Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications

One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information

Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication

The cause of symmetry is usually subtle, and its study often leads to a deeper understanding of the bearer of the symmetry. To gain insight into the dynamics driving the growth and evolution of genomes, we conducted a comprehensive study of textual symmetries in 786 complete chromosomes. We focused on symmetry based on our belief that, in spite of their extreme diversity, genomes must share common dynamical principles and mechanisms that drive their growth and evolution, and that the most robust footprints of such dynamics are symmetry related. We found that while complement and reverse symmetries are essentially absent in genomic sequences, inverse–complement plus reverse–symmetry is prevalent in complex patterns in most chromosomes, a vast majority of which have near maximum global inverse symmetry. We also discovered relations that can quantitatively account for the long observed but unexplained phenomenon of -mer skews in genomes. Our results suggest segmental and whole-genome inverse duplications are important mechanisms in genome growth and evolution, probably because they are efficient means by which the genome can exploit its double-stranded structure to enrich its code-inventory

Periodic correlation structures in bacterial and archaeal complete genomes

The periodic transference of nucleotide strings in bacterial and archaeal complete genomes is investigated by using the metric representation and the recurrence plot method. The generated periodic correlation structures exhibit four kinds of fundamental transferring characteristics: a single increasing period, several increasing periods, an increasing quasi-period and almost noincreasing period. The mechanism of the periodic transference is further analyzed by determining all long periodic nucleotide strings in the bacterial and archaeal complete genomes and is explained as follows: both the repetition of basic periodic nucleotide strings and the transference of non-periodic nucleotide strings would form the periodic correlation structures with approximately the same increasing periods.Comment: 23 pages, 6 figures, 2 table

Dynamics of transposable elements generates structure and symmetries in genetic sequences

Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a common origin for both features. However, the mechanism leading to this relationship is unknown. Here we investigate a biologically motivated dynamics for the evolution of genetic sequences. We show that a metastable (long-lived) regime emerges in which sequences have symmetry and structure interlaced in a way that matches that of extant genomes.Comment: 6 pagesm 4 figure

CA-NEAT: Evolved Compositional Pattern Producing Networks for Cellular Automata Morphogenesis and Replication

Cellular Automata (CA) are a remarkable example of morphogenetic system, where cells grow and self-organise through local interactions. CA have been used as abstractions of biological development and artificial life. Such systems have been able to show properties that are often desirable but difficult to achieve in engineered systems, e.g. morphogenesis and replication of regular patterns without any form of centralized coordination. However, cellular systems are hard to program (i.e. evolve) and control, especially when the number of cell states and neighbourhood increase. In this paper, we propose a new principle of morphogenesis based on Compositional Pattern Producing Networks (CPPNs), an abstraction of development that has been able to produce complex structural motifs without local interactions. CPPNs are used as Cellular Automata genotypes and evolved with a NeuroEvolution of Augmenting Topologies (NEAT) algorithm. This allows complexification of genomes throughout evolution with phenotypes emerging from self-organisation through development based on local interactions. In this paper, the problems of 2D pattern morphogenesis and replication are investigated. Results show that CA-NEAT is an appropriate means of approaching cellular systems engineering, especially for future applications where natural levels of complexity are targeted. We argue that CA-NEAT could provide a valuable mapping for morphogenetic systems, beyond cellular automata systems, where development through local interactions is desired

Complexity, BioComplexity, the Connectionist Conjecture and Ontology of Complexity\ud

This paper develops and integrates major ideas and concepts on complexity and biocomplexity - the connectionist conjecture, universal ontology of complexity, irreducible complexity of totality & inherent randomness, perpetual evolution of information, emergence of criticality and equivalence of symmetry & complexity. This paper introduces the Connectionist Conjecture which states that the one and only representation of Totality is the connectionist one i.e. in terms of nodes and edges. This paper also introduces an idea of Universal Ontology of Complexity and develops concepts in that direction. The paper also develops ideas and concepts on the perpetual evolution of information, irreducibility and computability of totality, all in the context of the Connectionist Conjecture. The paper indicates that the control and communication are the prime functionals that are responsible for the symmetry and complexity of complex phenomenon. The paper takes the stand that the phenomenon of life (including its evolution) is probably the nearest to what we can describe with the term “complexity”. The paper also assumes that signaling and communication within the living world and of the living world with the environment creates the connectionist structure of the biocomplexity. With life and its evolution as the substrate, the paper develops ideas towards the ontology of complexity. The paper introduces new complexity theoretic interpretations of fundamental biomolecular parameters. The paper also develops ideas on the methodology to determine the complexity of “true” complex phenomena.\u

Conspiracy in bacterial genomes

The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two parabolically) from the total GC content. The rank ordered distribution of the amino acids is fitted by a straight line. The Shannon entropy computed over all the codons is well fitted by a parabola in the GC content, while the partial entropies computed over subsets of the codons show peculiar different behavior, exhibiting therefore a first conspiracy effect. Moreover the sum of the codon usage frequencies over particular sets, e.g. with C and A (respectively G and U) as i-th nucleotide, shows a clear linear dependence from the GC content, exhibiting another conspiracy effect.Comment: revised version: introduction and conclusion enhanced, references added, figures added, some tables remove