Hypervariable Regions in 16S rRNA Genes for the Taxonomic Classification

Abstract

16S ribosomal RNA (rRNA) gene sequences are reliable markers for the taxonomic classification of microbes and widely used in environmental microbiology. Production of 16S rRNA gene amplicons in large amounts, encompassing the full length of genes is not yet feasible, because of the limitations of the current sequencing techniques. They are mostly in short reads of length less than 300 base pairs. Hence, the selection of the most efficient hypervariable regions for phylogenetic analysis and taxonomic classification is a current research area. It is found that nine hypervariable regions (V1–V9), resides in bacterial 16S ribosomal RNA (rRNA) genes. Family, genus, and species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations. In this study systematic studies that compare the relative advantage of hypervariable regions grouped as V1–V2–V3, V4–V5–V6, and V7–V8–V9 for specific diagnostic goals are done. In the present research, the built in function Longest–Common–Subsequence in computer algebra package MATHEMATICA is used to create an in silico pipeline to evaluate the taxonomic classification sensitivity of the hypervariable regions compared with the corresponding full-length sequences. Conclusions: Our results suggest that V4–V5–V6 region might be an optimal sub-region for the design of universal primers with superior phylogenetic resolution for bacterial phyla.