How conserved are the conserved 16S-rRNA regions?
Identifieur interne : 000C80 ( PubMed/Checkpoint ); précédent : 000C79; suivant : 000C81How conserved are the conserved 16S-rRNA regions?
Auteurs : Marcel Martinez-Porchas [Mexique] ; Enrique Villalpando-Canchola [Mexique] ; Luis Enrique Ortiz Suarez [Mexique] ; Francisco Vargas-Albores [Mexique]Source :
- PeerJ [ 2167-8359 ] ; 2017.
Abstract
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.
DOI: 10.7717/peerj.3036
PubMed: 28265511
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Desarrollo, A.C., Hermosillo, Sonora, Mexico.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora</wicri:regionArea><wicri:noRegion>Sonora</wicri:noRegion></affiliation></author><author><name sortKey="Ortiz Suarez, Luis Enrique" sort="Ortiz Suarez, Luis Enrique" uniqKey="Ortiz Suarez L" first="Luis Enrique" last="Ortiz Suarez">Luis Enrique Ortiz Suarez</name><affiliation wicri:level="1"><nlm:affiliation>Instituto Tecnológico de Morelia, Morelia, Michoacán, Mexico.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Instituto Tecnológico de Morelia, Morelia, Michoacán</wicri:regionArea><wicri:noRegion>Michoacán</wicri:noRegion></affiliation></author><author><name sortKey="Vargas Albores, Francisco" sort="Vargas Albores, Francisco" uniqKey="Vargas Albores F" first="Francisco" last="Vargas-Albores">Francisco Vargas-Albores</name><affiliation wicri:level="1"><nlm:affiliation>Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.</nlm:affiliation><country xml:lang="fr">Mexique</country><wicri:regionArea>Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora</wicri:regionArea><wicri:noRegion>Sonora</wicri:noRegion></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="ISSN">2167-8359</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">28265511</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2167-8359</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PeerJ</Title><ISOAbbreviation>PeerJ</ISOAbbreviation></Journal><ArticleTitle>How conserved are the conserved 16S-rRNA regions?</ArticleTitle><Pagination><MedlinePgn>e3036</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.3036</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y" EqualContrib="Y"><LastName>Martinez-Porchas</LastName><ForeName>Marcel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y" EqualContrib="Y"><LastName>Villalpando-Canchola</LastName><ForeName>Enrique</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ortiz Suarez</LastName><ForeName>Luis Enrique</ForeName><Initials>LE</Initials><AffiliationInfo><Affiliation>Instituto Tecnológico de Morelia, Morelia, Michoacán, Mexico.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vargas-Albores</LastName><ForeName>Francisco</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Sonora, Mexico.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>02</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PeerJ</MedlineTA><NlmUniqueID>101603425</NlmUniqueID><ISSNLinking>2167-8359</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Biodiversity</Keyword><Keyword MajorTopicYN="N">Conserved regions 16S</Keyword><Keyword MajorTopicYN="N">Kmers</Keyword><Keyword MajorTopicYN="N">Primer design</Keyword></KeywordList><CoiStatement>The authors declare there are no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>10</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>01</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>3</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>3</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>3</Month><Day>8</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28265511</ArticleId><ArticleId IdType="doi">10.7717/peerj.3036</ArticleId><ArticleId IdType="pii">3036</ArticleId><ArticleId IdType="pmc">PMC5333541</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>BMC 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uniqKey="Villalpando Canchola E" first="Enrique" last="Villalpando-Canchola">Enrique Villalpando-Canchola</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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