Deep selection shapes the intragenomic diversity of rRNA genes

Abstract

Ribosome biogenesis in eukaryotes is supported by hundreds of ribosomal RNA (rRNA) gene copies that are encoded in the ribosomal DNA (rDNA) and are thought to undergo frequent sequence homogenization by concerted evolution. Here, we present species-wide rDNA sequence analysis in Saccharomyces cerevisiae that challenges this model of evolution. We show that rDNA copies in yeast are far from homogeneous, both among and within isolates, and that rapid sequence homogenization is unlikely because many variants avoided fixation or elimination over evolutionary time. Instead, the diversity landscape across the rDNA shows clear functional stratification, suggesting that different copy-number thresholds for selection shape rDNA diversity. Notably, variants in the most highly conserved rDNA elements are sufficiently deleterious to exhibit signatures of purifying selection even when present in only 1% of rRNA gene copies. Our results portray a complex selection landscape that shapes rDNA diversity within a single species and reveal unexpectedly deep purifying selection of multi-copy genes.

Competing Interest Statement

The authors have declared no competing interest.

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