Integrative rDNAomics—Importance of the Oldest Repetitive Fraction of the Eukaryote Genome

Abstract

Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context.

High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes

“…The other classic tandem array sequences that are of great interest but extremely difficult to assemble are the ribosomal DNA (rDNA) clusters with hundreds of thousands of copies in the genome. This is evidenced by the fact that rDNAs have been mapped for their locations in over 500 fish species, but are only studied for their partial genomic sequences in three species [43]. Eukaryotic rRNA genes are divided into two classes of 45S (corresponding to the nucleolar organizer regions, NORs) and 5S rRNA genes.…”

Structural Variation of the X Chromosome Heterochromatin in the Anopheles gambiae Complex

“…In humans, the number of rDNA repeats can vary from 250 to 670 copies per diploid genome [86], and the changes in rDNA copy number can affect genome-wide gene expression [87]. Natural variation in rDNA and heterochromatin may contribute to genome evolution, formation of reproductive barriers, and eventually to diversification of species [88][89][90]. Genomics studies of the heterochromatin in natural populations of An.…”

The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum

“…The ND phenomenon consists of the reversible silencing of the 35S/45S rDNA loci that are inherited from one of the ancestral species, and has been described in allopolyploids and hybrids that belong to numerous and diverse plant genera (Pikaard, 2000). Although our understanding of the involvement of epigenetic modifications such as DNA methylation and histone deacetylation in establishing and maintaining the ND has advanced significantly in the last decades (Neves et al, 1995;Chen and Pikaard, 1997a;Lawrence et al, 2004;Earley et al, 2006;Costa-Nunes et al, 2010), the mechanisms by which one ancestral rDNA set is selected for silencing remain elusive (Symonova, 2019). The proposed explanations that the uniparental expression of 35S rDNA corresponds to the physical characteristics of its IGSs (the so-called enhancer imbalance hypothesis, originally proposed for Xenopus hybrids), or to differences in the affinity for transcription factors, are not supported in plants (Chen and Pikaard, 1997b;Frieman et al, 1999).…”