title: Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis.
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.
authors.affiliation: Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
authors.forename: Bo
authors.initials: B
authors.lastname: Yang
authors.affiliation: Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, San Ya, Hai Nan, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Division of Life Sciences, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong. boqianpy@ust.hk.
authors.forename: Pei-Yuan
authors.initials: PY
authors.lastname: Qian
mesh_terms: D001419:Bacteria / Q000235:genetics*; D016000:Cluster Analysis; D017931:DNA Primers / Q000378:metabolism; D030541:Databases, Genetic; D019143:Evolution, Molecular; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000145:classification / Q000235:genetics*
chemical_list: D017931:DNA Primers; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA; 16S rRNA gene; Geodesic distance; Phylogenetic; Primer; Variable regions