Lines and SINES in suids: The repetitive genomic landscape in sus scrofa and related pig species

H.J. Megens, R.P.M.A Crooijmans, O. Madsen, Y. Takeuchi, G. Faulkner, C. Rogel-Gaillard, J. Ma, L.B. Schook, M.A.M. Groenen
Plant and Animal Genome XIX Conference, January 15-19, 2011, San Diego, CA


Repetitive DNA elements in genomes are often regarded as a nuisance, though their relevance as a mutational force and role in generation of copy number variation and chromosomal rearrangements has been highlighted in the past decade. The completion of the pig genome offers the opportunity to investigate patterns of evolution of repetitive elements in Sus scrofa in relation to genome architecture. More than 40% of the porcine genome consists of repetitive elements. The largest families of repetitive elements are formed by LINE-1 (L1; ~16% of the genome) and by the SINE family PRE (~11% of the genome). As expected, GC-poor regions are notably enriched in L1, and depleted in PRE elements. Both L1 and PRE show an ancient peak of expansion. PRE activity seems to have gradually declined since then, although thousands of recent PREs are present in the Porcine genome. L1 showed several additional, smaller and more recent expansions. Hence, the amplification rates over time differ between these two major repetitive element families. Complete genomic sequencing of other Suids (a Chinese pig, Sus verucosus, Sus celebensis, Sus barbatus, and Phacochoerus africanus) allowed us to construct a preliminary catalog of transposable element insertion events over time and identify recent insertion sites that may be unique to pigs or certain populations of pigs. This not only allows us to assess a large number of unique events during Suid evolution, but also aids in understanding the dynamics of genome evolution and architecture in the pig.