Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota
Abstract
Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.
- Authors:
-
[1];
[2];
[2];
[3];
[3];
[2];
[5];
[3];
[2]
- Zhejiang Univ., Hangzhou (China)
- Vanderbilt Univ., Nashville, TN (United States)
- Univ. of Wisconsin, Madison, WI (United States)
- South China Agricultural Univ., Guangzhou (China)
- Westerdijk Fungal Biodiversity Inst. (Netherlands)
- Publication Date:
- Research Org.:
- Great Lakes Bioenergy Research Center (GLBRC), Madison, WI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1764995
- Alternate Identifier(s):
- OSTI ID: 1764996
- Grant/Contract Number:
- SC0018409
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Science Advances
- Additional Journal Information:
- Journal Volume: 6; Journal Issue: 45; Journal ID: ISSN 2375-2548
- Publisher:
- AAAS
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Shen, Xing-Xing, Steenwyk, Jacob L., LaBella, Abigail L., Opulente, Dana A., Zhou, Xiaofan, Kominek, Jacek, Li, Yuanning, Groenewald, Marizeth, Hittinger, Chris T., and Rokas, Antonis. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. United States: N. p., 2020.
Web. doi:10.1126/sciadv.abd0079.
Shen, Xing-Xing, Steenwyk, Jacob L., LaBella, Abigail L., Opulente, Dana A., Zhou, Xiaofan, Kominek, Jacek, Li, Yuanning, Groenewald, Marizeth, Hittinger, Chris T., & Rokas, Antonis. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. United States. https://doi.org/10.1126/sciadv.abd0079
Shen, Xing-Xing, Steenwyk, Jacob L., LaBella, Abigail L., Opulente, Dana A., Zhou, Xiaofan, Kominek, Jacek, Li, Yuanning, Groenewald, Marizeth, Hittinger, Chris T., and Rokas, Antonis. Wed .
"Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota". United States. https://doi.org/10.1126/sciadv.abd0079. https://www.osti.gov/servlets/purl/1764995.
@article{osti_1764995,
title = {Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota},
author = {Shen, Xing-Xing and Steenwyk, Jacob L. and LaBella, Abigail L. and Opulente, Dana A. and Zhou, Xiaofan and Kominek, Jacek and Li, Yuanning and Groenewald, Marizeth and Hittinger, Chris T. and Rokas, Antonis},
abstractNote = {Ascomycota, the largest and most well-studied phylum of fungi, contains three subphyla: Saccharomycotina (budding yeasts), Pezizomycotina (filamentous fungi), and Taphrinomycotina (fission yeasts). Despite its importance, we lack a comprehensive genome-scale phylogeny or understanding of the similarities and differences in the mode of genome evolution within this phylum. By examining 1107 genomes from Saccharomycotina (332), Pezizomycotina (761), and Taphrinomycotina (14) species, we inferred a robust genome-wide phylogeny that resolves several contentious relationships and estimated that the Ascomycota last common ancestor likely originated in the Ediacaran period. Comparisons of genomic properties revealed that Saccharomycotina and Pezizomycotina differ greatly in their genome properties and enabled inference of the direction of evolutionary change. The Saccharomycotina typically have smaller genomes, lower guanine-cytosine contents, lower numbers of genes, and higher rates of molecular sequence evolution compared with Pezizomycotina. These results provide a robust evolutionary framework for understanding the diversity and ecological lifestyles of the largest fungal phylum.},
doi = {10.1126/sciadv.abd0079},
journal = {Science Advances},
number = 45,
volume = 6,
place = {United States},
year = {Wed Nov 04 00:00:00 EST 2020},
month = {Wed Nov 04 00:00:00 EST 2020}
}
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journal, May 2019
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Phylogenomics and contrasting modes of genome evolution in Ascomycota
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- Zenodo