5S Ribosomal RNA Sequences from Zygomycotina and Evolutionary Implications

An eight-gene molecular phylogeny of the Kickxellomycotina, including the first phylogenetic placement of Asellariales

Kickxellomycotina is a recently described subphylum encompassing four zygomycete orders (Asellariales, Dimargaritales, Harpellales, Kickxellales). These fungi are united by the formation of disciform septal pores containing lenticular plugs. Morphological diversification and life history evolution has made the relationships within and among the four orders difficult to resolve on those grounds alone. Here we infer the phylogeny of the Kickxellomycotina based on an eight-gene supermatrix including both ribosomal rDNA (18S, 28S, 5.8S) and protein sequences (MCM7, TSR1, RPB1, RPB2, β-tubulin). The results of this study demonstrate that Kickxellomycotina is monophyletic and related to members of the Zoopagomycotina. Eight unique clades are distinguished in the Kickxellomycotina, including the four defined orders (Asellariales, Dimargaritales, Harpellales, Kickxellales) as well as four genera previously placed within two of these orders (Barbatospora, Orphella, Ramicandelaber, Spiromyces). Dimargaritales and Ramicandelaber are the earliest diverging members of the subphylum, although the relationship between these taxa remains uncertain. The remaining six clades form a monophyletic group, with Barbatospora diverging first. The next split divides the remaining members of the subphylum into two subclades: (i) Asellariales and Harpellales and (ii) Kickxellales, Orphella and Spiromyces. Estimation of ancestral states for four potentially informative morphological and ecological characters reveals that arthropod endosymbiosis might have been an important factor in the early evolution of the Kickxellomycotina.

Eccrinales (Trichomycetes) are not fungi, but a clade of protists at the early divergence of animals and fungi

The morphologically diverse orders Eccrinales and Amoebidiales have been considered members of the fungal class Trichomycetes (Zygomycota) for the last 50 years. These organisms either inhabit the gut or are ectocommensals on the exoskeleton of a wide range of arthropods--Crustacea, Insecta, and Diplopoda--in varied habitats. The taxonomy of both orders is based on a few micromorphological characters. One species, Amoebidium parasiticum, has been axenically cultured and this has permitted several biochemical and phylogenetic analyses. As a consequence, the order Amoebidiales has been removed from the Trichomycetes and placed in the class Mesomycetozoea. An affinity between Eccrinales and Amoebidiales was first suggested when the class Trichomycetes was erected by Duboscq et al. [Arch. Zool. Exp. Gen. 86 (1948) 29]. Subsequently, molecular markers have been developed to study the relationship of these orders to other groups. Ribosomal gene (18S and 28S) sequence analyses generated by this study do not support a close association of these orders to the Trichomycetes or to other fungi. Rather, Eccrinales share a common ancestry with the Amoebidiales and belong to the protist class Mesomycetozoea, placed at the animal-fungi boundary.

Hyaloraphidium curvatum is not a green alga, but a lower fungus; Amoebidium parasiticum is not a fungus, but a member of the DRIPs

The unicellular heterotrophic protist Hyaloraphidium is classified with a family of green algae, the Ankistrodesmaceae. The only species that exists in pure culture and that is available for taxonomic studies is H. curvatum. Comparative 18S ribosomal RNA sequence analyses showed that H. curvatum belongs to the fungi rather than to the algae. Within the fungi, H. curvatum preferentially clustered with Chytridiomycetes. Unlike Chytridiomycetes, H. curvatum propagates by autosporulation, and the presence of flagella has never been reported. Transmission electron microscopy indicated that H. curvatum in some respects resembles Chytridiomycetes, but no elements of a flagellar apparatus were detected. The habitus of H. curvatum is unlike that of other fungi except the trichomycete Amoebidium parasiticum. The cell wall sugar composition of H. curvatum was unique, but to some extent resembled that of A. parasiticum. However, H. curvatum and A. parasiticum are not closely related to each other according to 18S rRNA sequence data. Moreover, A. parasiticum clustered with protistan animals, the Mesomycetozoa (DRIPs). Combined molecular, ultrastructural and chemical data do not allow assignment of H. curvatum to any recognized clade of fungi. This suggests that H. curvatum may represent an independent evolutionary lineage within the fungi.

Phylogenetic association of Pneumocystis carinii with the 'Rhizopoda/Myxomycota/Zygomycota group' indicated by comparison of 5S ribosomal RNA sequences

The cytoplasmic 5S ribosomal RNA (5S rRNA) sequence from Pneumocystis carinii was determined. A sequence comparison matrix of 382 eukaryote 5S rRNA sequences and an evolutionary tree were constructed to establish the phylogenetic position of Pneumocystis. The data suggest that Pneumocystis is associated with the Rhizopoda/Myxomycota/Zygomycota group (= 'Protista fungi') but not with common fungi, such as Ascomycota or Basidiomycota, nor with other protozoa.

Evolution of organisms and organelles as studied by comparative computer and biochemical analyses of ribosomal 5S RNA structure

The results documented in this publication demonstrate that for evolutionary studies the ribosomal 5S rRNA is a suitable object for such an investigation and that as many methods as possible should be consulted. In this study the results of biochemical and chemical experiments were combined with those of computer sequence analyses, and they revealed that these methods complement each other nicely. We are currently at a state at which we are able to well define the secondary structures of the 5S rRNAs for eubacteria, organelles, archaebacteria, and eukaryotes and we are even able to propose a secondary structure for a Ur-5S rRNA. It is also clear that in the future the present studies should be continued and extended in such a way that the tertiary structures of these molecules will become known.

5 S and 5.8 S ribosomal RNA sequences and protist phylogenetics

More than 100 5 S 5.8 S rRNA sequences from protists, including fungi, are known. Through a combination of quantitative treeing and special consideration of "signature' nucleotide combinations, the most significant phylogenetic implications of these data are emphasized. Also, limitations of the data for phylogenetic inferences are discussed and other significant data are brought to bear on the inferences obtained. 5 S sequences from red algae are seen as the most isolated among eukaryotics. A 5 S sequence lineage consisting of oomycetes, euglenoids, most protozoa, most slime molds and perhaps dinoflagellates and mesozoa is defined. Such a lineage is not evident from 5.8 S rRNA or cytochrome c sequence data. 5 S sequences from Ascomycota and Basidiomycota are consistent with the proposal that each is derived from a mycelial form with a haploid yeast phase and simple septal pores, probably most resembling present Taphrinales. 5 S sequences from Chytridiomycota and Zygomycota are not clearly distinct from each other and suggest that a major lineage radiation occurred in the early history of each. Qualitative biochemical data clearly supports a dichotomy between an Ascomycota-Basidiomycota lineage and a Zygomycota-Chytridiomycota lineage.