Molecular phylogeny of Trametes and related genera based on internal transcribed spacer (ITS) and nearly complete mitochondrial small subunit ribosomal DNA (mt SSU rDNA) sequences

Abstract

Some species of Trametes and their related genera are so similar in microstructure characteristics that it is difficult to identify and separate them by traditional taxonomy. In this study, we elucidated relationships among Trametes through comparison of the nuclear internal transcribed spacer (ITS) and the nearly complete mitochondrial small subunit ribosomal DNA (mt SSU rDNA) sequences. Finally, phylogenetic trees were built. Phylogenetic analysis of the ITS and mt SSU rDNA sequences showed consensus results; most of the Trametes species clustered within a single clade and formed a main clade together with species of Pycnoporus. The genera Coriolopsis and Cerrena could be separated clearly from the main clade. The determination of secondary structure of the ITS1 and ITS2 domains of the representative species indicated that the conservative structure of some helices might be useful for resolving the phylogenetic relationship among some related species. The secondary structures of the variable domains V4 and V6 in mt SSU rDNA were also determined in this study. We found that both the conserved domains and the variable  domains all contained informative sites which could significantly contribute to resolving the phylogenetic relationships within the Trametes group. The length and sequences of the V4 and V6 domains were found to be constant within a species, but very different among species with significant inter-species variations. The major advantage of these species-specific markers is that we only need to study one isolate from one species to determine their phylogenetic position. Secondary structure information of the V4 and V6 domains is found to be a useful marker to resolve phylogenetic problems. Based on our study, we considered that the genus Pycnoporus had a close relationship with Trametes; Trametes trogii was grouped with Coriolopsis gallica, indicating that it might belong to Coriolopsis; Cerrena, as a separate genus, was placed far away from Trametes.

Key words: Trametes, internal transcribed spacer (ITS) sequences, nearly complete mitochondrial small subunit ribosomal DNA (mt SSU rDNA), secondary structure, phylogenetic analysis.