18S

18S refers to the 18S ribosomal RNA, a component of the small subunit of eukaryotic ribosomes. It is encoded by the 18S rRNA gene, the first of the ribosomal RNA genes arranged in tandem repeats within the nuclear rDNA cluster. The 18S rRNA gene is transcribed as part of a single large precursor that also includes the 5.8S and 28S rRNAs, separated by internal transcribed spacers ITS1 and ITS2, and is processed to yield the mature rRNA components. In most eukaryotes, the 18S rRNA gene is roughly 1,800 base pairs long, and the mature 18S rRNA is about 1,900 nucleotides. The gene contains conserved regions suitable for universal primer binding and several hypervariable regions (often designated as V1–V9) that provide varying levels of taxonomic resolution across eukaryotes.

Applications of the 18S rRNA gene include its use as a molecular marker for eukaryotes in phylogenetic analyses and environmental sequencing. It is widely employed in environmental DNA and metabarcoding studies to profile eukaryotic community composition, including protists and other microeukaryotes. In clinical and environmental microbiology, 18S sequences aid in identifying eukaryotic pathogens and symbionts, and they are often used alongside other markers such as 28S or mitochondrial genes when higher resolution is required. Large sequence databases, such as SILVA, PR2, and GenBank, provide extensive 18S rRNA sequence collections for alignment, classification, and phylogenetic inference.

Limitations include uneven taxonomic resolution across groups, potential intragenomic variation due to multiple rDNA copies, and primer biases that affect detection of certain taxa. Short-read sequencing can limit species-level discrimination, while longer reads can improve accuracy. In practice, 18S is frequently paired with additional markers to enhance resolution and ecological interpretation. See also: 16S rRNA, 28S rRNA.