Diversity Arrays Technology (DArT) for Pan-Genomic Evolutionary Studies of Non-Model Organisms

Background: High-throughput tools for pan-genomic study, especially the DNA microarray platform, have sparked a remarkable increase in data production and enabled a shift in the scale at which biological investigation is possible. The use of microarrays to examine evolutionary relationships and processes, however, is predominantly restricted to model or near-model organisms. Methodology/Principal Findings: This study explores the utility of Diversity Arrays Technology (DArT) in evolutionary studies of non-model organisms. DArT is a hybridization-based genotyping method that uses microarray technology to identify and type DNA polymorphism. Theoretically applicable to any organism (even one for which no prior genetic data are available), DArT has not yet been explored in exclusively wild sample sets, nor extensively examined in a phylogenetic framework. DArT recovered 1349 markers of largely low copy-number loci in two lineages of seed-free land plants: the diploid fern Asplenium viride and the haploid moss Garovaglia elegans. Direct sequencing of 148 of these DArT markers identified 30 putative loci including four routinely sequenced for evolutionary studies in plants. Phylogenetic analyses of DArT genotypes reveal phylogeographic and substrate specificity patterns in A. viride, a lack of phylogeographic pattern in Australian G. elegans, and additive variation in hybrid or mixed samples. Conclusions/Significance: These results enable methodological recommendations including procedures for detecting and analysing DArT markers tailored specifically to evolutionary investigations and practical factors informing the decision to use DArT, and raise evolutionary hypotheses concerning substrate specificity and biogeographic patterns. Thus DArT is a demonstrably valuable addition to the set of existing molecular approaches used to infer biological phenomena such as adaptive radiations, population dynamics, hybridization, introgression, ecological differentiation and phylogeography

The Nucleotide-sequence of the Small Ribosomal-subunit Rna of the Yeast Candida-albicans and the Evolutionary Position of the Fungi Among the Eukaryotes

Up to now the small ribosomal subunit RNA sequences of about 50 different eukaryotes have been published, of which only three belong to the fungi. We determined the complete srRNA sequence of the imperfect yeast Candida albicans. The sequence is 1788 nucleotides long and was determined at the DNA level using the dideoxy method with a set of primers specific for conserved sequences of small ribosomal subunit RNA. An evolutionary tree, comprising 58 organisms including C. albicans, was constructed. This tree shows a number of early diverging lineages such as a diplomonad, a microsporidian, an amoeba, slime molds, an euglenoid, kinetoplastids and sporozoans. Next within a relatively short time interval there is a radiation into a number of clusters composed of ciliates, metazoa, fungi and green plants. C. albicans was previously classified in the artificial taxon of imperfect fungi. The evolutionary tree presented in this paper clearly shows C. albicans to belong to the ascomycetous yeasts. An additional aim of this study was the refinement of the srRNA secondary structure model. Although the outline of this model is now well established, no consensus model exists in certain eukaryote-specific areas of high structural variability. The srRNA sequence of xC. albicans was fitted into the secondary structure model and the existence of a pseudoknot is proposed in one of these eukaryote-specific areas

Phylogenetic Analysis of 5 Medically Important Candida Species As Deduced On the Basis of Small Ribosomal-subunit Rna Sequences

The classification of species belonging to the genus Candida Berkhout is problematic. Therefore, we have determined the small ribosomal subunit RNA (srRNA) sequences of the type strains of three human pathogenic Candida species; Candida krusei, C. lusitaniae and C. tropicalis. The srRNA sequences were aligned with published eukaryotic srRNA sequences and evolutionary trees were inferred using a matrix optimization method. An evolutionary tree comprising all available eukaryotic srRNA sequences, including two other pathogenic Candida species, C. albicans and C. glabrata, showed that the yeasts diverage rather late in the course of eukaryote evolution, namely at the same depth as green plants, ciliates and some smaller taxa. The cluster of the higher fungi consists of 10 ascomycetes and ascomycete-like species with the first branches leading to Neurospora crassa, Pneumocystis carinii, Candida lusitaniae and C. krusei, in that order. Next there is a dichotomous divergence leading to a group consisting of Torulaspora delbrueckii, Saccharomyces cerevisiae, C. glabrata and Kluyveromyces lactis and a smaller group comprising C. tropicalis and C. albicans. The divergence pattern obtained on the basis of srRNA sequence data is also compared to various other chemotaxonomic data