title: Ancient DNA sequence revealed by error-correcting codes.
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 Arabidopsis thaliana 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. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.
authors.affiliation: 1] Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil [2] Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13400-918, Piracicaba, SP, Brazil.
authors.forename: Marcelo M
authors.initials: MM
authors.lastname: Brandão
authors.affiliation: Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13400-918, Piracicaba, SP, Brazil.
authors.forename: Larissa
authors.initials: L
authors.lastname: Spoladore
authors.affiliation: Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas, 13081-970, Campinas, SP, Brazil.
authors.forename: Luzinete C B
authors.initials: LC
authors.lastname: Faria
authors.affiliation: Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas, 13081-970, Campinas, SP, Brazil.
authors.forename: Andréa S L
authors.initials: AS
authors.lastname: Rocha
authors.affiliation: Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13400-918, Piracicaba, SP, Brazil.
authors.forename: Marcio C
authors.initials: MC
authors.lastname: Silva-Filho
authors.affiliation: Departamento de Telemática, Faculdade de Engenharia Elétrica e de Computação, Universidade Estadual de Campinas, 13081-970, Campinas, SP, Brazil.
authors.forename: Reginaldo
authors.initials: R
authors.lastname: Palazzo
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000201:enzymology / Q000235:genetics; D001499:Bayes Theorem; D003062:Codon; D004247:DNA / Q000032:analysis* / Q000737:chemistry; D019143:Evolution, Molecular; D008291:Malate Dehydrogenase / Q000145:classification / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
chemical_list: D003062:Codon; D004247:DNA; D008291:Malate Dehydrogenase