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Intragenomic Variation and Evolution of the Internal Transcribed Spacer of the rRNA Operon in Bacteria

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Abstract

Variation in the internal transcribed spacer (ITS) of the rRNA (rrn) operon is increasingly used to infer population-level diversity in bacterial communities. However, intragenomic ITS variation may skew diversity estimates that do not correct for multiple rrn operons within a genome. This study characterizes variation in ITS length, tRNA composition, and intragenomic nucleotide divergence across 155 Bacteria genomes. On average, these genomes encode 4.8 rrn operons (range: 2–15) and contain 2.4 unique ITS length variants (range: 1–12) and 2.8 unique sequence variants (range: 1–12). ITS variation stems primarily from differences in tRNA gene composition, with ITS regions containing tRNA-Ala + tRNA-Ile (48% of sequences), tRNA-Ala or tRNA-Ile (10%), tRNA-Glu (11%), other tRNAs (3%), or no tRNA genes (27%). Intragenomic divergence among paralogous ITS sequences grouped by tRNA composition ranges from 0% to 12.11% (mean: 0.94%). Low divergence values indicate extensive homogenization among ITS copies. In 78% of alignments, divergence is <1%, with 54% showing zero variation and 81% containing at least two identical sequences. ITS homogenization occurs over relatively long sequence tracts, frequently spanning the entire ITS, and is largely independent of the distance (basepairs) between operons. This study underscores the potential contribution of interoperon ITS variation to bacterial microdiversity studies, as well as unequivocally demonstrates the pervasiveness of concerted evolution in the rrn gene family.

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Acknowledgments

We thank Rob Young, Scott Edwards, and members of the Cavanaugh lab for their critical comments and support during the preparation of the manuscript. This work was supported by National Science Foundation Grants EF-0412205 and OCE-0453901 awarded to C. Cavanaugh and by the Genetics and Genomics Training Program (GGT) at Harvard University.

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  1. Department of Organismic and Evolutionary Biology, Harvard University, The Biological Laboratories, 16 Divinity Avenue, Cambridge, MA, 02138, USA

    Frank J. Stewart & Colleen M. Cavanaugh

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Correspondence to Colleen M. Cavanaugh.

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Stewart, F.J., Cavanaugh, C.M. Intragenomic Variation and Evolution of the Internal Transcribed Spacer of the rRNA Operon in Bacteria. J Mol Evol 65, 44–67 (2007). https://doi.org/10.1007/s00239-006-0235-3

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