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Title: Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Abstract

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system,more » or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Finally, among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.« less

Authors:
 [1];  [1];  [1];  [2];  [3];  [3];  [3];  [3];  [3]; ORCiD logo [4];  [5];  [3]; ORCiD logo [6]; ORCiD logo [1]
  1. Ruhr-Univ., Bochum (Germany)
  2. Centre for Genomic Regulation (CRG), Barcelona (Spain)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Georg-August Univ., Gottingen (Germany)
  5. Centre for Genomic Regulation (CRG), Barcelona (Spain); Univ. Pompeu Fabra (UPF), Barcelona (Spain); Inst. Catalana de Recerca i Estudis Avancats (ICREA), Barcelona (Spain)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); German Research Foundation (DFG)
OSTI Identifier:
1619142
Grant/Contract Number:  
AC02-05CH11231; NO407/7-1
Resource Type:
Accepted Manuscript
Journal Name:
Genetics
Additional Journal Information:
Journal Volume: 213; Journal Issue: 4; Journal ID: ISSN 0016-6731
Publisher:
Genetics Society of America
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; fruiting body development; Ascodesmis nigricans; Sordaria macrospora; Puronema confluens; comparative transcriptomics

Citation Formats

Lütkenhaus, Ramona, Traeger, Stefanie, Breuer, Jan, Carreté, Laia, Kuo, Alan, Lipzen, Anna, Pangilinan, Jasmyn, Dilworth, David, Sandor, Laura, Pöggeler, Stefanie, Gabaldón, Toni, Barry, Kerrie, Grigoriev, Igor V., and Nowrousian, Minou. Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes. United States: N. p., 2019. Web. https://doi.org/10.1534/genetics.119.302749.
Lütkenhaus, Ramona, Traeger, Stefanie, Breuer, Jan, Carreté, Laia, Kuo, Alan, Lipzen, Anna, Pangilinan, Jasmyn, Dilworth, David, Sandor, Laura, Pöggeler, Stefanie, Gabaldón, Toni, Barry, Kerrie, Grigoriev, Igor V., & Nowrousian, Minou. Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes. United States. https://doi.org/10.1534/genetics.119.302749
Lütkenhaus, Ramona, Traeger, Stefanie, Breuer, Jan, Carreté, Laia, Kuo, Alan, Lipzen, Anna, Pangilinan, Jasmyn, Dilworth, David, Sandor, Laura, Pöggeler, Stefanie, Gabaldón, Toni, Barry, Kerrie, Grigoriev, Igor V., and Nowrousian, Minou. Tue . "Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes". United States. https://doi.org/10.1534/genetics.119.302749. https://www.osti.gov/servlets/purl/1619142.
@article{osti_1619142,
title = {Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes},
author = {Lütkenhaus, Ramona and Traeger, Stefanie and Breuer, Jan and Carreté, Laia and Kuo, Alan and Lipzen, Anna and Pangilinan, Jasmyn and Dilworth, David and Sandor, Laura and Pöggeler, Stefanie and Gabaldón, Toni and Barry, Kerrie and Grigoriev, Igor V. and Nowrousian, Minou},
abstractNote = {Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Finally, among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.},
doi = {10.1534/genetics.119.302749},
journal = {Genetics},
number = 4,
volume = 213,
place = {United States},
year = {2019},
month = {12}
}

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