Abstract
Eukaryotic genomes are rich in repetitive DNA sequences grouped in two classes regarding their genomic organization: tandem repeats and dispersed repeats. In tandem repeats, copies of a short DNA sequence are positioned one after another within the genome, while in dispersed repeats, these copies are randomly distributed. In this review we provide evidence that both tandem and dispersed repeats can have a similar organization, which leads us to suggest an update to their classification based on the sequence features, concretely regarding the presence or absence of retrotransposons/transposon specific domains. In addition, we analyze several studies that show that a repetitive element can be remodeled into repetitive non-coding or coding sequences, suggesting (1) an evolutionary relationship among DNA sequences, and (2) that the evolution of the genomes involved frequent repetitive sequence reshuffling, a process that we have designated as a “DNA remodeling mechanism”. The alternative classification of the repetitive DNA sequences here proposed will provide a novel theoretical framework that recognizes the importance of DNA remodeling for the evolution and plasticity of eukaryotic genomes.
Highlights
Eukaryotic genomes contain a high diversity of repetitive DNA sequences [1,2]
We suggest that the repetitive sequences should not be divided as tandem repeats and dispersed repeats, once repeats organized in tandem could present a dispersed organization, and vice-versa
Different studies show that a repetitive element can be remodelled into a different sequence, repetitive or not, which proves an evolutionary relationship among DNA sequences, and suggests that the evolution of the genome is characterized by a frequent repetitive sequence reshuffling, a process that we have called a “DNA remodelling mechanism”
Summary
Eukaryotic genomes contain a high diversity of repetitive DNA sequences [1,2]. The amplification/. Despite the increasing evidence pointing to a functional significance of the repetitive DNA fraction, there are still limitations to characterizing their role in different biological processes due to their high diversity, genomic abundance, complex evolution mode, and difficulty in isolation and sequencing [29,30,31]. This review presents a compilation of evidence on the organization and evolutionary relationship between different classes of repetitive sequences, and between repetitive sequences and genes This evidence shows that the classification of repetitive sequences based on its genomic organization as “in tandem” or “dispersed repeats” is not “as black and white”, which reinforces the need for an updated classification. This new way to face the classification and study of the repetitive sequences will contribute to a better understanding of genomic plasticity and its contribution to eukaryotic species evolution and adaptation to environment
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