Genome architecture modulates 35S and 5S rDNA homogenization in Asteraceae

Concerted evolution is the model by which multicopy gene families are homogenized across genomes, with ribosomal DNA (rDNA) as its textbook example. However, the extent and efficiency of this process may vary depending on genomic factors. The plant family Asteraceae provides a natural comparative system to address the evolutionary dynamics of rDNA, as it is uniquely characterized by the coexistence of two contrasting genomic arrangements: a separate (S-type) and a linked (L-type) organization of 5S and 35S rRNA genes. Here we analyzed rDNA arrangements in 71 representative Asteraceae species (50 S-type and 21 L-type) and, using WGS data and repeatome analyses, we have reconstructed full rDNA units and quantified the intragenomic variability across coding (genic) and non-coding (spacer) regions. No intermediate (coexisting L-type+S-type) genotypes were found. Our results reveal contrasting patterns of 5S rDNA variation depending on its genomic context. S-type species exhibit high levels of 5S polymorphism in both genic and spacer regions, while L-type species show near-complete sequence homogeneity, consistent with variation in homogenization efficiency and selective constraints related to copy number and chromosomal position of 5S rRNA genes. In contrast, 35S rDNA shows a low polymorphism level overall. The findings support a context-dependent view of concerted evolution across rDNA and highlight the influence of genome architecture on rDNA evolution. In particular, the contrasting behavior of 5S (highly conserved when linked but highly variable when separate) emerges as a key example of how structural genomic context shapes the evolution of even the most conserved housekeeping genes.