How conserved are the conserved 16S-rRNA regions?
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 o...
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PeerJ Inc.
2017-02-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/3036.pdf |
| _version_ | 1797425532597436416 |
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| author | Marcel Martinez-Porchas Enrique Villalpando-Canchola Luis Enrique Ortiz Suarez Francisco Vargas-Albores |
| author_facet | Marcel Martinez-Porchas Enrique Villalpando-Canchola Luis Enrique Ortiz Suarez Francisco Vargas-Albores |
| author_sort | Marcel Martinez-Porchas |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T08:16:31Z |
| format | Article |
| id | doaj.art-3d32a9da5594497b997a55b38c89f3c5 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:16:31Z |
| publishDate | 2017-02-01 |
| publisher | PeerJ Inc. |
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| spelling | doaj.art-3d32a9da5594497b997a55b38c89f3c52023-12-02T22:01:10ZengPeerJ Inc.PeerJ2167-83592017-02-015e303610.7717/peerj.3036How conserved are the conserved 16S-rRNA regions?Marcel Martinez-Porchas0Enrique Villalpando-Canchola1Luis Enrique Ortiz Suarez2Francisco Vargas-Albores3Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, MexicoCentro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, MexicoInstituto Tecnológico de Morelia, Morelia, Michoacán, MexicoCentro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, MexicoThe 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.https://peerj.com/articles/3036.pdfKmersBiodiversityConserved regions 16SPrimer design |
| spellingShingle | Marcel Martinez-Porchas Enrique Villalpando-Canchola Luis Enrique Ortiz Suarez Francisco Vargas-Albores How conserved are the conserved 16S-rRNA regions? PeerJ Kmers Biodiversity Conserved regions 16S Primer design |
| title | How conserved are the conserved 16S-rRNA regions? |
| title_full | How conserved are the conserved 16S-rRNA regions? |
| title_fullStr | How conserved are the conserved 16S-rRNA regions? |
| title_full_unstemmed | How conserved are the conserved 16S-rRNA regions? |
| title_short | How conserved are the conserved 16S-rRNA regions? |
| title_sort | how conserved are the conserved 16s rrna regions |
| topic | Kmers Biodiversity Conserved regions 16S Primer design |
| url | https://peerj.com/articles/3036.pdf |
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