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Cited by 560Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyBacterial Identification and Susceptibility Testing

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Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

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Yang, Bo, Wang, Yong, Qian, Pei-Yuan·2016·BMC Bioinformatics
DOI 10.1186/s12859-016-0992-yPMC PMC4802574
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Abstract

Background: 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. Results: 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. Conclusions: 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.

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  • The changes added by human players tend to agree with the 16S structural model, especially in regions linked to important functional sites, such as S8 and S15 binding sites, and a region that undergoes conformational readjustment during 30S assembly.

    “In Fig. 4, we show that the changes added by human players tend to agree with the 16S structural model, especially in regions linked to important functional sites, such as S8 and S15 binding sites, and a region that undergoes conformational readjustment during 30S assembly44–49.”

    From Improving microbial phylogeny with citizen science within a mass-market video game (2025) · cites this paper as [49]

    The Results and discussion section links some 16S rRNA regions to structural and functional sites, but it does not discuss changes made by human players or their agreement with a structural model. Searches for S8 and S15 binding sites and conformational readjustment during 30S assembly found no passage addressing those details in our copy; no page numbers were provided. (LLM, conf=0.76)

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Metadata

Authors
Yang, B., Wang, Y., & Qian, P.-Y.
Affiliations
  • Hong Kong University of Science and Technology (HK)
  • Chinese Academy of Sciences (CN)
Corresponding author
Qian, Pei-Yuan
ORCID
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2016-03-22
Volume
17
Issue
1
Pages
135-135
ISSN
1471-2105 (ISSN-L)
DOI
10.1186/s12859-016-0992-y
PMC
PMC4802574
OpenAlex
W2306610272
Cited by
560
References
2
Citations by year
2026: 28 · 2025: 40 · 2024: 53 · 2023: 65 · 2022: 63 · 2021: 75 · 2020: 63 · 2019: 65 · 2018: 66 · 2017: 36 · 2016: 4
FWCI
29.61
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Bioinformatics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
Funders
  • National Natural Science Foundation of China (973 Program, 31460001, 41476104, No. 41476104)
  • National Key Research and Development Program of China (2012CB417304)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Health Sciences › Medicine › Microbiology (medical) › Bacterial Identification and Susceptibility Testing
Keywords
16S rRNA, hypervariable region, geodesic distance, phylogenetic resolution, primer design, bacterial taxonomy, prokaryotic phylogeny
MeSH terms
Bacteria, Nucleic Acid Conformation, Phylogeny, RNA, Ribosomal, 16S, Cluster Analysis, DNA Primers, Evolution, Molecular, Databases, Genetic

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