18S ribosomal RNA

18S ribosomal RNA (abbreviated 18S rRNA) is a part of the ribosomal RNA in eukaryotes. It is a component of the Eukaryotic small ribosomal subunit (40S) and the cytosolic homologue of both the 12S rRNA in mitochondria and the 16S rRNA in plastids and prokaryotes. Similar to the prokaryotic 16S rRNA, the genes of the 18S ribosomal RNA haven been widely used for phylogenetic studies and biodiversity screening of eukaryotes.

Research history
Along with the 28S and 5.8S rRNA in eukaryotes, the 18S rRNA was early identified as integral structural element of ribosomes which were first characterized by their sedimentation properties and named according to measured Svedberg units.

Given its ubiquitous presence in eukaryotic life, the evolution of the 18S rRNA was soon proposed as marker for phylogenetic studies to resolve the evolution of eukaryotes.

Structure and function
The 18S ribosomal RNA is the structural RNA of the small subunit in the eukaryotic cytoplasmic ribosome.

The genomic sequence of the 18S rRNA is organized in a group with the 28S and 5.8S rRNA, separated and flanked by the ITS-1, ITS-2 and ETS spacer regions. These regions of ribosomal DNA (rDNA) are present with several hundred copies in the active genome, clustered in nucleolus organizer regions (NORs). In ribosome biogenesis, these genes are transcribed together by the RNA polymerase I and are processed in the nucleolus structure of the nucleus.

The length of the 18S rRNA varies considerably in the eukaryotic phylogenetic tree, corresponding to a range of 16S-19S in Svedberg units, with the average length commonly given as around 2000 nucleotides. The 18S rRNA of humans has a length of 1869 nucleotides.

Uses
The universal presence of the 18S rRNA in eukaryotes and generally high degree of conservation in evolution allow the construction of universal primers for DNA amplification by polymerase chain reaction. The possible applications mirror molecular methods involving 16S rRNA of prokaryotes.

Biodiversity screening
Primers binding in highly conserved regions of the 18S rRNA are an important marker for biodiversity screening, allowing the amplification of unspecified or random targets from environmental samples as well as uncharacterized specimens from collections for DNA sequencing. Subsequent sequence alignment covering the less strictly conserved segments then allows the assignment of a sample to biologic clades.

In the case of 18S rRNA, retrieval of DNA is improved by the abundance of repeating sequences of the rDNA within eukaryotic cells, promoting the sensitivity of the analysis.

Phylogenetics
Genomic sequence data of the 18S rRNA is widely used to reconstruct the evolutionary history of organisms, especially in vertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences.

The 18S gene is part of the ribosomal functional core and is exposed to similar selective forces in all living beings. Thus, when the first large-scale phylogenetic studies based on 18S sequences were published (e.g. by Field et al., 1988), the gene was celebrated as the prime candidate for reconstructing the metazoan tree of life. 18S sequences later provided evidence for the splitting of Ecdysozoa and Lophotrochozoa clades (monophyletic group of organisms composed of a common ancestor and all its lineal descendants), thus contributing to a revolutionary change in our understanding of metazoan relationships.

During the latter part of the 2000s, and with increased numbers of taxa included into molecular phylogenies, however, two problems became apparent. First, there are prevailing sequencing impediments in representatives of certain taxa, such as the mollusk classes Solenogastres and Tryblidia, selected bivalve taxa, and the enigmatic crustacean class Remipedia. Failure to obtain 18S sequences of single taxa is considered a common phenomenon but is rarely ever reported. Secondly, in contrast to initially high hopes, 18S cannot resolve nodes at all taxonomic levels and its efficacy varies considerably among clades. This has been discussed as an effect of rapid ancient radiation within short periods. Multigene analyses are currently thought to give more reliable results for tracing deep branching events in Metazoa but 18S still is extensively used in phylogenetic analyses.