Reconstruction of Segmental Duplication Rates and Associated Genomic Features by Network Analysis

Segmental duplications are long genomic duplications that are fixed in a genome. Segmental duplications play an important evolutionary role because entire genes can be duplicated along with regulatory sequences. The ancestral segmental duplications of the human lineage gave rise to genes that are involved in the development of the human brain and provided sites for further genomic rearrangements. While some duplicated loci have been extensively studied, the universal principles and biological factors underlying the spread of segmental duplications remain unclear. Here, we represent segmental duplications in a network, with edges corresponding to duplication events and nodes corresponding to affected genomic sites. This representation allowed us to estimate how many duplications had occurred at each locus, and thereby enabling the prediction of genomic features associated with increased duplication rates. Our comprehensive study of genomic features associated with duplications and those associated with increased duplication rates allowed us to identify several biological factors affecting a segmental duplication process. In our study, we describe genomic features associated with increased duplication rates, three signatures of the duplication process and associations of segmental duplications with different classes of high-copy repeats. Furthermore our method is readily implemented and can easily be applied to segmental duplications of other genomes to build a network of segmental duplications or to predict real duplication events.