Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1a a, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.Key Words-Chytridiomycota; Fungi; Microsporidia; molecular phylogeny; nSSU rDNA; RPB1; Zygomycota J. Gen. Appl. Microbiol., 51, 267-276 (2005) Invited Review * Present address, and address reprint requests to: Dr. Junta Sugiyama, TechnoSuruga Co., Ltd. (formerly NCIMB Japan), Tokyo Office, Ogawamachi Kita Bldg. 4F, 1-8-3 Kanda Ogawamachi, Chiyoda-ku, Tokyo 101-0052, Japan. E-mail: jsugiyam@tecsrg.co.jp basal fungal phyla as suggested by accumulating molecular phylogenetic studies, especially emphasizing supra-ordinal relationships.
Non-monophyletic nature of ChytridiomycotaCurrently, the Chytridiomycota contains five orders: the Blastocladiales, Chytridiales, Neocallimastigales, Monoblepharidales, and Spizellomycetales (Hawksworth et al., 1995). This classification scheme is based primarily on zoospore ultrastructure (Barr, 1990). Results of molecular phylogenetic analyses of rDNA sequences suggest that the Spizellomycetales, Neocallimastigales, and Monoblepharidales are monophyletic (James et al., 2000;Li and Heath, 1992), supporting the validity of the proposed chytrid higher-level taxonomy. The Chytridiales, however, appears to be polyphyletic as are some chytrid genera (e.g., Rhizophydium; James et al., 2000). rDNA analyses, however, have not resolved the interordinal relationships of the Chytridiomycota, which might be due to the lack of phylogenetic signal within rDNA sequences (James et al., 2000). Although taxon sampling has been limited, analysis of complete mitochondrial genome sequences has provided a clearer framework of chytridiomycete phylogeny. This analysis suggests that the Monoblepharidales branched earlier than a well-supported Chytridiales-Spizellomycetales lineage (Bullerwell et al., 2003a). In the mtDNA analysis, the phylogenetic position of the Blastocladiales is not statistically re- Barr (1980) a This classification sche...