Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales

Abstract

Phylogenetic relationships of Rhizoctonia fungi within the order Cantharellales were studied using sequence data from portions of the ribosomal DNA cluster regions ITS-LSU, rpb2, tef1, and atp6 for 50 taxa, and public sequence data from the rpb2 locus for 165 taxa. Data sets were analysed individually and combined using Maximum Parsimony, Maximum Likelihood, and Bayesian Phylogenetic Inference methods. All analyses supported the monophyly of the family Ceratobasidiaceae, which comprises the genera Ceratobasidium and Thanatephorus. Multi-locus analysis revealed 10 well-supported monophyletic groups that were consistent with previous separation into anastomosis groups based on hyphal fusion criteria. This analysis coupled with analyses of a larger sample of 165 rpb2 sequences of fungi in the Cantharellales supported a sister relationship between the Botryobasidiaceae and Ceratobasidiaceae and a sister relationship of the Tulasnellaceae with the rest of the Cantharellales. The inclusion of additional sequence data did not clarify incongruences observed in previous studies of Rhizoctonia fungi in the Cantharellales based on analyses of a single or multiple genes. The diversity of ecological and morphological characters associated with these fungi requires further investigation on character evolution for re-evaluating homologous and homoplasious characters.

Keywords: Fungal plant pathogens; Multi-locus phylogeny; Rhizoctonia anamorphs; Rhizoctonia solani.

Fig 1

Phylogenetic hypothesis of the Cantharellales based on nucleotide sequences of rpb2. The tree is a Bayesian 50% majority-rule consensus tree and produced from a data set of 165 sequences and 487 nucleotide characters. Only support values for main clades and the thanatephoroid clade within the Ceratobasidiaceae are shown. Posterior probabilities are indicated to the left, and ML bootstrap values to the right. Taxa marked in bold were those used in multi-locus analyses.

Fig 2

Hypotheses of inferred relationships of Rhizoctonia fungi obtained with: i) Maximum Parsimony (MP), ii) Maximum Likelihood (ML) and iii) Bayesian Phylogenetic Inference (BPI) for concatenated data set of four genomic regions (ITS-LSU, rpb2, tef1 and atp6). Taxa shaded in grey are the members of the family Ceratobasidiaceae. Nodes that collapsed in the strict consensus tree are marked with an asterisk. Scale bar for ML and BPI represents nucleotide substitution per site, and for MP the number of steps. Values for support above 80% for two of three metrics (MP bootstrap, ML bootstrap or PP) are shown as thick branches.

Fig 3

Phylogenetic relationships of Rhizoctonia fungi based on parsimony analysis of the concatenated data set of four genomic regions (ITS-LSU, rpb2, tef1 and atp6). Values for support above 80% for at least two metrics (MP bootstrap/ML bootstrap/PP) are reported along the branches. Roman numerals (I-X) indicate supported clades (>80%) with all three metrics. Circles below branches indicate concordance factors above 0.5.

Fig 4

ML phylogeny of the Cantharellales showing genomic support. Left tree shows internode certainty (IC and ICA values respectively). Right tree shows the number of genomic regions (ITS-LSU, rpb2, tef1, atp6) that support a specific clade. Numbers at the left are concordant genes, at right those that are in conflict.