The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Current rDNA databases focus on short DNA markers, limiting phylogenetic resolution in environmental sequencing.
• Advances in long-read DNA sequencing necessitate longer rDNA reference sequences for improved phylogenetic analysis.

Purpose of the Study:

• To introduce the Ribosomal Operon Database (ROD), a novel resource of eukaryotic full-length rDNA operons.
• To provide researchers with comprehensive, long-read rDNA sequences for enhanced phylogenetic studies.

Main Methods:

• Collected full-length rDNA operons from publicly available eukaryotic genome assemblies in NCBI.
• Detected and analyzed operon presence, copy number, and variant clustering across diverse eukaryotic genomes.
• Evaluated the taxonomic resolution of different rDNA regions within full-length operons.

Main Results:

• Full-length rDNA operons were found in 34.1% of examined eukaryotic genomes.
• Significant intragenomic operon variability and extensive length variation (4136–16,463 bp) were observed.
• The 18S, V4, and V9 regions showed the highest conservation, offering valuable taxonomic resolution.

Conclusions:

• The ROD database successfully compiles eukaryotic full-length rDNA operons, supporting advanced phylogenetic research.
• The database will be regularly updated to incorporate new data and expand its utility.
• Understanding operon variability and length is crucial for mitigating PCR bias and interpreting phylogenetic data.