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Title: Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids

Abstract

Most plant species form symbioses with mycorrhizal fungi and this relationship is especially important for orchids. Fungi in the genera Tulasnella, Ceratobasidium, and Serendipita are critically important for orchid germination, growth and development. The goals of this study are to understand the phylogenetic relationships of mycorrhizal fungi and to improve the taxonomic resources for these groups. We identified 32 fungal isolates with the internal transcribed spacer region and used shallow genome sequencing to functionally annotate these isolates. We constructed phylogenetic trees from 408 orthologous nuclear genes for 50 taxa representing 14 genera, 11 families, and five orders in Agaricomycotina. While confirming relationships among the orders Cantharellales, Sebacinales, and Auriculariales, our results suggest novel relationships between families in the Cantharellales. Consistent with previous studies, we found the genera Ceratobasidium and Thanatephorus of Cerabotasidiaceae to not be monophyletic. Within the monophyletic genus Tulasnella, we found strong phylogenetic signals that suggest a potentially new species and a revision of current species boundaries (e.g. Tulasnella calospora); however it is premature to make taxonomic revisions without further sampling and morphological descriptions. There is low resolution of Serendipita isolates collected. More sampling is needed from areas around the world before making evolutionary-informed changes in taxonomy. Ourmore » study adds value to an important living collection of fungi isolated from endangered orchid species, but also informs future investigations of the evolution of orchid mycorrhizal fungi.« less

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [2];  [2]; ORCiD logo [3]; ORCiD logo [3];  [3]; ORCiD logo [3]; ORCiD logo [4]
  1. Univ. of Missouri, Columbia, MO (United States)
  2. Illinois College, Jacksonville, IL (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of California, Riverside, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF); National Institutes of Health (NIH); Defense Threat Reduction Agency (DTRA)
OSTI Identifier:
1619144
Grant/Contract Number:  
AC02-05CH11231; MRI-1429826; 1S10OD016290-01A1
Resource Type:
Accepted Manuscript
Country of Publication:
United States
Language:
English

Citation Formats

Unruh, Sarah A., Pires, J. Chris, Zettler, Lawrence, Erba, Luigi, Grigoriev, Igor, Barry, Kerrie, Daum, Christopher, Lipzen, Anna, and Stajich, Jason E.. Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids. United States: N. p., 2019. Web. https://doi.org/10.1101/862763.
Unruh, Sarah A., Pires, J. Chris, Zettler, Lawrence, Erba, Luigi, Grigoriev, Igor, Barry, Kerrie, Daum, Christopher, Lipzen, Anna, & Stajich, Jason E.. Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids. United States. https://doi.org/10.1101/862763
Unruh, Sarah A., Pires, J. Chris, Zettler, Lawrence, Erba, Luigi, Grigoriev, Igor, Barry, Kerrie, Daum, Christopher, Lipzen, Anna, and Stajich, Jason E.. Tue . "Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids". United States. https://doi.org/10.1101/862763. https://www.osti.gov/servlets/purl/1619144.
@article{osti_1619144,
title = {Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids},
author = {Unruh, Sarah A. and Pires, J. Chris and Zettler, Lawrence and Erba, Luigi and Grigoriev, Igor and Barry, Kerrie and Daum, Christopher and Lipzen, Anna and Stajich, Jason E.},
abstractNote = {Most plant species form symbioses with mycorrhizal fungi and this relationship is especially important for orchids. Fungi in the genera Tulasnella, Ceratobasidium, and Serendipita are critically important for orchid germination, growth and development. The goals of this study are to understand the phylogenetic relationships of mycorrhizal fungi and to improve the taxonomic resources for these groups. We identified 32 fungal isolates with the internal transcribed spacer region and used shallow genome sequencing to functionally annotate these isolates. We constructed phylogenetic trees from 408 orthologous nuclear genes for 50 taxa representing 14 genera, 11 families, and five orders in Agaricomycotina. While confirming relationships among the orders Cantharellales, Sebacinales, and Auriculariales, our results suggest novel relationships between families in the Cantharellales. Consistent with previous studies, we found the genera Ceratobasidium and Thanatephorus of Cerabotasidiaceae to not be monophyletic. Within the monophyletic genus Tulasnella, we found strong phylogenetic signals that suggest a potentially new species and a revision of current species boundaries (e.g. Tulasnella calospora); however it is premature to make taxonomic revisions without further sampling and morphological descriptions. There is low resolution of Serendipita isolates collected. More sampling is needed from areas around the world before making evolutionary-informed changes in taxonomy. Our study adds value to an important living collection of fungi isolated from endangered orchid species, but also informs future investigations of the evolution of orchid mycorrhizal fungi.},
doi = {10.1101/862763},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2019},
month = {12}
}

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