Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis
By Bo Yang, Yong Wang, Pei-Yuan Qian. BMC Bioinformatics, 2016
506 citations recorded by the source corpus.
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. 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. The 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. Our 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.
Subfields: Genetics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/fb10767c998121a55d23136cec60eb1b0cd9d7c1
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In Genetics
In Molecular Biology
- Sandra Reitmeier
- Isabel Abellan-Schneyder
- A. Abdelfattah
- Markus List
- Zeno Sewald
- Alina Sommer
- S. O. Cacciola
- A. Malacrinò
Citations in the corpus
- Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, background): “The consensus of these studies suggest that V4-V6 is the optimal sub-regions for the design of universal primers with superior phylogenetic resolution for bacterial phyla (Yang et al., 2016).”
- Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing (2021, background): “(14) suggested the V4-V5 region to be a good match based on its robustness in repre-”