Y. Van de Peer

Phylogenetic analysis of ten black yeast species using nuclear small subunit rRNA gene sequences

The nuclear small subunit rRNA genes of authentic strains of the black yeastsExophiala dermatitidis, Wangiella dermatitidis, Sarcinomyces phaeomuriformis, Capronia mansonii, Nadsoniella nigra var.hesuelica, Phaeoannellomyces elegans, Phaeococcomyces exophialae, Exophiala jeanselmei var.jeanselmei andE. castellanii were amplified by PCR and directly sequenced. A putative secondary structure of the nuclear small subunit rRNA ofExophiala dermatitidis was predicted from the sequence data. Alignment with corresponding sequences fromNeurospora crassa andAureobasidium pullulans was performed and a phylogenetic tree was constructed using the neighbor-joining method. The obtained topology of the tree was confirmed by bootstrap analysis. Based upon this analysis all fungi studied formed a well-supported monophyletic group clustering as a sister group to one group of the Plectomycetes (Trichocomaceae and Onygenales). The analysis confirmed the close relationship postulated betweenExophiala dermatitidis, Wangiella dermatitidis andSarcinomyces phaeomuriformis. This monophyletic clade also contains the teleomorph speciesCapronia mansonii thus confirming the concept of a teleomorph connection of the genusExophiala to a member of the Herpotrichiellaceae. However,Exophiala castellanii did not belong to this clade. Therefore, this species is not the anamorph ofCapronia mansonii as it was postulated.

5S ribosomal ribonucleic acid sequences in Bacteroides and Fusobacterium: evolutionary relationships within these genera and among eubacteria in general

The 5S ribosomal ribonucleic acid (rRNA) sequences were determined for Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides capillosus, Bacteroides veroralis, Porphyromonas gingivalis, Anaerorhabdus furcosus, Fusobacterium nucleatum, Fusobacterium mortiferum, and Fusobacterium varium. A dendrogram constructed by a clustering algorithm from these sequences, which were aligned with all other hitherto known eubacterial 5S rRNA sequences, showed differences as well as similarities with respect to results derived from 16S rRNA analyses. In the 5S rRNA dendrogram, Bacteroides clustered together with Cytophaga and Fusobacterium, as in 16S rRNA analyses. Intraphylum relationships deduced from 5S rRNAs suggested that Bacteroides is specifically related to Cytophaga rather than to Fusobacterium, as was suggested by 16S rRNA analyses. Previous taxonomic considerations concerning the genus Bacteroides, based on biochemical and physiological data, were confirmed by the 5S rRNA sequence analysis.

Inferring Eubacterial Phylogeny from SS Ribosomal RNA Structure Analysis

Based on analysis of 165 ribosomal RNA oligonucleotide catalogs of about 400 eubacterial species Woese et al. (1985) made a proposal to divide the eubacterial primary kingdom into 10 major phyla. Two years later with over 500 species characterized and with more than 50 nearly complete sequences, the earlier conclusions were significantly refined and extended (Woese, 1967). The picture obtained is substantially different from the classification system based on morphological and metabolic data In the 8th edition of Bergey’s Manual (Buchanan and Gibbons, 1974). Investigation of another universally occurring molecule such as 55 ribosomal RNA ought to help clarify this matter. So far about 160 eubacterial 55 RNA sequences have been published, but the distribution over the 10 major phyla is very uneven as can be seen from Table 1. For example, in the phylum of purple bacteria and relatives almost 80 species have been examined, whereas in the phylum of green sulfur bacteria, along with 4 other major phyla, no representatives whatsoever have been investigated. It is our aim to Lessen these gaps, in order to make possible a comparison with the view based on 165 ribosomal RNA. Rt present, progress has been made for several phyla, while work has started on others (Table 1). In this paper we present a tree derived from the weighted pairwise grouping of over 180 eubacterial 55 RNA sequences including several sequences of formerly undocumented phyla.