Origin and evolution of genes and genomes. Crucial role of triplet expansions

Abstract

A novel concept on mechanisms of evolution of genes and genomes is suggested: the sequences evolve largely by local events of triplet expansion and subsequent mutational changes in the repeats. The immediate memory about the earlier expansion events still resides in the sequences, in form of the frequently occurring segments of tandemly repeating codons. Other predicted fossils of the original repeats are: (I) the expanding triplets should be accompanied by their point mutation derivatives and (II) the remaining excess of codons formerly belonging to the tandem repeats should be reflected in overall codon usage biases. Both predictions are confirmed by analysis of largest available database of non-redundant protein coding sequences, of total size ∼5 × 10⁹ codons. One important conclusion also follows from the results. Life which, presumably, started with replication of expanding triplets and their subsequent mutational changes, is continuing to emerge within the genes and genomes, in form of new events of triplet expansion.

Keywords:

• triplet expansion
• repeats
• codon usage
• gene evolution

Acknowledgements

The work has been supported by Fellowship of SoMoPro (South Moravian Program, Czech Republic) with financial contribution of European Union within the 7th framework program (FP/2007-2013, Grant Agreement No. 229,603), and by the project “CEITEC – Central European Institute of Technology” (CZ.1.05/1.1.00/02.0068) from European Regional Development Fund.