Junta Sugiyama

The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits

We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Is Penicillium monophyletic? An evaluation of phylogeny in the family Trichocomaceae from 18S, 5.8S and ITS ribosomal DNA sequence data.

AbstractUsing ribosomal DNA sequences from 17 fungi, we evaluated the monophylly of Penicillium and the phylogeny in the ascomycete family Trichocomaceae (= Eurotiaceae). We determined the 5.8S and...

Molecular phylogeny of Zygomycota based on EF-1α and RPB1 sequences: limitations and utility of alternative markers to rDNA

Earlier molecular phylogenetic analyses based on nuclear small subunit ribosomal DNA (nSSU rDNA) suggest that the Zygomycota are polyphyletic within the Chytridiomycota. However, these analyses failed to resolve almost all interordinal relationships among basal fungi (Chytridiomycota and Zygomycota), due to lack of sufficient characters within the nSSU rDNA. To further elucidate the higher-level phylogeny of Zygomycota, we have sequenced partial RPB1 (DNA dependent RNA polymerase II largest subunit) and EF-1alpha (translation elongation factor 1 alpha) genes from 10 and 3 zygomycete fungi, respectively. Independent molecular phylogenetic analyses were performed based on each sequence by distance and maximum likelihood methods. Although deep phylogenetic relationships among basal fungi still remain poorly resolved using either gene, the RPB1-based phylogeny identified a novel monophyletic clade consisting of the Dimargaritales, Harpellales, and Kickxellales. This result suggests that regularly formed septa (cross walls that divide hyphae into segments) with a lenticular cavity are plesiomorphic for this clade, and indicates the importance of septal pore ultrastructure in zygomycete phylogeny. In addition, a peculiar mucoralean genus Mortierella, which was considered to be distantly related to the other Mucorales based on previous nSSU rDNA analyses, was resolved as the basal most divergence within the Mucorales, consistent with traditional phenotypic-based taxonomy. Although the taxa included in our analysis are restricted, the monophyly of each order suggested by nSSU rDNA phylogeny is supported by the present RPB1-based analysis. These results support the potential use of RPB1 as an alternative marker for fungal phylogenetic studies. Conversely, the overall fungal phylogeny based on EF-1alpha sequence is poorly resolved. A comparison of numbers of observed substitutions versus inferred substitutions within EF-1alpha indicates that this gene is much more saturated than RPB1. This result suggests that the EF-1alpha gene is unsuitable for resolving higher-level phylogenetic relationships within the Fungi.

Archiascomycetes : detection of a major new lineage within the Ascomycota

For phylogenetic analysis of the higher fungi, we sequenced the nuclear small subunit rRNA (18S rRNA) gene fromTaphrina populina, the type species of the genusTaphrina, andProtomyces lactucae-debilis. The molecular phylogeny inferred from these 2 sequences and 75 sequences from the DNA data bank divided the Ascomycota into three major lineages: the hemiascomycetes, the euascomycetes, and the archiascomycetes, newly described herein. The former two lineages are monophyletic, whereas the archiascomycetes, which originated first and are comprised ofTaphrina, Protomyces, Saitoella, Schizosaccharomyces, andPneumocystis, may not be monophyletic. Among the archiascomycetes, theTaphrina/Protomyces branch is monophyletic. Confirmation of the archiascomycetes as a monophyletic taxonomic class will require comparison of additional genetically defined characters.

Phylogenetic divergence of the entomophthoralean fungi: Evidence from nuclear 18S ribosomal RNA gene sequences

To analyze the phylogeny and molecular evolution of the entomophthoralean fungi, we deter? mined the small subunit nuclear ribosomal RNA gene sequences for four representative species of the En- tomophthorales and the trichomycete Smittium culi- setae (Harpellales) in the Zygomycota. Ten published reference sequences were added to this analysis. The phylogeny, inferred from the aligned 1480 positions and using the choanoflagellate Diaphanoeca grandis (Choanoflagellida) as an outgroup, divided seven zyg- omycete species into four clusters. The four species in the Entomophthorales were placed in two clusters, i.e., Basidiobolus ranarum in one cluster containing Chy? tridium, Spizellomyces and Neocallimastix, and the re- maining three species Conidiobolus coronatus, Entomo- phthora muscae, and Zoophthora radicans in another clus? ter containing Mucor. Glomus etunicatum is basal to ascomycetes and basidiomycetes, and Smittium culi- setae was placed close to the divergence of Entomo?

