Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics

Abstract

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...

A higher-level phylogenetic classification of the Fungi

“…These groups have long been recognized to be polyphyletic, based on analyses of rRNA, tef1, and rpb1 (James et al 2000;Nagahama et al 1995;Tanabe et al 2004Tanabe et al , 2005. The recent multilocus analyses of James et al (2006) and others now provide the sampling, resolution, and support necessary to structure new classifications of these early-diverging groups, although significant questions remain.…”

Temporal variation of the small eukaryotic community in two freshwater lakes: emphasis on zoosporic fungi

“…The LSU gene has been widely used in the taxonomy of lower fungi (i.e. zoosporic fungi) (Tanabe et al 2005, Letcher et al 2005, 2006, 2008a,b,c, James et al 2006a,b, Hibbett et al 2007, Mozley-Standridge et al 2009, Wakefield et al 2010. Thus, because of the greater availability of LSU sequences, we expected our retrieved sequences to primarily fall into described taxa of zoosporic fungi.…”

The Evolution of Sex: a Perspective from the Fungal Kingdom

“…The recent Fungal Tree of Life project supports the Chytridiomycota and Zygomycota as early-diverged fungi (124,177), although the two lineages are not monophyletic (122,282). Animals and fungi evolved from a single-celled and flagellate ancestor, from which the choanoflagellate outgroup to the metazoans also descends (151).…”