Phylogenetic analysis of Antrodia and related taxa based on partial mitochondrial SSU rDNA sequences

Evolutionary dynamics of host specialization in wood-decay fungi

Background

The majority of wood decomposing fungi are mushroom-forming Agaricomycetes, which exhibit two main modes of plant cell wall decomposition: white rot, in which all plant cell wall components are degraded, including lignin, and brown rot, in which lignin is modified but not appreciably removed. Previous studies suggested that brown rot fungi tend to be specialists of gymnosperm hosts and that brown rot promotes gymnosperm specialization. However, these hypotheses were based on analyses of limited datasets of Agaricomycetes. Overcoming this limitation, we used a phylogeny with 1157 species integrating available sequences, assembled decay mode characters from the literature, and coded host specialization using the newly developed R package, rusda.

Results

We found that most brown rot fungi are generalists or gymnosperm specialists, whereas most white rot fungi are angiosperm specialists. A six-state model of the evolution of host specialization revealed high transition rates between generalism and specialization in both decay modes. However, while white rot lineages switched most frequently to angiosperm specialists, brown rot lineages switched most frequently to generalism. A time-calibrated phylogeny revealed that Agaricomycetes is older than the flowering plants but many of the large clades originated after the diversification of the angiosperms in the Cretaceous.

Conclusions

Our results challenge the current view that brown rot fungi are primarily gymnosperm specialists and reveal intensive white rot specialization to angiosperm hosts. We thus suggest that brown rot associated convergent loss of lignocellulose degrading enzymes was correlated with host generalism, rather than gymnosperm specialism. A likelihood model of host specialization evolution together with a time-calibrated phylogeny further suggests that the rise of the angiosperms opened a new mega-niche for wood-decay fungi, which was exploited particularly well by white rot lineages.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1229-7) contains supplementary material, which is available to authorized users.

Revisiting the taxonomy of Phanerochaete (Polyporales, Basidiomycota) using a four gene dataset and extensive ITS sampling

We amplified RPB1, RPB2, and the ITS and LSU ribosomal genes from species mostly in the phlebioid clade, focusing heavily in phanerochaetoid taxa. We performed Maximum Likelihood and Bayesian analyses for different combinations of datasets. Our results provide a strongly supported phylogenetic picture of the phlebioid clade, representing 89 species in the four genes analyses, of which 49 represent phanerochaetoid taxa. Phanerochaete sensu lato is polyphyletic and distributed across nine lineages in the phlebioid clade. Six of these lineages are associated to already described genera, while we describe the new genus Phaeophlebiopsis to accommodate Phlebiopsis-like species in one of the remaining lineages. We also propose three taxonomic transfers and describe nine new species, with four of those species currently placed in Phanerochaete sanguinea or Phanerochaete velutina. Finally, the placement of Leptoporus mollis along with other potential brown-rot species in the phlebioid clade suggests that, in addition to the Antrodia clade, brown-rot fungi may have evolved more than once in Polyporales.

Re-evaluation of the Genus Antrodia (Polyporales, Basidiomycota) in Korea

The wood decay fungi Antrodia P. Karst. play important ecological roles and have significant industrial and economic impacts as both wood degraders and sources of pharmaceutical and biotechnological products. Although each Antrodia species has distinct morphological characteristics, the misidentification rate is especially high due to their simple morphological characters. A combination of morphological and internal transcribed spacer region sequence analyses revealed that 27 of 89 specimens previously identified by morphology alone were correct, whereas 35 of these specimens were misidentified as other Antrodia species. We report here that seven Antrodia species exist in Korea (A. albida, A. heteromorpha, A. malicola, A. serialis, A. sinuosa, A. sitchensis, and A. xantha) and based on these specimens, we provide taxonomic descriptions of these species, except for A. serialis, which was only confirmed by isolate.

A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales)

Phylogenetic relationships among members of the antrodia clade were investigated with molecular data from two nuclear ribosomal DNA regions, LSU and ITS. A total of 123 species representing 26 genera producing a brown rot were included in the present study. Three DNA datasets (combined LSU-ITS dataset, LSU dataset, ITS dataset) comprising sequences of 449 isolates were evaluated with three different phylogenetic analyses (maximum likelihood, maximum parsimony, Bayesian inference). We present a phylogenetic overview of the five main groups recovered: the fibroporia, laetiporus, postia, laricifomes and core antrodia groups. Not all of the main groups received strong support in the analyses, requiring further research. We were able to identify a number of well supported clades within the main groups.