Automated sequencing of PCR-amplified 16S rDNA on ‘Hydrolink’ gels

Abstract A commercially available high-performance gel solution, ‘Hydrolink Long Ranger’, was used for direct automated sequencing of PCR-amplified double-stranded 16S rDNA. The 1.5 kb rDNA fragments were amplified directly from bacterial cell lysates and sequenced by using Tth DNA polymerase with the linear PCR sequencing protocol. Sequencing reactions were analyzed on an automated laser fluorescent DNA sequencer with Hydrolink gels compared to standard polyacrylamide gels. Automated Hydrolink gel electrophoresis allowed high sequencing speeds and resulted in a marked increase in readable sequences. Upon this electrophoresis, an average of 540 bases of nucleotides was resolved by automated reading in a single sequencing run, and the resolved sequence was extended up to 600 to 700 bases by manual correction of the errors and ambiguities. This sequencing strategy is useful for the analysis of long sequences of more than 500 bases and makes it possible to obtain entire 16S rDNA sequence data for several strains within 2 days, using an automated DNA sequencer with the one dye detection system.

Relatedness, phylogeny, and evolution of the fungi

Recent advances in fungal systematics are reviewed in relation to our previous studies. The usefulness of the integrated analysis of genotypic (especially 18S rRNA gene sequence comparisons) and phenotypic (especially ultrastructural and chemotaxonomic data) characters has been emphasized for the major groups and selected taxa of the fungi, and the impact to fungal systematics and evolution is discussed. Our noteworthy studies and findings are: 1) polyphyly of the chytridiomycetes and zygomycetes, 2) phylogenetic origin of the entomophthoralean fungi includingBasidiobolus, 3) detection of a major new lineage “Archiascomycetes,” comprisingTaphrina, Protomyces andSaitoella, Schizosaccharomyces, andPneumocystis, within the Ascomycota, and its phylogenetic and evolutionary significance, 4) polyphyletic origins of species in the anamorphic genusGeosmithia, and 5) phylogenetic placement ofMixia osmundae, species correctly and incorrectly assigned to the genusTaphrina, and basidiomyceotus yeasts. The newest 18S rDNA sequence-based neighbor-joining trees of the Ascomycota are demonstrated.

A taxonomic study of Antarctic yeasts.

SUMMARYYeast species isolated from samples of water, soil, algae, mosses, penguin dung, etc., from Lakes Vanda, Bonney, Miers, and Fryxell in the Dry Valley region of South Victoria Land, and from ...

Polyphyletic origins of species of the anamorphic genus Geosmithia and the relationships of the cleistothecial genera: Evidence from 18S, 5S and 28S rDNA sequence analyses

The anamorphic genus Geosmithia, with the type species G. lavendula, includes species strictly lacking a teleomorph as well as species associated with the teleomorphs Talaromyces and Chromocleista. Our 18S rDNA sequence-based tree, inferred from 1586 alignable sites from 57 selected taxa within the Ascomycota and using two basidiomycetes as out- groups, clearly demonstrates that Geosmithia is a poly- phyletic taxon with evolutionary affinities to at least three groups of the euascomycete lineage within the

The Higher Fungus Protomyces inouyei has Two Group I Introns in the 18S rRNA Gene

The nucleotide sequence of the small-subunit rRNA (18S rRNA) coding gene in the higher fungus Protomyces inouyei contains two group I introns. This is the first report of two group I introns in the 18S rRNA coding region. Based on the comparison of the two introns of Protomyces inouyei with those of the green alga Ankistrodesmus stipitatus, and the other two higher fungi Pneumocystis carinii and Ustilago maydis, the Protomyces introns are group I introns containing the highly conserved sequence elements P, Q, R, and S. Intron A of Protomyces inouyei is located in the same position as in Pneumocystis carinii while intron B shares the location with that in Ustilago maydis. The phylogenetic relationships strongly support horizontal transfer of these group I introns.