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Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences.

ABSTRACT: Since the sequencing of large genomes, many statistical features of their sequences have been found. One intriguing feature is that certain subsequences are much more abundant than others. In fact, abundances of subsequences of a given length are distributed with a scale-free power-law tail, resembling properties of human texts, such as Zipf's law. Despite recent efforts, the understanding of this phenomenon is still lacking. Here we find that selfish DNA elements, such as those belonging to the Alu family of repeats, dominate the power-law tail. Interestingly, for the Alu elements the power-law exponent increases with the length of the considered subsequences. Motivated by these observations, we develop a model of selfish DNA expansion. The predictions of this model qualitatively and quantitatively agree with the empirical observations. This allows us to estimate parameters for the process of selfish DNA spreading in a genome during its evolution. The obtained results shed light on how evolution of selfish DNA elements shapes non-trivial statistical properties of genomes.

SUBMITTER: Sheinman M

PROVIDER: S-EPMC4973250 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences.

Sheinman Michael M Ramisch Anna A Massip Florian F Arndt Peter F PF

Scientific reports 20160804

Since the sequencing of large genomes, many statistical features of their sequences have been found. One intriguing feature is that certain subsequences are much more abundant than others. In fact, abundances of subsequences of a given length are distributed with a scale-free power-law tail, resembling properties of human texts, such as Zipf's law. Despite recent efforts, the understanding of this phenomenon is still lacking. Here we find that selfish DNA elements, such as those belonging to the ...[more]

PMID: 27488939

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Project description:BackgroundWhole genome duplication (WGD) and tandem duplication (TD) provide two critical sources of raw genetic material for genome complexity and evolutionary novelty. Little is known about the complexity of the Sesamum indicum genome after it diverged from a common ancestor with the paleodiploid Vitis vinifera and further experienced WGD and TD events.ResultsHere, we analyzed the functional divergence of different classes of inter- and intra-genome gene pairs from ancestral events to uncover multiple-layers of evolutionary dynamics acting during the process of forming the modern S. indicum genome. Comprehensive inter-genome analyses revealed that 60% and 70% of syntenic orthologous gene pairs were retained among the two subgenomes in S. indicum compared to V. vinifera, although there was no evidence of significant differences under selection pressure. For the intra-genomic analyses, 5,932 duplicated gene pairs experienced fractionation, with the remaining 1,236 duplicated gene pairs having undergone functional divergence under diversifying selection. Analysis of the TD events indicated that 2,945 paralogous gene pairs, from 1,089 tandem arrays of 2-16 genes, experienced functional divergence under diversifying selection. Sequence diversification of different classes of gene pairs revealed that most of TD events occurred after the WGD event, with others following the ancestral gene order indicating ancient TD events at some time prior to the WGD event. Our comparison-of-function analyses for different classes of gene pairs indicated that the WGD and TD evolutionary events were both responsible for introducing genes that enabled exploration of novel and complementary functionalities, whilst maintaining individual plant ruggedness.ConclusionsIn this study, we first investigated functional divergence of different classes of gene pairs to characterize the dynamic processes associated with each evolutionary event in S. indicum. The data demonstrated massive and distinct functional divergence among different classes of gene pairs, and provided a genome-scale view of gene function diversification explaining the complexity of the S. indicum genome. We hope this provides a biological model to study the mechanism of plant species formation, particularly in the context of the evolutionary history of flowering plants, and offers novel insights for the study of angiosperm genomes.

Dataset Information

Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences.

Publications

Evolutionary dynamics of selfish DNA explains the abundance distribution of genomic subsequences.

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