Universal Global Imprints of Genome Growth and Evolution – Equivalent Length and Cumulative Mutation Density

Abstract

BackgroundSegmental duplication is widely held to be an important mode of genome growth and evolution. Yet how this would affect the global structure of genomes has been little discussed.Methods/Principal FindingsHere, we show that equivalent length, or , a quantity determined by the variance of fluctuating part of the distribution of the -mer frequencies in a genome, characterizes the latter's global structure. We computed the s of 865 complete chromosomes and found that they have nearly universal but (-dependent) values. The differences among the of a chromosome and those of its coding and non-coding parts were found to be slight.ConclusionsWe verified that these non-trivial results are natural consequences of a genome growth model characterized by random segmental duplication and random point mutation, but not of any model whose dominant growth mechanism is not segmental duplication. Our study also indicates that genomes have a nearly universal cumulative “point” mutation density of about 0.73 mutations per site that is compatible with the relatively low mutation rates of (15)10/site/Mya previously determined by sequence comparison for the human and E. coli genomes.

Human–chimpanzee alignment: Ortholog exponentials and paralog power laws

“…The quantitative study of monoscale substitution/duplication dynamics was revitalised by the work of H.C. Lee and collaborators with their apt characterisation of "nature as the blind plagiariser" [6]. Although these authors did not investigate the steady state duplication length distributions yielded by their models, subsequent research revealed that similar classes of models yield algebraic length distributions that resemble those often exhibited by duplicated sequence in self-alignment and self-intersection of natural genomes [9,16,24].…”

Fractal genome sequences

“…The individual differences between the GA-sequences suggest that point mutations and other scrambling influences have also been instrumental in shaping the blocks. In this sense, the self-similar GA-blocks seem to be good candidates for the mechanisms suggested by Chen et al (2010). Nevertheless, the individual members of each block are very different from each other and may point to a special, not yet known mechanism to generate the specific spectrum of sequence properties that characterized each block pattern.…”

“…Even purely mathematical models have successfully joined the debate among geneticists and added most valuable insights into the roles of oligomers, duplications, point mutations, deletions in shaping genomes during evolutionary times (Chen et al, 2010;Messer et al, 2005;Hsieh et al, 2003). We should like to add inversions and inverted transpositions as major factors to the list as they can explain the universal strand symmetry (Albrecht-Buehler, 2006).…”

Primary orthologs from local sequence context

“…To evaluate the effectiveness of the method introduced in section 2.3 under certain models of genome evolution, we implement a series of numerical simulations with a "genome growth model" that is characterized by two dynamical elements only: random segmental duplication and random point substitution; obviously, evolutionary selection is absent from these dynamics. This model was earlier proposed by Chen et al; by "growth model" the authors referred to "a computer algorithm for generating, from an initial sequence, a target sequence that has a given profile and other specific genome-like attributes" (Chen et al 2010). In 2013, Massip and Arndt (Massip and Arndt 2013; see also Koroteev and Miller, unpublished data, http://arxiv.org/abs/1304.1409v3, last accessed October 29, 2013) reported that such a model yields repetitive sequences within a single genome whose length distribution at stationarity resembles those observed in natural genomes (Gao and Miller 2011; see also Koroteev and Miller 2011).…”

“…The common ancestor's genome was generated from a 4-base random sequence of length L =10 ! nucleotide bases by a genome growth model(Chen et al 2010) with parameters m/n = 0.01(Massip and Arndt 2013); starting from this common ancestor's genome, two subsequent lineages evolve independently: within each time unit, m random segmental duplications of length K=1000 nucleotides and n random point substitutions are introduced to each lineage.…”