Phylogenetic and phylogenomic overview of the Polyporales

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 e...

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Bibliographic Details
Published in:Mycologia 2013-11, Vol.105 (6), p.1350-1373
Main Authors: Binder, Manfred, Justo, Alfredo, Riley, Robert, Salamov, Asaf, Lopez-Giraldez, Francesc, Sjökvist, Elisabet, Copeland, Alex, Foster, Brian, Sun, Hui, Larsson, Ellen, Larsson, Karl-Henrik, Townsend, Jeffrey, Grigoriev, Igor V., Hibbett, David S.
Format: Article
Language:English
Subjects:
Biological Sciences
Biological Systematics
Biological taxonomies
Biologisk systematik
Biologiska vetenskaper
Bjerkandera adusta
Coriolaceae
Datasets
Evolution, Molecular
Fungal Proteins - genetics
Ganoderma
Genomes
Genomics
new molecular markers
Phanerochaete
Phylogenetics
Phylogeny
Polyporales
Polyporales - classification
Polyporales - genetics
SPECIAL SECTION: GENOMICS OF POLYPORALES
Taxa
taxonomy
Trametes
Tyromyces
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Summary: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.
ISSN:0027-5514
1557-2536
DOI:10.3852/13-003