Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb

Abstract

In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes (<20 %) encode functional rRNA. The most common SNPs were C > T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.Electronic supplementary materialThe online version of this article (doi:10.1007/s00412-015-0556-3) contains supplementary material, which is available to authorized users.

Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.)

“…Indeed, in some plant species most rRNA genes were converted into pseudogenes [74]. However, we have no evidence for such significant erosion in Esox 5S rDNA despite its high methylation (methylation-induced mutations were not significantly enriched in Esox 5S rDNA, p  > 0.05).…”

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

“…Such a mutation pattern could be explained by the presence of putative pseudogenized 35S rDNA copies in the B. stacei genome. In support, the mutations affecting the abundant Cycas revoluta (gymnosperm) rDNA pseudogenes occurred at nearly the same frequency in the coding and non-coding subregions (Wang et al, 2016). Of note, the pseudogenized rDNA sequences were found in the human genome, mostly in the proximal regions (Robicheau et al, 2017).…”

The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants

“…Although this prolongs computation times (typically 5-6 hours on the MetaCentrum ELIXIR computer clusters) we were able to reconstruct 5S rDNA units in the large (50 GB) Fritillaria imperialis genome (Zonneveld, 2010) although, in this case, the number of reads in the cluster was too low, preventing graph analysis. High coverages may also help to reveal rare 5S rDNA variants and pseudogenes that are frequent in gymnosperms (Wang et al, 2016;Wang et al, 2019) while they rarely occur in angiosperms. In interspecific comparisons, the usage of a standard fraction of genome (0.1-1.0%) is recommended to prevent biases in interspecific comparisons.…”