Мақола

Phylogenetic and phylogenomic overview of the Polyporales

Manfred BinderBiology Department, Clark University, 950 Main Street, Worcester, Massachusetts 01610, and CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, the NetherlandsAlfredo JustoBiology Department, Clark University, 950 Main Street, Worcester, Massachusetts 01610Robert Riley#N#3US DOE Joint Genome Institute, Walnut Creek, California, United States of America#N#Asaf SalamovUS Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, California 94598Francesc López‐GiráldezDepartment of Ecology and Evolutionary Biology, Yale University, Osborne Memorial Labs 226, 165 Prospect Street, New Haven, Connecticut 06520-8106Elisabet SjökvistDeptartment of Biological and Environmental sciences, University of Gothenburg, PO Box 461, SE 40530 Göteborg, SwedenAlex Copeland#N#3US DOE Joint Genome Institute, Walnut Creek, California, United States of America#N#Brian Foster#N#3US DOE Joint Genome Institute, Walnut Creek, California, United States of America#N#Hui SunUS Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, California 94598Ellen LarssonDeptment of Biological and Environmental sciences, University of Gothenburg, PO Box 461, SE 40530 Göteborg, SwedenKarl‐Henrik LarssonNatural History Museum, University of Oslo, PO Box 1172 Blindern, NO 0318 Oslo, NorwayJeffrey P. TownsendDepartment of Ecology and Evolutionary Biology, Yale University, Osborne Memorial Labs 226, 165 Prospect Street, New Haven, Connecticut 06520-8106Igor V. GrigorievUS Department of Energy Joint Genome Institute, 2800 Michell Drive, Walnut Creek, California 94598David S. HibbettBiology Department, Clark University, 950 Main Street, Worcester, Massachusetts 01610

2013en

ABI

Аннотация

We present a phylogenetic and phylogenomic overview of the Polyporales. The newly sequenced genomes of Bjerkandera adusta, Ganoderma sp., and Phlebia brevispora are introduced and an overview of 10 currently available Polyporales genomes is provided. The new genomes are 39 500 000-49 900 00 bp and encode for 12 910-16 170 genes. We searched available genomes for single-copy genes and performed phylogenetic informativeness analyses to evaluate their potential for phylogenetic systematics of the Polyporales. Phylogenomic datasets (25, 71, 356 genes) were assembled for the 10 Polyporales species with genome data and compared with the most comprehensive dataset of Polyporales to date (six-gene dataset for 373 taxa, including taxa with missing data). Maximum likelihood and Bayesian phylogenetic analyses of genomic datasets yielded identical topologies, and the corresponding clades also were recovered in the 373-taxa dataset although with different support values in some datasets. Three previously recognized lineages of Polyporales, antrodia, core polyporoid and phlebioid clades, are supported in most datasets, while the status of the residual polyporoid clade remains uncertain and certain taxa (e.g. Gelatoporia, Grifola, Tyromyces) apparently do not belong to any of the major lineages of Polyporales. The most promising candidate single-copy genes are presented, and nodes in the Polyporales phylogeny critical for the suprageneric taxonomy of the order are identified and discussed.

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DOI: 10.3852/13-003

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