Abstract
BackgroundSegmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copies in a genome. There are several well-studied mechanisms responsible for segmental duplications: non-allelic homologous recombination, non-homologous end joining and replication slippage. Such duplications play an important role in evolution, however, we do not have a full understanding of the dynamic properties of the duplication process.ResultsWe study segmental duplications through a graph representation where nodes represent genomic regions and edges represent duplications between them. The resulting network (the SD network) is quite complex and has distinct features which allow us to make inference on the evolution of segmantal duplications. We come up with the network growth model that explains features of the SD network thus giving us insights on dynamics of segmental duplications in the human genome. Based on our analysis of genomes of other species the network growth model seems to be applicable for multiple mammalian genomes.ConclusionsOur analysis suggests that duplication rates of genomic loci grow linearly with the number of copies of a duplicated region. Several scenarios explaining such a preferential duplication rates were suggested.
Highlights
Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity
In the remainder of the text we will denote genomic regions that correspond to nodes of the SD network as duplicated regions and will associate network characteristics to those regions directly, for example, we consider a number of neighbors of a node as a node degree of the corresponding duplicated region
Through our mathematical considerations we were able to identify a model that can while making minimal assumptions on the general dynamics reproduce the network characteristics of the SD network
Summary
Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. There are several well-studied mechanisms responsible for segmental duplications: non-allelic homologous recombination, non-homologous end joining and replication slippage. Such duplications play an important role in evolution, we do not have a full understanding of the dynamic properties of the duplication process. Segmental duplications (SDs) are conventionally defined as long duplications of a genomic region (> 1 kbp) within one genome and with a relatively high level of sequence identity (> 90%). Segmental duplications should not be confused with simple genomic repeats which are present in higher copy number, are usually shorter, and have other mechanisms of propagation in a genome (Sup. Figure 1).
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