The driving force behind genomic diversity

The driving force behind genomic diversity Salla Jaakkola1, Sedeer El-Showk1, Arto Annila1,2,3,* 1Department of Biosciences, 2Institute of Biotechnology and 3Department of Physics, FI-00014 University of Helsinki, Finland Abstract Eukaryote genomes contain excessively introns, inter-genic and other non-genic sequences that appear to have no vital functional role or phenotype manifestation. Their existence, a long-standing puzzle, is viewed from the principle of increasing entropy. According to thermodynamics of open systems, genomes evolve toward diversity by various mechanisms that increase, decrease and distribute genomic material in response to thermodynamic driving forces. Evolution results in an excessive genome, a high-entropy ecosystem of its own, where copious non-coding segments associate with low-level functions and conserved sequences code coordinated activities. The rate of entropy increase, equivalent to the rate of free energy decrease, is identified with the universal fitness criterion of natural selection that governs populations of genomic entities as well as other species. Keywords: Entropy; Evolution; Junk DNA; Natural process; Natural selection; Selfish DNA The discovery of mobile genetic elements by McClintock in the 1940s and introns by Sharp and Roberts in 1977 challenged the once predominant view of a genome as a plain repository of biological information [1,2,3]. Since then, many mechanisms have been found - particularly in eukaryotes - which are capable of increasing, decreasing and redistributing genomic material [4] beyond simple insertion and deletion; examples include gene duplication, transfer of genetic material, polyploidy, genesis of genes [5], exon shuffling [6], intron gain and loss [7,8]. Despite increasing understanding of evolutionary mechanisms that shape the genome, the vast amount of non-coding sequences such as B-chromosomes, pseudogenes, transposons, short repeats, introns and miscellaneous unique sequences, remains perplexing. Also it is puzzling, why the size of genome does not correlate with the complexity of an organism [4]. The selfish DNA theory takes a bold stance by picturing all sequences as replicating entities in mutual competition for survival [9,10,11]. The view of a genome as an ecosystem of its own is insightful and consistent with the theory of evolution by natural selection [12]. Obviously the genome is open to external influence, e.g., affecting allele frequencies but the genome-centric view, despite considering externalities only implicitly, provides understanding to the evolution of a genome toward diversity. In this study we consider the possibility that genomes are driven to the diversity of sequences in the quest of increasing entropy. The general thermodynamic principle underlies many spontaneous phenomena that are referred to as natural processes [13]. Since no system, irrespective of its evolutionary mechanisms, can escape the 2nd law of thermodynamics, also processes in a genome should be described as diminishing potential energy differences, i.e., as consuming free energy in interactions. This is the essence of theory of evolution by natural selection [12] that was recently formulated in thermodynamic terms [14] to account for diverse natural phenomena and puzzle of nature [15,16,17]. We consider the imperative of increasing entropy as a sufficient reason to explain why genomes organize into nested hierarchies of diverse sequences and display skewed distributions of coding and non-coding sequences. 1. Genome as a thermodynamic system The 2nd law of thermodynamics merely states that potential energy differences tend to vanish in mutual interactions. Increase in entropy means dispersal of energy, not univocally increasing disorder as is often erroneously assumed. The principle of increasing entropy makes no difference between abiotic and biotic, although we tend to label as living those systems that attain and maintain high- entropy non-equilibrium states by coupling to external 2 energy. The external energy provides the potential gradient that is consumed in raising the concentrations of complex entities, such as genes, beyond those at equilibrium. The complex just as simple entities are mechanisms that diminish the potential energy differences in interactions. They exist due to their functional properties that contribute to the consumption of free energy in the quest for stationary state in their surroundings. Now that the 2nd law of thermodynamics has been formulated as an equation of motion [14], an evolutionary course, such as growth of a genome, can be understood and simulated. The evolution of a genome can be regarded as an energy-powered dissipative motion via chemical reactions. The seemingly dull quest for increased entropy is in fact a highly functional criterion. It selects from diverse energy transduction mechanisms those that will consume free energy most rapidly. Genes associate with powerful energy tra

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