Genomic architecture of 5S rDNA cluster and its variations within and between species

Qiutao Ding, Runsheng Li, Xiaoliang Ren, Lu yan Chan, Vincy W.S. Ho, Dongying Xie, Pohao Ye, Zhongying Zhao*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

4 Citations (Scopus)


Background: Ribosomal DNAs (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosomes during generation of genome assembly. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution. Results: Here we generate ultra-long Oxford Nanopore Technologies (ONT) and short NGS reads to delineate the architecture and variation of the 5S rDNA cluster in the different strains of C. elegans and C. briggsae. We classify the individual rDNA’s repeating units into 25 types based on the unique sequence variations in each unit of C. elegans (N2). We next perform assembly of the cluster by taking advantage of the long reads that carry these units, which led to an assembly of 5S rDNA cluster consisting of up to 167 consecutive 5S rDNA units in the N2 strain. The ordering and copy number of various rDNA units are consistent with the separation time between strains. Surprisingly, we observed a drastically reduced level of variation in the unit composition in the 5S rDNA cluster in the C. elegans CB4856 and C. briggsae AF16 strains than in the C. elegans N2 strain, suggesting that N2, a widely used reference strain, is likely to be defective in maintaining the 5S rDNA cluster stability compared with other wild isolates of C. elegans or C. briggsae. Conclusions: The results demonstrate that Nanopore DNA sequencing reads are capable of generating assembly of highly repetitive sequences, and rDNA units are highly dynamic both within and between population(s) of the same species in terms of sequence and copy number. The detailed structure and variation of the 5S rDNA units within the rDNA cluster pave the way for functional and evolutionary studies.

Original languageEnglish
Article number238
Number of pages20
JournalBMC Genomics
Issue number1
Publication statusPublished - 27 Mar 2022

Scopus Subject Areas

  • Biotechnology
  • Genetics

User-Defined Keywords

  • 18S-5.8S-26S
  • 5S
  • 5S rDNA cluster
  • C. briggsae
  • Caenorhabditis elegans
  • Oxford Nanopore technologies


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