Phylogeny Based on 16S rRNA/DNA

Abstract

Polyphasic systematics of prokaryotes is guided by the results of comparative analysis of the evolutionary conservative 16S ribosomal ribonucleic acid (RNA) genes. Certain genes coding for ‘housekeeping’ proteins support the phylogenetic outline but most of these genes are either not ubiquitous or they are evolving too rapidly to embrace all higher taxa. Dendrograms of phylogenetic relatedness show the order at which organisms evolved in time, thus providing the frame for their classification. The delineation and circumscription of taxa should not be solely based on the topology of dendrograms but it is advised to include a wide range of molecular, chemical and metabolic properties, which need to be assessed and evaluated in the light of novel taxonomic information.

Key concepts:

  • The results of comparative 16S ribosomal ribonucleic acid (rRNA) gene sequence analysis shattered the dogma of the bifurcation of higher life form categories, that is prokaryotes versus eukaryotes.

  • The advantage of rRNA genes over genes coding for proteins is a combination of properties: universal presence, easy accessibility and polymerase chain reaction (PCR) amplification, rare lateral gene transfer and broad coverage of taxa between domain and species.

  • The only taxonomic category where the 16S rRNA gene sequence fails to unravel detailed evolutionary insights into the structure of its members is the taxon ‘species’.

  • Taxonomy of a strain is more than the analysis of a few sequences: it is a pragmatic concept that takes into account the results of its evolutionary history leading to changes at the genomic, epigenetic and phenotypic levels.

  • Classification is a process in which the database of a strain is compared to the network of strains already classified. Its place in the system is found when this dataset matches most closely the dataset of an already classified taxon. In this process the 16S rRNA sequence guides the affiliation to the genus level.

Keywords: semantides; evolution; phylogeny; taxonomy; systematics; classification

Figure 1.

Secondary structure of a 16S rRNA molecule based on the Escherichia coli structure (Maidak et al., ; available in the public domain Ribosomal Database Project). Highly variable regions are red; highly conservative stretches are green. Binding sites of primers used in PCR amplification of the rRNA gene are blue, with the direction of amplification indicated by arrows. The other nucleotides are black.

Figure 2.

Phylogenetic distribution of peptidoglycan amino acids as a salient chemotaxonomic property. Type strains of Microbacterium (M.) with ornithine in their peptidoglycan are indicated in red, those with lysine are indicated in blue. Neighbour‐Joining dendrograms of relationship of genes coding for 16S rRNA (1A), rpoB (1B), recA (1C), gyrB (1D), ppk (1E) and a concatenated dataset (1F), containing the gene sequences that formed the basis for genes displayed in Figure A–E. Bootstrap values of >30% are indicated at relevant branching points. Agromyces albus DSM 15934T served as a root. Scale bar indicates 2% inferred nucleotide changes. Reprinted from Richert et al., www.elsevier.com/locate/sam. Copyright (2007) with permission from Elsevier.

Figure 3.

The phylogenetic tripartition of living organisms based on the analysis of genes coding for small subunit rRNA (16S and 18S rRNA). Within the prokaryotic domains most of the main lines of descent, called kingdoms in the domain Archaea, and phyla in the domain Bacteria, are indicated. The origin of the evolutionary lineages appears to be located close to the branching point of the lineage of the Bacteria (indicated by a circle). The bar represents 5 nucleotide substitutions per 100 nucleotides.

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How to Cite close
Stackebrandt, Erko(Sep 2009) Phylogeny Based on 16S rRNA/DNA. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000462.pub2]