How conserved are the conserved 16S-rRNA regions?
| Autor: | Luis Enrique Ortiz Suarez, Enrique Villalpando-Canchola, Francisco Vargas-Albores, Marcel Martínez-Porchas |
|---|---|
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Conserved regions 16S Nucleotide frequency 030106 microbiology lcsh:Medicine Biology General Biochemistry Genetics and Molecular Biology Conserved sequence 03 medical and health sciences Master key Gene Contig General Neuroscience lcsh:R Computational Biology Biodiversity Genomics General Medicine 16S ribosomal RNA Hypervariable region 030104 developmental biology Evolutionary biology Primer design Kmers Primer (molecular biology) General Agricultural and Biological Sciences |
| Zdroj: | PeerJ PeerJ, Vol 5, p e3036 (2017) |
| ISSN: | 2167-8359 |
| Popis: | The 16S rRNA gene has been used as master key for studying prokaryotic diversity in almost every environment. Despite the claim of several researchers to have the best universal primers, the reality is that no primer has been demonstrated to be truly universal. This suggests that conserved regions of the gene may not be as conserved as expected. The aim of this study was to evaluate the conservation degree of the so-called conserved regions flanking the hypervariable regions of the 16S rRNA gene. Data contained in SILVA database (release 123) were used for the study. Primers reported as matches of each conserved region were assembled to form contigs; sequences sizing 12 nucleotides (12-mers) were extracted from these contigs and searched into the entire set of SILVA sequences. Frequency analysis shown that extreme regions, 1 and 10, registered the lowest frequencies. 12-mer frequencies revealed segments of contigs that were not as conserved as expected (≤90%). Fragments corresponding to the primer contigs 3, 4, 5b and 6a were recovered from all sequences in SILVA database. Nucleotide frequency analysis in each consensus demonstrated that only a small fraction of these so-called conserved regions is truly conserved in non-redundant sequences. It could be concluded that conserved regions of the 16S rRNA gene exhibit considerable variation that has to be considered when using this gene as biomarker. |
| Databáze: | OpenAIRE |
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