With a moderate molecular size and low mutation rate, 16S rDNA is the most commonly used marker in the study of bacterial systematics. The 16S rDNA sequence consists of 9 variable regions and 10 conservative regions, the conserved region sequences reflect the genetic relationships between species, while the variable region sequences reflect the difference between species. Like 16S rDNA, 18S rDNA sequence also consists of conservative regions and variable regions (V1-V9, absence of V6). In short, the main steps of 16S/18S/ITS amplicon sequencing include library construction, sequencing and bioinformatics analysis. For example, if you chose V4 for analysis, the PE250 sequencing is needed, but for V1-V3 regions, the sequencing strategy should be PE300.