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Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex

Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination pro...

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Autores principales: Chand Dakal, Tikam, Giudici, Paolo, Solieri, Lisa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976873/
https://www.ncbi.nlm.nih.gov/pubmed/27501051
http://dx.doi.org/10.1371/journal.pone.0160744
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author Chand Dakal, Tikam
Giudici, Paolo
Solieri, Lisa
author_facet Chand Dakal, Tikam
Giudici, Paolo
Solieri, Lisa
author_sort Chand Dakal, Tikam
collection PubMed
description Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5’ end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding.
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spelling pubmed-49768732016-08-25 Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex Chand Dakal, Tikam Giudici, Paolo Solieri, Lisa PLoS One Research Article Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5’ end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding. Public Library of Science 2016-08-08 /pmc/articles/PMC4976873/ /pubmed/27501051 http://dx.doi.org/10.1371/journal.pone.0160744 Text en © 2016 Chand Dakal et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Chand Dakal, Tikam
Giudici, Paolo
Solieri, Lisa
Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex
title Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex
title_full Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex
title_fullStr Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex
title_full_unstemmed Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex
title_short Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex
title_sort contrasting patterns of rdna homogenization within the zygosaccharomyces rouxii species complex
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976873/
https://www.ncbi.nlm.nih.gov/pubmed/27501051
http://dx.doi.org/10.1371/journal.pone.0160744
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