The phylogenetic position of Postia s.l. (Polyporales, Basidiomycota) from Patagonia, Argentina

We investigated the phylogenetic relationships of Postia species from Patagonia with rDNA ITS and LSU sequences, together with morphological, cultural and biological features. All species in the genus were included in a "Postia clade" irrespective of whether their spores were thin- or thick-walled. This clade is characterized by tetrapolar mating, a normal nuclear behavior, metachromatic generative hyphae and absence of fiber hyphae in culture. One subclade merged the austral taxa P. pelliculosa and P. punctata, but otherwise no distinct relationships were found regarding spore shape, spore wall thickness and geographical distribution of taxa. The austral P. venata and the endemic P. carbophila, with thin-walled basidiospores, occupied variable positions in both analyses. Postia caesia from Patagonia grouped within the P. caesia species complex but on a separate branch. In contrast, P. rennyi and P. balsamea from Patagonia corresponded well with strains from other geographic areas. The two austral species in Ryvardenia, R. cretacea and R. campyla, characterized by non-metachromatic hyphae, bipolar mating and an astatocoenocytic nuclear behavior, formed an independent subclade among the dimitic genera of the "Antrodia clade", far from other Postia taxa within which they had been placed previously, supporting their inclusion in a genus of their own. Postia carbophila grouped with other Postia species and not with Postia (Rhodonia) placenta as suggested previously on the basis of morphological comparisons. Instead, the latter species grouped with taxa in the dimitic genus Amyloporia with which it shares heterocytic nuclear behavior. A separation between specimens of Postia pelliculosa and Ryvardenia cretacea from either side of the Pacific (i.e. SE Australia/New Zealand and S Argentina/S Chile) suggests they could be considered different at the species level from a phylogenetic point of view.

Molecular phylogenetics of the Gloeophyllales and relative ages of clades of Agaricomycotina producing a brown rot

The Gloeophyllales is a recently described order of Agaricomycotina containing a morphologically diverse array of polypores (Gloeophyllum), agarics (Neolentinus, Heliocybe) and resupinate fungi (Veluti-Veluticeps, Boreostereum, Chaetodermella), most of which have been demonstrated to produce a brown-rot mode of wood decay and are found preferentially on coniferous substrates. Multiple phylogenetic studies have included taxa of Gloeophyllales, but none have sampled the order thoroughly, and so far only ribosomal RNA genes have been used. Consequently the limits and higher level placement of the Gloeophyllales are obscure. We obtained sequence data for three protein-coding genes (rpb2, atp6, tef1) and three rRNA regions (nuc-ssu, nuc-lsu, 5.8S) in 19 species of Gloeophyllales representing seven genera and analyzed them together with a diverse set of Agaricomycotina, emphasizing Polyporales. Boreostereum, which is suspected to produce a white rot, is the sister group of the rest of the Gloeophyllales, all of which produce a brown rot. Gloeophyllum contains at least two independent clades, one of which might correspond to the genus Osmoporus. White rot and resupinate fruiting bodies appear to be plesiomorphic in Gloeophyllales. Relaxed molecular clock analyses suggest that the Gloeophyllales arose in the Cretaceous, after the origin of Pinaceae.

Phylogenetic analysis of Antrodia species and Antrodia camphorata inferred from internal transcribed spacer region

The species of Antrodia are one of the difficult-to-classify and obscure groups of poroid Aphyllophorales based on morphological appearance. However, it is becoming increasingly important to reliably identify the entire suite of Antrodia camphorata strains and Antrodia species due to the potential pharmaceutical value of their biologically active ingredients. In this study, the internal transcribed spacer (ITS) region of the ribosomal RNA gene (rDNA) was sequenced and phylogenetically analyzed in a number of Antrodia fungal species and strains. ITS amplicons from the Antrodia species tested ranged in size from 543 to 610 bp; the size of the ITS of A. camphorata strains ranged from 592 to 596 bp. The overall sizes of ITS2 and 5.8S ribosomal RNA gene of all A. camphorata strains tested in this study were shown to be 217 and 158 bp, respectively. A phylogenetic analysis of ITS data generated, which included sequences of 11 A. camphorata strains and nine other Antrodia species, showed three clearly distinct groups. Group 1 includes A. camphorata, Antrodia salmonea, and Antrodia carbinca strains. Within Group 2, Antrodia sinuosa and Antrodia xantha were clustered together. Group 3 contained Antrodia albida, A. heteromorpha, A. serialis, and A. malicola. The observed sequence diversity among ITS alleles provided an effective tool for differentiating strains of A. camphorata, A. salmonea, A. xantha, A. sinuosa, or A. serialis. Polymorphisms arising within the ITS1-5.8S-ITS2 region can provide practical markers for establishing a foundation for the further expansion of an ITS sequence database of medically important fungi.