title: Ribosomal DNA sequence heterogeneity reflects intraspecies phylogenies and predicts genome structure in two contrasting yeast species.
abstract: The ribosomal RNA encapsulates a wealth of evolutionary information, including genetic variation that can be used to discriminate between organisms at a wide range of taxonomic levels. For example, the prokaryotic 16S rDNA sequence is very widely used both in phylogenetic studies and as a marker in metagenomic surveys and the internal transcribed spacer region, frequently used in plant phylogenetics, is now recognized as a fungal DNA barcode. However, this widespread use does not escape criticism, principally due to issues such as difficulties in classification of paralogous versus orthologous rDNA units and intragenomic variation, both of which may be significant barriers to accurate phylogenetic inference. We recently analyzed data sets from the Saccharomyces Genome Resequencing Project, characterizing rDNA sequence variation within multiple strains of the baker's yeast Saccharomyces cerevisiae and its nearest wild relative Saccharomyces paradoxus in unprecedented detail. Notably, both species possess single locus rDNA systems. Here, we use these new variation datasets to assess whether a more detailed characterization of the rDNA locus can alleviate the second of these phylogenetic issues, sequence heterogeneity, while controlling for the first. We demonstrate that a strong phylogenetic signal exists within both datasets and illustrate how they can be used, with existing methodology, to estimate intraspecies phylogenies of yeast strains consistent with those derived from whole-genome approaches. We also describe the use of partial Single Nucleotide Polymorphisms, a type of sequence variation found only in repetitive genomic regions, in identifying key evolutionary features such as genome hybridization events and show their consistency with whole-genome Structure analyses. We conclude that our approach can transform rDNA sequence heterogeneity from a problem to a useful source of evolutionary information, enabling the estimation of highly accurate phylogenies of closely related organisms, and discuss how it could be extended to future studies of multilocus rDNA systems. [concerted evolution; genome hydridisation; phylogenetic analysis; ribosomal DNA; whole genome sequencing; yeast].
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK; Bioinformatics, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Claire
authors.initials: C
authors.lastname: West
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK; Bioinformatics, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: James
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK; Bioinformatics, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UKNational Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK; Bioinformatics, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Robert P
authors.initials: RP
authors.lastname: Davey
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK; Bioinformatics, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UKNational Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK; Bioinformatics, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Jo
authors.initials: J
authors.lastname: Dicks
authors.affiliation: National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK; Bioinformatics, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK; Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK ian.roberts@ifr.ac.uk.
authors.forename: Ian N
authors.initials: IN
authors.lastname: Roberts
mesh_terms: D004271:DNA, Fungal / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics*; D018740:Genetic Heterogeneity; D014644:Genetic Variation; D016681:Genome, Fungal / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012440:Saccharomyces / Q000145:classification* / Q000235:genetics*
chemical_list: D004271:DNA, Fungal; D004275:DNA, Ribosomal