Catawba – Rhododendron catawbiense

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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.[1]

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.[2]

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.[3]

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, of which several hundred copies form the nucleolus organizer regions (NORs).[2] In ribosome biogenesis, these genes are transcribed together by the RNA polymerase I and are processed in the nucleolus structure of the nucleus.

18S rRNA nucleotide length of selected species
Species Size [nt]
Saccharomyces cerevisiae 1,789[4]
Xenopus laevis 1,825[5]
Homo sapiens 1,869[6]
Drosophila melanogaster 1,995[7]

The length of the 18S rRNA varies considerably in the eukaryotic phylogenetic tree, corresponding to a range of 16S-19S in Svedberg units,[2] with the average length commonly given as around 2000 nucleotides.[2] The 18S rRNA of humans has a length of 1869 nucleotides.[6]

Uses

Phylogenetics

The genes coding for 18S rRNA are referred to as 18S rRNA genes. Sequence data from these genes is widely used in molecular analysis to reconstruct the evolutionary history of organisms, especially in vertebrates, as its slow evolutionary rate makes it suitable to reconstruct ancient divergences.

The small subunit (SSU) 18S rRNA gene is one of the most frequently used genes in phylogenetic studies and an important marker for random target polymerase chain reaction (PCR) in environmental biodiversity screening.[1] In general, rRNA gene sequences are easy to access due to highly conserved flanking regions allowing for the use of universal primers.[1] Their repetitive arrangement within the genome provides excessive amounts of template DNA for PCR, even in the smallest organisms. 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),[3] the gene was celebrated as the prime candidate for reconstructing the metazoan tree of life.[1] 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.[1]

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.[1] Failure to obtain 18S sequences of single taxa is considered a common phenomenon but is rarely ever reported.[1] 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.[1]

References

This article incorporates CC-By-2.0 text from the reference.[1]

  1. ^ a b c d e f g h i Meyer A, Todt C, Mikkelsen NT, Lieb B (2010). "Fast evolving 18S rRNA sequences from Solenogastres (Mollusca) resist standard PCR amplification and give new insights into mollusk substitution rate heterogeneity". BMC Evolutionary Biology. 10 70: 70. doi:10.1186/1471-2148-10-70. PMC 2841657. PMID 20214780.
  2. ^ a b c d Graw, Jochen (2015). Genetik [Genetics] (in German) (6th ed.). Berlin, Heidelberg: Springer-Verlag Berlin Heidelberg. doi:10.1007/978-3-662-44817-5. ISBN 978-3-662-44816-8.
  3. ^ a b Field KG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT, Raff EC, Pace NR, Raff RA (1988). "Molecular phylogeny of the animal kingdom". Science. 239 (4841): 748–753. doi:10.1126/science.3277277.
  4. ^ Rubtsov PM, Musakhanov MM, Zakharyev VM, Krayev AS, Skryabin KG, Bayev AA (1980). "The structure of the yeast ribosomal RNA genes. I. The complete nucleotide sequence of the 18S ribosomal RNA gene from Saccharomyces cerevisiae". Nucleic Acids Research. 8 (23): 5779–5794. doi:10.1093/nar/8.23.5779. PMID 7008030.
  5. ^ Salim M, Maden EH (1981). "Nucleotide sequence of Xenopus laevis 18S ribosomal RNA inferred from gene sequence". Nature. 291: 205–208. doi:10.1038/291205a0. PMID 7015146.
  6. ^ a b Page Homo sapiens RNA, 18S ribosomal N5 (RNA18SN5), ribosomal RNA on "Homo sapiens 18S ribosomal RNA". National Library of Medicine. 25 March 2023. Retrieved 2024-06-29.
  7. ^ Tautz D, Hancock JM, Webb DA, Tautz C, Dover GA (1988). "Complete sequences of the rRNA genes of Drosophila melanogaster". Molecular biology and evolution. 5: 366–376. doi:10.1093/oxfordjournals.molbev.a040500. PMID 3136294.
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