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Ribotin: automated assembly and phasing of rDNA morphs
1Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
Bioinformatics (Oxford, England)
|March 5, 2024
Summary
Ribotin assembles full-length ribosomal DNA (rDNA) copies, resolving variations missed by other methods. This tool accurately recovers rDNA sequences from human and nonhuman genomes, improving genetic variation studies.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Ribosomal DNA (rDNA) arrays are repetitive and homogenous, posing challenges for current sequencing assembly methods.
- Incomplete assembly of rDNA arrays limits the study of genetic variation within these crucial genomic regions.
Purpose of the Study:
- To develop a novel computational tool, ribotin, for assembling full-length ribosomal DNA (rDNA) copies (morphs).
- To accurately resolve and study the variation between different rDNA morphs within eukaryotic genomes.
Main Methods:
- Ribotin utilizes a combination of highly accurate long reads and extremely long Oxford Nanopore reads.
- The tool is designed to overcome the limitations of existing assembly methods for repetitive DNA regions.
Main Results:
- Ribotin successfully assembles full-length rDNA copies, recovering the most abundant morphs in both human and nonhuman genomes.
- Analysis revealed that genome-wide consensus sequences often generate mosaic rDNA sequences not present in the actual genome.
Conclusions:
- Ribotin provides a robust solution for assembling complex rDNA arrays, enabling detailed studies of rDNA variation.
- The findings highlight potential inaccuracies in previous rDNA analyses based on consensus sequences.
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