Ancient DNA sequence revealed by error-correcting codes
Identifieur interne : 000190 ( Main/Exploration ); précédent : 000189; suivant : 000191Ancient DNA sequence revealed by error-correcting codes
Auteurs : Marcelo M. Brandão [Brésil] ; Larissa Spoladore [Brésil] ; Luzinete C. B. Faria [Brésil] ; Andréa S. L. Rocha [Brésil] ; Marcio C. Silva-Filho [Brésil] ; Reginaldo Palazzo [Brésil]Source :
- Scientific Reports [ 2045-2322 ] ; 2015.
Abstract
A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the
Url:
DOI: 10.1038/srep12051
PubMed: 26159228
PubMed Central: 4498232
Affiliations:
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Brandão</name><affiliation wicri:level="1"><nlm:aff id="a1"><institution>Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas</institution>, Campinas, SP,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo</institution>, 13400-918, Piracicaba, SP,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Spoladore, Larissa" sort="Spoladore, Larissa" uniqKey="Spoladore L" first="Larissa" last="Spoladore">Larissa Spoladore</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo</institution>, 13400-918, Piracicaba, SP,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Faria, Luzinete C B" sort="Faria, Luzinete C B" uniqKey="Faria L" first="Luzinete C. B." last="Faria">Luzinete C. B. Faria</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas</institution>, 13081-970, Campinas, SP,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Rocha, Andrea S L" sort="Rocha, Andrea S L" uniqKey="Rocha A" first="Andréa S. L." last="Rocha">Andréa S. L. Rocha</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas</institution>, 13081-970, Campinas, SP,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Silva Filho, Marcio C" sort="Silva Filho, Marcio C" uniqKey="Silva Filho M" first="Marcio C." last="Silva-Filho">Marcio C. Silva-Filho</name><affiliation wicri:level="1"><nlm:aff id="a2"><institution>Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo</institution>, 13400-918, Piracicaba, SP,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Palazzo, Reginaldo" sort="Palazzo, Reginaldo" uniqKey="Palazzo R" first="Reginaldo" last="Palazzo">Reginaldo Palazzo</name><affiliation wicri:level="1"><nlm:aff id="a3"><institution>Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas</institution>, 13081-970, Campinas, SP,<country>Brazil</country></nlm:aff><country xml:lang="fr">Brésil</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Scientific Reports</title><idno type="eISSN">2045-2322</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the <italic>Arabidopsis thaliana</italic> malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. 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Schultz Gact</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Z" uniqKey="Yang Z">Z. Yang</name></author><author><name sortKey="Roberts, D" uniqKey="Roberts D">D. Roberts</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Edgar, R C" uniqKey="Edgar R">R. C. Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Edgar, R C" uniqKey="Edgar R">R. C. Edgar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hedges, S B" uniqKey="Hedges S">S. B. Hedges</name></author><author><name sortKey="Blair, J E" uniqKey="Blair J">J. E. Blair</name></author><author><name sortKey="Venturi, M L" uniqKey="Venturi M">M. L. Venturi</name></author><author><name sortKey="Shoe, J L" uniqKey="Shoe J">J. L. Shoe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Heckman, D S" uniqKey="Heckman D">D. S. Heckman</name></author><author><name sortKey="Geiser, D M" uniqKey="Geiser D">D. M. Geiser</name></author><author><name sortKey="Eidell, B R" uniqKey="Eidell B">B. R. Eidell</name></author><author><name sortKey="Stauffer, R L" uniqKey="Stauffer R">R. L. Stauffer</name></author><author><name sortKey="Kardos, N L" uniqKey="Kardos N">N. L. Kardos</name></author><author><name sortKey="Hedges, S B" uniqKey="Hedges S">S. B. Hedges</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sanderson, M J" uniqKey="Sanderson M">M. J. Sanderson</name></author><author><name sortKey="Thorne, J L" uniqKey="Thorne J">J. L. Thorne</name></author><author><name sortKey="Wikstrom, N" uniqKey="Wikstrom N">N. Wikstrom</name></author><author><name sortKey="Bremer, K" uniqKey="Bremer K">K. Bremer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Drummond, A J" uniqKey="Drummond A">A. J. Drummond</name></author><author><name sortKey="Rambaut, A" uniqKey="Rambaut A">A. Rambaut</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Brésil</li></country></list><tree><country name="Brésil"><noRegion><name sortKey="Brandao, Marcelo M" sort="Brandao, Marcelo M" uniqKey="Brandao M" first="Marcelo M." last="Brandão">Marcelo M. Brandão</name></noRegion><name sortKey="Brandao, Marcelo M" sort="Brandao, Marcelo M" uniqKey="Brandao M" first="Marcelo M." last="Brandão">Marcelo M. Brandão</name><name sortKey="Faria, Luzinete C B" sort="Faria, Luzinete C B" uniqKey="Faria L" first="Luzinete C. B." last="Faria">Luzinete C. B. Faria</name><name sortKey="Palazzo, Reginaldo" sort="Palazzo, Reginaldo" uniqKey="Palazzo R" first="Reginaldo" last="Palazzo">Reginaldo Palazzo</name><name sortKey="Rocha, Andrea S L" sort="Rocha, Andrea S L" uniqKey="Rocha A" first="Andréa S. L." last="Rocha">Andréa S. L. Rocha</name><name sortKey="Silva Filho, Marcio C" sort="Silva Filho, Marcio C" uniqKey="Silva Filho M" first="Marcio C." last="Silva-Filho">Marcio C. Silva-Filho</name><name sortKey="Spoladore, Larissa" sort="Spoladore, Larissa" uniqKey="Spoladore L" first="Larissa" last="Spoladore">Larissa Spoladore</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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