Short Interrupted Repeats Cassette ensembles of plant nuclear genomes reflect evolutionary route of species

Short Interrupted Repeats Cassettes (SIRCs) are recently discovered eukaryotic DNA elements possessing many traits of satellite DNA and mobile genetic elements, and consisting of short direct repeats interspersed with diverse spacer sequences. The SIRC ensemble of individual species is highly heterogenous and cannot be studied using alignment methods. It was found that number of similar SIRC sequences in a given pair of species is in general correlated with their taxonomic distance, and, at the same time, closely related species can possess very diverged SIRC ensembles, which makes SIRC evolutionary patterns closer to the mobile genetic element type. The SIRC sequences make up clusters with comparable sequence patterns, that are likely to demonstrate the doublet evolutionary model which strongly supports that the SIRC structures are undergoing evolutionary selection. Several SIRC sequences of Arabidopsis were found to be of ancient origin with traceable evolution history as far as to the moss clade. We carried out unbiased detection of SIRC ensembles in 10 plant nuclear genomes and found that, despite very high intraspecies heterogeneity, SIRC sets possess strong interspecies phylogenetic signal. This paper consists of a brief Introduction, Results that reveal the intra- and inter-organismal relationships of the studied sequences, the Discussion section, and the Materials and Methods section that presents the existing bioinformatics approaches used, as well as the development of an R package for the detection of SIRCs.