Study reveals widespread variation in ribosomal DNA structure across vertebrate species
Researchers used chromosome-scale genome assemblies from the Vertebrate Genomes Project to conduct a broad comparative analysis of the 45S ribosomal DNA locus across vertebrates. The study found that rDNA organization, copy number, and sequence evolution vary dramatically across vertebrate lineages, with mammals and birds showing compact arrangements while amphibians and some fish display highly dispersed architectures. The findings reframe rDNA as a multi-layered evolutionary system rather than a simple indicator of ribosome production capacity.
A new preprint on bioRxiv presents a comprehensive comparative analysis of the 45S ribosomal DNA (rDNA) locus across vertebrates, leveraging chromosome-scale genome assemblies from the Vertebrate Genomes Project. The study reveals wide variation in how rDNA is organized across vertebrate clades: mammals and birds typically confine rDNA to a small number of often terminal chromosomal loci, while amphibians and certain fish lineages show highly dispersed arrangements spanning dozens of chromosomes. Copy number varies by more than an order of magnitude and does not correlate simply with repeat-unit size or predicted ribosome demand, suggesting rDNA acts as a flexible genomic reservoir rather than a direct functional gauge. At the sequence level, the ribosomal RNA-encoding genes (18S, 5.8S, 28S) are highly conserved and retain strong phylogenetic signal, whereas the internal transcribed spacers diverge rapidly and show pronounced asymmetry between ITS1 and ITS2. Structure-informed phylogenetic methods provided modest but consistent improvements in accuracy under conditions of high sequence divergence, underscoring their utility when conventional sequence signals weaken. Together, the results characterize the 45S rDNA locus as integrating deep evolutionary conservation with structural plasticity, offering new insights into genome organization and vertebrate evolution.
What's missing
As a preprint, this study has not yet undergone formal peer review, so findings should be interpreted with caution. The authors do not fully address the functional consequences of the observed copy number and architectural variation, nor do they resolve whether dispersed rDNA arrangements in amphibians and fish reflect adaptive advantages or neutral drift. The mechanisms driving lineage-specific expansion of internal transcribed spacers also remain unexplained.
What different sources said
- bioRxivCenter
Interspecies variation of 45S ribosomal DNA in vertebrates
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