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Phylogenetic and phylogenomic overview of the Polyporales

Journal article
Authors Manfred Binder
Alfredo Justo
Robert Riley
Asaf Salamov
Francesc Lopez-Giraldez
Elisabet Sjökvist
Alex Copeland
Brian Foster
Hui Sun
Ellen Larsson
Karl-Henrik Larsson
Jeffrey Townsend
Igor V. Grigoriev
David S. Hibbett
Published in Mycologia
Volume 105
Issue 6
Pages 1350-1373
ISSN 0027-5514
Publication year 2013
Published at Department of Biological and Environmental Sciences
Pages 1350-1373
Language en
Links dx.doi.org/10.3852/13-003
Keywords 'genomics, new molecular markers, Polyporales, taxonomy'
Subject categories Biological Sciences, Biological Systematics

Abstract

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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