Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)
Abstract
Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.
- Authors:
-
- Univ. of Michigan, Ann Arbor, MI (United States)
- Univ. of Florida, Gainesville, FL (United States)
- Univ. of California, Riverside, CA (United States)
- Oregon State Univ., Corvallis, OR (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1594914
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Molecular Phylogenetics and Evolution
- Additional Journal Information:
- Journal Volume: 133; Journal Issue: C; Journal ID: ISSN 1055-7903
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Acaulopage tetraceros; Cochlonema odontosperma; single cell; Stylopage hadra; Zoopage; Zoophagus insidians
Citation Formats
Davis, William J., Amses, Kevin R., Benny, Gerald L., Carter-House, Derreck, Chang, Ying, Grigoriev, Igor, Smith, Matthew E., Spatafora, Joseph W., Stajich, Jason E., and James, Timothy Y. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). United States: N. p., 2019.
Web. doi:10.1016/j.ympev.2019.01.006.
Davis, William J., Amses, Kevin R., Benny, Gerald L., Carter-House, Derreck, Chang, Ying, Grigoriev, Igor, Smith, Matthew E., Spatafora, Joseph W., Stajich, Jason E., & James, Timothy Y. Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi). United States. https://doi.org/10.1016/j.ympev.2019.01.006
Davis, William J., Amses, Kevin R., Benny, Gerald L., Carter-House, Derreck, Chang, Ying, Grigoriev, Igor, Smith, Matthew E., Spatafora, Joseph W., Stajich, Jason E., and James, Timothy Y. Fri .
"Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)". United States. https://doi.org/10.1016/j.ympev.2019.01.006. https://www.osti.gov/servlets/purl/1594914.
@article{osti_1594914,
title = {Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)},
author = {Davis, William J. and Amses, Kevin R. and Benny, Gerald L. and Carter-House, Derreck and Chang, Ying and Grigoriev, Igor and Smith, Matthew E. and Spatafora, Joseph W. and Stajich, Jason E. and James, Timothy Y.},
abstractNote = {Previous genome-scale phylogenetic analyses of Fungi have under sampled taxa from Zoopagales; this order contains many predacious or parasitic genera, and most have never been grown in pure culture. We sequenced the genomes of 4 zoopagalean taxa that are predators of amoebae, nematodes, or rotifers and the genome of one taxon that is a parasite of amoebae using single cell sequencing methods with whole genome amplification. Each genome was a metagenome, which was assembled and binned using multiple techniques to identify the target genomes. We inferred phylogenies with both super matrix and coalescent approaches using 192 conserved proteins mined from the target genomes and performed ancestral state reconstructions to determine the ancestral trophic lifestyle of the clade. Our results indicate that Zoopagales is monophyletic. Ancestral state reconstructions provide moderate support for mycoparasitism being the ancestral state of the clade.},
doi = {10.1016/j.ympev.2019.01.006},
journal = {Molecular Phylogenetics and Evolution},
number = C,
volume = 133,
place = {United States},
year = {Fri Jan 11 00:00:00 EST 2019},
month = {Fri Jan 11 00:00:00 EST 2019}
}
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