16s/18s/ITS

The full length of bacteria 16S rDNA is about 1540bp, including 10 conserved regions and 9 hypervariable regions, in which the difference of conserved region in bacteria is not significant while the hypervariable region has high specificity. Therefore, some hypervariable regions (usually V3 and V4 regions) can be sequenced for analyzing the bacterial community diversity.

18S rRNA is commonly used in fungi for phylogenetics since it has more hypervariable domains than 16S. In addition to this, the ITS (Internal Transcribed Spacer) region, removed in the posttranscriptional process of nuclear rRNA cistron, has been widely regarded as a universal fungi barcode marker for a successful identification for the broadest range of fungi. And compared to 18S, ITS is more variable and hence more suitable as the genetic marker for measuring intraspecific genetic diversity.