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Varying strength of selection contributes to the intragenomic diversity of rRNA genes

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  • Daniel Sultanov

    (New York University)

  • Andreas Hochwagen

    (New York University)

Abstract

Ribosome biogenesis in eukaryotes is supported by hundreds of ribosomal RNA (rRNA) gene copies that are encoded in the ribosomal DNA (rDNA). The multiple copies of rRNA genes are thought to have low sequence diversity within one species. Here, we present species-wide rDNA sequence analysis in Saccharomyces cerevisiae that challenges this view. We show that rDNA copies in this yeast are heterogeneous, both among and within isolates, and that many variants avoided fixation or elimination over evolutionary time. The sequence diversity landscape across the rDNA shows clear functional stratification, suggesting different copy-number thresholds for selection that contribute to rDNA diversity. Notably, nucleotide variants in the most conserved rDNA regions are sufficiently deleterious to exhibit signatures of purifying selection even when present in only a small fraction of rRNA gene copies. Our results portray a complex evolutionary landscape that shapes rDNA sequence diversity within a single species and reveal unexpectedly strong purifying selection of multi-copy genes.

Suggested Citation

  • Daniel Sultanov & Andreas Hochwagen, 2022. "Varying strength of selection contributes to the intragenomic diversity of rRNA genes," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34989-w
    DOI: 10.1038/s41467-022-34989-w
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    2. Jinfan Wang & Jing Wang & Byung-Sik Shin & Joo-Ran Kim & Thomas E. Dever & Joseph D. Puglisi & Israel S. Fernández, 2020. "Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex," Nature Communications, Nature, vol. 11(1), pages 1-8, December.
    3. Jason Sims & Giovanni Sestini & Christiane Elgert & Arndt von Haeseler & Peter Schlögelhofer, 2021. "Sequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
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