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Mitochondrial 16S and nuclear 28S ribosomal DNA phylogenies of three species of mollusks belonging to the genus Waldo.

28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and thus one of the basic components of all eukaryotic cells. It has a size of 25S in plants and 28S in mammals, hence the alias of 25S–28S rRNA.[1]

Combined with 5.8S rRNA to the 5' side, it is the eukaryotic nuclear homologue of the prokaryotic 23S and mitochondrial 16S ribosomal RNAs.[2][3][4]

Use in phylogeny

The genes coding for 28S rRNA are referred to as 28S rDNA. The comparison of the sequences from these genes are sometimes used in molecular analysis to construct phylogenetic trees, for example in protists,[5] fungi,[6] insects,[7] arachnids,[8] tardigrades,[9] and vertebrates.[10][11]


The 28S rRNA is typically 4000–5000 nt long.[12]

Some eukaryotes cleave 28S rRNA into two parts before assembling both into the ribosome, a phenomenon termed the "hidden break".[12]


Several databases provide alignments and annotations of LSU rRNA sequences for comparative purposes:


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  6. ^ James, Timothy Y.; Kauff, Frank; Schoch, Conrad L.; Matheny, P. Brandon; Hofstetter, Valérie; Cox, Cymon J.; Celio, Gail; Gueidan, Cécile; Fraker, Emily (2006). "Reconstructing the early evolution of Fungi using a six-gene phylogeny". Nature. 443 (7113): 818–822. Bibcode:2006Natur.443..818J. doi:10.1038/nature05110. PMID 17051209. S2CID 4302864.
  7. ^ Whiting, Michael F.; Carpenter, James C.; Wheeler, Quentin D.; Wheeler, Ward C. (1997-03-01). "The Strepsiptera Problem: Phylogeny of the Holometabolous Insect Orders Inferred from 18S and 28S Ribosomal DNA Sequences and Morphology". Systematic Biology. 46 (1): 1–68. doi:10.1093/sysbio/46.1.1. ISSN 1063-5157. PMID 11975347.
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  10. ^ Le, Hoc Lanh Vân; Lecointre, Guillaume; Perasso, Roland (1993-03-01). "A 28S rRNA-Based Phylogeny of the Gnathostomes: First Steps in the Analysis of Conflict and Congruence with Morphologically Based Cladograms". Molecular Phylogenetics and Evolution. 2 (1): 31–51. doi:10.1006/mpev.1993.1005. PMID 8081546.
  11. ^ Mallatt, Jon; Sullivan, Jack (December 1998). "28S and 18S rDNA sequences support the monophyly of lampreys and hagfishes". Molecular Biology and Evolution. 15 (12): 1706–1718. doi:10.1093/oxfordjournals.molbev.a025897. PMID 9866205.
  12. ^ a b Natsidis, Paschalis; Schiffer, Philipp H.; Salvador-Martínez, Irepan; Telford, Maximilian J. (December 2019). "Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers". Scientific Reports. 9 (1): 19477. Bibcode:2019NatSR...919477N. doi:10.1038/s41598-019-55573-1. PMC 6925239. PMID 31863008.
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