Phylogeny Based on 16 S r RNA / DNA

Abstract

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.