Prevalence and dynamics of ribosomal DNA micro-heterogeneity are linked to population history in two contrasting yeast species

James, Stephen A, West, Claire ORCID: https://orcid.org/0000-0001-7649-9600, Davey, Robert P, Dicks, Jo and Roberts, Ian N (2016) Prevalence and dynamics of ribosomal DNA micro-heterogeneity are linked to population history in two contrasting yeast species. Scientific Reports, 6. ISSN 2045-2322

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Abstract

Despite the considerable number and taxonomic breadth of past and current genome sequencing projects, many of which necessarily encompass the ribosomal DNA, detailed information on the prevalence and evolutionary significance of sequence variation in this ubiquitous genomic region are severely lacking. Here, we attempt to address this issue in two closely related yet contrasting yeast species, the baker's yeast Saccharomyces cerevisiae and the wild yeast Saccharomyces paradoxus. By drawing on existing datasets from the Saccharomyces Genome Resequencing Project, we identify a rich seam of ribosomal DNA sequence variation, characterising 1,068 and 970 polymorphisms in 34 S. cerevisiae and 26 S. paradoxus strains respectively. We discover the two species sets exhibit distinct mutational profiles. Furthermore, we show for the first time that unresolved rDNA sequence variation resulting from imperfect concerted evolution of the ribosomal DNA region follows a U-shaped allele frequency distribution in each species, similar to loci that evolve under non-concerted mechanisms but arising through rather different evolutionary processes. Finally, we link differences between the shapes of these allele frequency distributions to the two species' contrasting population histories.

Item Type:	Article
Additional Information:	This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Uncontrolled Keywords:	fungal evolution,molecular evolution,genome informatics
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Population Health
Depositing User:	Pure Connector
Date Deposited:	24 Sep 2016 00:42
Last Modified:	06 Jun 2024 14:56
URI:	https://ueaeprints.uea.ac.uk/id/eprint/60190
DOI:	10.1038/srep28555

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