Phylogenetic and phylogenomic overview of the Polyporales

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.

Phylogenetic position and taxonomy of Kusaghiporia usambarensis gen. et sp. nov. (Polyporales)

“…Despite the strong support of Laetiporaceae Jülich (Figure 2) K. usambarensis, L. persicinus, W. cocos, Phaoelus , and Crustoderma together with Pycnoporellus displayed long branches indicating a high genetic divergence. A high genetic divergence of L. persicinus has previously been reported (Binder et al 2013; Ortiz-Santana et al 2013; Han et al 2016; Justo et al 2017). Lindner and Banik (2008) suggested placing L. persicinus in a separate genus due to its genetic remoteness as compared to other species of Laetiporus .…”

“…In earlier studies (Binder et al 2013; Zhao et al 2015), seven clades were found in Polyporales : the “core polyporoid clade”; the “residual polyporoid clade”; the “antrodia clade”; the “gelatoporia clade”; the “phlebioid clade”; the “tyromyces clade” and the “fragiliporia clade”. Justo et al (2017) recognised six clades, excluding the “fragiliporia clade” reported by Zhao et al (2015).…”

“…However, Justo et al (2017) recognised 37 families in Polyporales . Seven clades have been recognised in Polyporales : the “antrodia”; “core polyporoid”; “residual polyporoid”; “phlebioid”; “tyromyces”; “gelatoporia” and “fragiliporia” clades (Binder et al 2013; Zhao et al 2015). …”

“…Recent taxonomic and phylogenetic studies, including that of Lindner and Banik (2008), have presented molecular phylogenies of the clade. In a study of Laetiporus and other polypores, Banik et al (2010) inferred relationships among North American and Japanese Laetiporus isolates; Ortiz-Santana et al (2013) presented a phylogenetic overview of the “antrodia clade” and Binder et al (2013) used genomic data and a six-gene data set for evaluating phylogenetic relationships in Polyporales . Further studies include those of Han et al (2014) in which two new species of Fomitopsis from China were described, and Zhao et al (2015) used a multi-gene dataset to support the recognition of Fragiliporiaceae , a new family of Polyporales .…”

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

“…We have selected (a) 14 popular white rot fungal strains – Ceriporiopsis subvermispora B (Fernandez-Fueyo et al 2012), Heterobasidion annosum v2.0 (Olson et al 2012), Fomitiporia mediterranea v1.0 (Floudas et al 2012), Phanerochaete carnosa HHB-10118 (Suzuki et al 2012), Pycnoporus cinnabarinus BRFM 137 (Levasseur et al 2014), Phanerochaete chrysosporium R78 v2.2 (Martinez et al 2004; Ohm et al 2014), Dichomitus squalens LYAD-421 SS1 (Floudas et al 2012), Trametes versicolor v1.0 (Floudas et al 2012), Punctularia strigosozonata v1.0 (Floudas et al 2012), Phlebia brevispora HHB-7030 SS6 (Binder et al 2013), Botrytis cinerea v1.0 (Amselem et al 2011), Pleurotus ostreatus PC15 v2.0 (Riley et al 2014; Alfaro et al 2016; Castanera et al 2016), Stereum hirsutum FP-91666 SS1 v1.0 (Floudas et al 2012), Pleurotus eryngii ATCC90797 (Guillen et al 1992; Camarero et al 1999; Ruiz‐Dueñas et al 1999; Matheny et al 2006); (b) 15 popular brown rot fungal strains – Postia placenta MAD 698-R v1.0 (Martinez et al 2009), Fibroporia radiculosa TFFH 294 (Tang et al 2012), Wolfiporia cocos MD-104 SS10 v1.0 (Floudas et al 2012), Dacryopinax primogenitus DJM 731 SSP1 v1.0 (Floudas et al 2012), Daedalea quercina v1.0 (Nagy et al 2015), Laetiporus sulphureus var v1.0 (Nagy et al 2015), Postia placenta MAD-698-R-SB12 v1.0 (Martinez et al 2009), Neolentinus lepideus v1.0 (Nagy et al 2015), Serpula lacrymans S7.9 v2.0 (Eastwood et al 2011), Calocera cornea v1.0 (Eastwood et al 2011), Gloeophyllum trabeum v1.0 (Floudas et al 2012), Fistulina hepatica v1.0 (Floudas et al 2015), Fomitopsis pinicola FP-58527 SS1 (Floudas et al 2015), Hydnomerulius pinastri v2.0 (Kohler et al 2015) and Coniophora puteana v1.0 (Kohler et al 2015); (c) 13 popular soft rot fungal strains – Trichoderma reesei v 2.0 (Martinez et al 2008), Rhizopus oryzae 99-880 from Broad (Ma et al 2009), Aspergillus wentii v1.0 (De Vries et al 2017), Penicillium chrysogenum Wisconsin 54-1255 (Van Den Berg et al 2008), Daldinia eschscholzii EC12 v1.0, Hypoxylon sp. CI-4A v1.0 (Wu et al 2017), Aspergillus niger ATCC 1015 v4.0 (Andersen et al 2011), Hypoxylon sp.…”