In almost all organisms the small ribosomal subunit contains a single RNA species. In eukaryotes 18S rRNA and elsewhere it is 16S rRNA.
Ribosomal RNA's are Highly conserved in structure and presumed function across all of evolution. Particularly the small subunit rRNA, have become the most commonly used markers for establishing phylogenetic relationships between organisms. Mutations in the conserved core regions of the rRNA are heavily biased toward nucleotide substitution, rather than deletion and insertion. This, together with the existence of a universal secondary structure, considerably facilitates the sequence alignment process.
OBased on the Molecular phylogeny of rRNA sequence led to the conclusion that there are three domains of life such as Bacteria (Eubacteria), Archaea (Archaebacteria) and Eukaryotes (Eukarya). Most models predict that during evolution from the Progenote (the first organisms able to replicate their genomes) the Archaea and eukaryotes arose from a common ancestor, following their separation from the bacterial line (see Figure 4). Trees with different topology have been derived based on a variety of protein sequences, probably as a consequence of the relatively high levels of lateral gene transfer that is now thought to have occurred during evolution.
18s rRNA /ITS gene sequencing methods are commonly used for molecular identification of Eukaryotes. It helps in classification and quantitation of microbes within complex biological mixture such as environmental samples (eg., marine water) and gut samples (eg., human gut microbiome). These genes have very high degree of variation even between closely related species.
18S rRNA / ITS Sequencing Technical Advantages: