pöggeler, Stefanie
Stajich, Jason E.
Nowrousian, Minou
author_facet Traeger, Stefanie
Altegoer, Florian
Freitag, Michael
Gabaldon, Toni
Kempken, Frank
Kumar, Abhishek
Marcet-Houben, Marina
Pöggeler, Stefanie
Stajich, Jason E.
Nowrousian, Minou
author_sort Traeger, Stefanie
collection PubMed
description 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.
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spelling pubmed-37780142013-09-25 The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution Traeger, Stefanie Altegoer, Florian Freitag, Michael Gabaldon, Toni Kempken, Frank Kumar, Abhishek Marcet-Houben, Marina Pöggeler, Stefanie Stajich, Jason E. Nowrousian, Minou PLoS Genet Research Article 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. Public Library of Science 2013-09-19 /pmc/articles/PMC3778014/ /pubmed/24068976 http://dx.doi.org/10.1371/journal.pgen.1003820 Text en © 2013 Traeger et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Traeger, Stefanie
Altegoer, Florian
Freitag, Michael
Gabaldon, Toni
Kempken, Frank
Kumar, Abhishek
Marcet-Houben, Marina
Pöggeler, Stefanie
Stajich, Jason E.
Nowrousian, Minou
The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
title The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
title_full The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
title_fullStr The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
title_full_unstemmed The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
title_short The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
title_sort genome and development-dependent transcriptomes of pyronema confluens: a window into fungal evolution
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778014/
https://www.ncbi.nlm.nih.gov/pubmed/24068976
http://dx.doi.org/10.1371/journal.pgen.1003820
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