Abstract
BackgroundProkaryotic 16S ribosomal RNA (rRNA) sequences are widely used in environmental microbiology and molecular evolution as reliable markers for the taxonomic classification and phylogenetic analysis of microbes. Restricted by current sequencing techniques, the massive sequencing of 16S rRNA gene amplicons encompassing the full length of genes is not yet feasible. Thus, the selection of the most efficient hypervariable regions for phylogenetic analysis and taxonomic classification is still debated. In the present study, several bioinformatics tools were integrated to build an in silico pipeline to evaluate the phylogenetic sensitivity of the hypervariable regions compared with the corresponding full-length sequences.ResultsThe correlation of seven sub-regions was inferred from the geodesic distance, a parameter that is applied to quantitatively compare the topology of different phylogenetic trees constructed using the sequences from different sub-regions. The relationship between different sub-regions based on the geodesic distance indicated that V4-V6 were the most reliable regions for representing the full-length 16S rRNA sequences in the phylogenetic analysis of most bacterial phyla, while V2 and V8 were the least reliable regions.ConclusionsOur results suggest that V4-V6 might be optimal sub-regions for the design of universal primers with superior phylogenetic resolution for bacterial phyla. A potential relationship between function and the evolution of 16S rRNA is also discussed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-0992-y) contains supplementary material, which is available to authorized users.
Highlights
Prokaryotic 16S ribosomal RNA sequences are widely used in environmental microbiology and molecular evolution as reliable markers for the taxonomic classification and phylogenetic analysis of microbes
Full-length 16S ribosomal RNA (rRNA) gene sequences consist of nine hypervariable regions that are separated by nine highly conserved regions [11, 12]
The pairwise distances of V2-VT and V8-VT were larger than the others, indicating that the phylogenetic relationships inferred from the V2 and V8 subregions were very different from the VT-based results
Summary
Prokaryotic 16S ribosomal RNA (rRNA) sequences are widely used in environmental microbiology and molecular evolution as reliable markers for the taxonomic classification and phylogenetic analysis of microbes. Several bioinformatics tools were integrated to build an in silico pipeline to evaluate the phylogenetic sensitivity of the hypervariable regions compared with the corresponding full-length sequences. The 16S rRNA gene sequence was first used in 1985 for phylogenetic analysis [9] Because it contains both highly conserved regions for primer design and hypervariable regions to identify phylogenetic characteristics of microorganisms, the 16S rRNA gene sequence became the most widely used marker gene for profiling bacterial communities [10]. Full-length 16S rRNA gene sequences consist of nine hypervariable regions that are separated by nine highly conserved regions [11, 12]. The 16S rRNA gene sequences used in most studies are partial sequences
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