Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics
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Resolving the Mortierellaceae phylogeny through synthesis of multi‑gene phylogenetics and phylogenomics Natalie Vandepol1 · Julian Liber2 · Alessandro Desirò3 · Hyunsoo Na4 · Megan Kennedy4 · Kerrie Barry4 · Igor V. Grigoriev4 · Andrew N. Miller5 · Kerry O’Donnell6 · Jason E. Stajich7 · Gregory Bonito1,3 Received: 17 February 2020 / Accepted: 25 July 2020 © MUSHROOM RESEARCH FOUNDATION 2020
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 sequence data for multi-gene phylogenetics. 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 multi-gene phylogenetics 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. Keywords Mortierellaceae · Phylogenomics · Molecular systematics · Taxonomy · Multi-locus sequence typing
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13225-020-00455-5) contains supplementary material, which is available to authorized users. * Gregory Bonito [email protected] 1
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
2
Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
3
Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
4
Joint Genome Institute, Berkeley, CA 94720, USA
5
Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL 61820, USA
6
United States Department of Agriculture, Agricultural Research Service, Peoria, IL 61604, USA
7
Department of Microbiology and Plant Pathology & Institute for Integrative Genome Biology, University of California-Riverside, Riverside, CA 92521, USA
Early diverging fungi belonging to Mortierellomycotina are diverse in ecology and species richness, and are classified within a single order (Mortierellales) and as belonging to a single family (Mortierellaceae). Phylogenetically, this lineage is c
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