RDNAbased

RDNAbased refers to approaches in biology and bioinformatics that rely on ribosomal DNA sequences as molecular markers for identifying organisms, inferring phylogeny, and surveying biodiversity. The term emphasizes the use of conserved and variable regions within ribosomal RNA gene repeats (rDNA) to distinguish taxa across life forms. In bacteria and archaea, the most common target is the 16S rRNA gene; in fungi, the internal transcribed spacer (ITS) region and portions of the 18S rRNA gene are frequently used; in other eukaryotes, 18S rRNA remains a standard marker. rDNA regions are present in multiple copies, allowing sensitive detection, and exhibit both conserved and hypervariable segments suitable for taxonomic discrimination at different levels.

RDNAbased methods underpin many culture-independent techniques, including amplicon sequencing to profile microbial communities, environmental DNA surveys, and preliminary taxonomic assignment in metagenomics. Analyses typically involve PCR amplification of target regions, sequencing, and comparison against reference databases such as SILVA, Greengenes, or UNITE. Limitations include amplification bias from primer choice, variation in rDNA copy number among taxa, and limited resolution for closely related species. Additionally, intragenomic variation and chimeric artifacts can complicate interpretation.

Despite these caveats, RDNAbased strategies remain foundational in ecology, clinical microbiology, and environmental monitoring, especially where rapid, cost-effective identification is needed or when genomes are not yet available. The term distinguishes these methods from genome-resolved approaches that analyze whole genomes or metagenomes.