A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations |
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| Affiliation: | 1. School of Biological Sciences, University of Auckland, Auckland, New Zealand;2. Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France;3. ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, ACT 2601, Australia;4. Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia;5. Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia;6. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia;7. Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3168, Australia;8. Liggins Institute, University of Auckland, Auckland, New Zealand;9. Maurice Wilkins Center, University of Auckland, New Zealand;10. MRC Lifecourse Unit, University of Southampton, United Kingdom;11. Brain Research New Zealand, The University of Auckland, Auckland, New Zealand |
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| Abstract: | Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties in quantifying copy number mean we lack a comprehensive understanding of how copy number evolves and the consequences. Here we present a genomic sequence read approach to estimate rDNA copy number based on modal coverage to help overcome limitations with existing mean coverage-based approaches. We validated our method using Saccharomyces cerevisiae strains with known rDNA copy numbers. Application of our pipeline to a global sample of S. cerevisiae isolates showed that different populations have different rDNA copy numbers. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations. |
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