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ARS Home » Midwest Area » Peoria, Illinois » National Center for Agricultural Utilization Research » Mycotoxin Prevention and Applied Microbiology Research » Research » Publications at this Location » Publication #375158

Research Project: Management and Characterization of Agriculturally and Biotechnologically Important Microbial Genetic Resources and Associated Information

Location: Mycotoxin Prevention and Applied Microbiology Research

Title: Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics

item VANDEPOL, NATALIE - Michigan State University
item LIBER, JULIAN - Michigan State University
item DESIRO, ALESSANDRO - Michigan State University
item NA, HYUNSOO - Joint Genome Institute
item KENNEDY, MEGAN - Joint Genome Institute
item BARRY, KERRIE - Joint Genome Institute
item GRIGORIEV, IGOR - Joint Genome Institute
item MILLER, ANDREW - University Of Illinois
item O Donnell, Kerry
item STAJICH, JASON - University Of California
item BONITO, GREGORY - Michigan State University

Submitted to: Fungal Diversity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2020
Publication Date: 9/16/2020
Citation: Vandepol, N., Liber, J., Desiro, A., Na, H., Kennedy, M., Barry, K., Grigoriev, I.V., Miller, A.N., O'Donnell, K., Stajich, J.E., Bonito, G. 2020. Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics. Fungal Diversity. 104:267-289.

Interpretive Summary: Mortierella, a group of structurally simple fungi, includes several species that are prolific producers of polyunsaturated fatty acids that are highly valued by the nutraceutical and bioenergy industries. These fungi are notoriously difficult to identify accurately with a microscope. This research developed a high-throughput method using DNA sequencing to rapidly and accurately identify Mortierella species. New reference DNA sequence and ecological databases will greatly facilitate identification of isolates that are of value to biotechnology industries.

Technical Abstract: Early efforts to classify Mortierellaceae were based on macro- and micromorphology, but sequencing and phylogenetic studies with ribosomal DNA (rDNA) markers have demonstrated conflicting taxonomic groupings and polyphyletic genera. Although some taxonomic confusion in the family has been clarified, rDNA data alone is unable to resolve higher level phylogenetic relationships within Mortierellaceae. In this study, we applied two parallel approaches to resolve the Mortierellaceae phylogeny: low coverage genome (LCG) sequencing and high-throughput, multiplexed targeted amplicon sequencing to generate multi-locus sequence data (MLST). We then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon dataset. Resolving the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera, 7 of which are newly proposed. Low-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence phylogeny. The MLST approach enabled much greater sampling depth and breadth than the LCG approach, but has limitations too. We present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.