title: Circular code motifs in genomes of eukaryotes.
abstract: A set X of 20 trinucleotides was identified in genes of bacteria, eukaryotes, plasmids and viruses, which has in average the highest occurrence in reading frame compared to its two shifted frames (Michel, 2015; Arquès and Michel, 1996). This set X has an interesting mathematical property as X is a circular code (Arquès and Michel, 1996). Thus, the motifs from this circular code X, called X motifs, have the property to always retrieve, synchronize and maintain the reading frame in genes. In this paper, we develop several statistical analyzes of X motifs in 138 available complete genomes of eukaryotes in which genes as well as non-gene regions are examined. Large X motifs (with lengths of at least 15 consecutive trinucleotides of X and compositions of at least 10 different trinucleotides of X among 20) have the highest occurrence in genomes of eukaryotes compared to its 23 large bijective motifs, its two large permuted motifs and large random motifs. The largest X motifs identified in eukaryotic genomes are presented, e.g. an X motif in a non-gene region of the genome Solanum pennellii with a length of 155 trinucleotides (465 nucleotides) and an expectation E=10(-71). In the human genome, the largest X motif occurs in a non-gene region of the chromosome 13 with a length of 36 trinucleotides and an expectation E=10(-11). X motifs in non-gene regions of genomes could be evolutionary relics of primitive genes using the circular code for translation. However, the proportion of X motifs (with lengths of at least 10 consecutive trinucleotides of X and compositions of at least 5 different trinucleotides of X among 20) in genes/non-genes of the 138 complete eukaryotic genomes is about 8. Thus, the X motifs occur preferentially in genes, as expected from the previous works of 20 years.
authors.affiliation: Theoretical bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France. Electronic address: kelsoufi@unistra.fr.
authors.forename: Karim
authors.initials: K
authors.lastname: El Soufi
authors.affiliation: Theoretical bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France. Electronic address: c.michel@unistra.fr.
authors.forename: Christian J
authors.initials: CJ
authors.lastname: Michel
mesh_terms: D004270:DNA, Circular; D056890:Eukaryota / Q000235:genetics*; D016678:Genome / Q000235:genetics; D059372:Nucleotide Motifs / Q000235:genetics*; D016364:Reading Frames / Q000235:genetics
chemical_list: D004270:DNA, Circular
keywords: Bijective transformation circular code; Circular code; Circular code motifs; Genomes of eukaryotes; Permuted circular code