Ancient DNA sequence revealed by error-correcting codes.

Andréa S L Rocha,Marcio C Silva-Filho,Reginaldo Palazzo,Marcelo M Brandão,Larissa Spoladore,Luzinete C B Faria

doi:10.1038/srep12051

Andréa S L Rocha, Marcio C Silva-Filho + Show 4 more

Open Access

https://doi.org/10.1038/srep12051

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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.

Highlights

Code; or 2) it is a sequence belonging to the set of neighboring sequences differing by at least one nucleotide from the corresponding codeword of a G-linear code
In this study the DNA sequence generation algorithm was applied as a computational tool to provide strong evidence of the evolution of the genetic code, in special on nucleotide and amino acid site specific polymorphism, by showing the existence of a mathematical structure underlying the actual DNA sequences and by investigating the real biological meaning of the difference in the specific position pointed out by the code-generated sequences
The code-generated sequences that had a single nucleotide alteration, causing a residue change in the translated protein, were used in a Blastx analysis to verify if the alteration suggested by the error-correcting code (ECC) could be found in other sequences

Summary

Results and Discussion

In this study the DNA sequence generation algorithm was applied as a computational tool to provide strong evidence of the evolution of the genetic code, in special on nucleotide and amino acid site specific polymorphism, by showing the existence of a mathematical structure underlying the actual DNA sequences and by investigating the real biological meaning of the difference in the specific position pointed out by the code-generated sequences. Analyses were run for the code generated sequences of the Saccharomyces YMR193 gene (GI 45269853), the Triticum aestivum wPR4 gene (GI 78096542), the Nicotiana tabacum antifungal CBP 20 gene (GI 632733), the Citrus sinensis chlorophyllase gene (GI 7328566), the Arabidopsis thaliana hevein-like protein PR4 gene (GI 186509758), the Saccharomyces cerevisiae OXA gene (GI 832917) and the Homo sapiens F1F0 ATP-synthase gene (GI 12587). Tables S02.a) S02.b) S02.c) S02.d) S02.e) S02.f ) S02.g) S02.h) S02.i) S02.j) 2a and b 3.a) 3.b) 3.c) 3.d)

DNA sequences

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