A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations

Sharma, D; Hermann-Le Denmat, S; Matzke, NJ; Hannan, K; Hannan, RD; O&#39;Sullivan, JM; Ganley, ARD

Author(s): Sharma, D; Hermann-Le Denmat, S; Matzke, NJ; Hannan, K; Hannan, RD; O'Sullivan, JM; Ganley, ARD;
Details: Publication Year 2022-07,Volume 114,Issue #4,Page 110430
Journal Title: Genomics
Publication Type: Research article
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.
Keywords: DNA Copy Number Variations; DNA, Ribosomal/genetics; RNA, Ribosomal/genetics; *Saccharomyces cerevisiae/genetics; *Saccharomyces cerevisiae Proteins/genetics; Bioinformatics method; Copy number; Ribosomal DNA; Saccharomyces cerevisiae; Sequence read coverage; Tandem repeats
Department(s): Laboratory Research
PubMed ID: 35830947
Publisher's Version: https://doi.org/10.1016/j.ygeno.2022.110430
Open Access at Publisher's Site: https://doi.org/10.1016/j.ygeno.2022.110430
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2025-04-04 12:33:49

Last Modified: 2025-04-04 12:35:17