Characterization of the Different Levels of Variation in 45S rRNA Genes

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 rema...

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Bibliographic Details
Published inMethods in molecular biology (Clifton, N.J.) Vol. 2484; p. 363
Main Author Rabanal, Fernando A
Format Journal Article
LanguageEnglish
Published United States 2022
Subjects
DNA, Ribosomal - genetics
Genes, rRNA
Humans
RNA, Ribosomal - genetics
45S rDNA
Copy number variation
Natural variation
Polymorphisms
Ribosomes
rRNA genes
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Summary: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.
ISSN:1940-6029
DOI:10.1007/978-1-0716-2253-7_24