16S ribosomal RNA gene

A 16S ribosomal RNA gene is a DNA sequence transcribed to produce16S ribosomal RNA, a structural and functional RNA of the small ribosomal subunit in bacteria and archaea. It is an RNA-coding gene, rather than a gene whose final product is a protein. The Escherichia coli rrsA annotation supplies a concrete example: NCBI records its gene type as rRNA and its product as16S ribosomal RNA.^[ref]

Sequence comparison makes the 16S ribosomal RNA gene useful as a marker of microbial relationships. The historical motivation includes a1977 analysis by Carl R. Woese and George E. Fox using ribosomal RNA sequence characterization to distinguish deep lineages. That experiment analysed RNA sequence information; it should not be described as a modern polymerase chain reaction survey.^[ref]

Gene copy number complicates abundance interpretation. A2004 genome comparison examined both variable copy numbers and sequence differences between16S copies in one genome.^[ref] In an invented ideal assay,100 cells with one target copy each contribute100 templates, while100 cells with four copies contribute400. Equal cell counts then give20percent and80percent of templates. Extraction, primer matching and amplification can introduce further differences. A sequence-read fraction is consequently not automatically a cell fraction.