The repetitive DNA landscape in sheep

Repetitive DNA sequences, representing the majority of most mammalian genomes, can be broadly divided into tandemly repeated or satellite sequences (mostly located in the heterochromatin) and transposable elements (TEs) dispersed over the genome. Some repetitive DNA sequences are highly conserved but other sequences show substantial diversification in copy number, sequence and organization between individuals, breeds, and related species. Here, we report the repetitive DNA landscape of sheep (Ovis aries) based on de novo analysis of >6Gbp of sequence from each of five individuals. Major classes of repetitive DNA sequences were identified and quantified by network analysis (using the program RepeatExplorer), frequency analysis of short motifs (K-mers), and alignment to reference genome assemblies. The genomic organization of the major repetitive motifs was characterized by in situ hybridization to chromosomes. The well-known c. 816 bplong centromere-associated satellite SatI represented 4 to 6 % of the genome while SatII (c. 600 bp long) was 1 to 2 % of the genome. Notably, these satellites showed contrasting behaviour at meiotic prophase: Sat I sequences cover a larger area indicating a looser chromatin loop organization. While, Sat II sequences are tightly organized and are attached to the synaptonemal complex (SC) at a more distal position than SatI sequences at the end of SCs of acrocentric chromosomes. The repetitive sequence analysis identified other much less abundant satellite sequences and simple repeats, some with novel genomic distributions. Families of non-LTR retrotransposons including LINEs (L1 and RTE) and derived SINEs represented more than 25 % of the genome. Non-LTR families showed characteristic distributions on chromosomes with some showing greater abundance on metacentric autosomes or on sex chromosomes. Endogenous retrovirus classes grouped into clusters with some families showing centromeric and others more dispersed distributions. Rapidly evolving repetitive sequences allow us to study processes of chromosome or genome evolution and diversification in sheep, and more broadly across the Bovidae.