Abstract
Although commonly regarded as nearly identical in sequence, 45S ribosomal RNA genes represent a massive source of genetic variation at different levels. Unfortunately, due to their repetitive nature and the difficulty to assemble their multiple copies in tandem, these important genomic elements remain largely unexplored in sequencing projects. Here, I describe how to exploit next generation sequencing data to estimate their copy number in an organism and detect true polymorphic sites within and among individuals. Furthermore, for species that carry multiple 45S ribosomal RNA gene clusters, I show how to make use of experimental populations to assign some of these variants to their cluster of origin.
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Acknowledgments
This work has been supported by a Human Frontiers Science Program (HFSP) Long-Term Fellowship (LT000819/2018-L) to FAR and by the Max Planck Society. I thank Sonja Kersten and Ilja Bezrukov for proofreading the manuscript and testing the code.
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Rabanal, F.A. (2022). Characterization of the Different Levels of Variation in 45S rRNA Genes. In: Lambing, C. (eds) Plant Gametogenesis. Methods in Molecular Biology, vol 2484. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2253-7_24
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DOI: https://doi.org/10.1007/978-1-0716-2253-7_24
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