Comparative analysis of Alu repeats in primate genomes

Abstract

Using bacteria artificial chromosome (BAC) end sequences (16.9 Mb) and high-quality alignments of genomic sequences (17.4 Mb), we performed a global assessment of the divergence distributions, phylogenies, and consensus sequences for Alu elements in primates including lemur, marmoset, macaque, baboon, and chimpanzee as compared to human. We found that in lemurs, Alu elements show a broader and more symmetric sequence divergence distribution, suggesting a steady rate of Alu retrotransposition activity among prosimians. In contrast, Alu elements in anthropoids show a skewed distribution shifted toward more ancient elements with continual declining rates in recent Alu activity along the hominoid lineage of evolution. Using an integrated approach combining mutation profile and insertion/deletion analyses, we identified nine novel lineage-specific Alu subfamilies in lemur (seven), marmoset (one), and baboon/macaque (one) containing multiple diagnostic mutations distinct from their human counterparts-Alu J, S, and Y subfamilies, respectively. Among these primates, we show that that the lemur has the lowest density of Alu repeats (55 repeats/Mb), while marmoset has the greatest abundance (188 repeats/Mb). We estimate that ;70% of lemur and 16% of marmoset Alu elements belong to lineage-specific subfamilies. Our analysis has provided an evolutionary framework for further classification and refinement of the Alu repeat phylogeny. The differences in the distribution and rates of Alu activity have played an important role in subtly reshaping the structure of primate genomes. The functional consequences of these changes among the diverse primate lineages over such short periods of evolutionary time are an important area of future investigation.

Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus

“…These landscape changes in the close vicinity of XIST/Xist further reinforce the malleability of this region, as has been underscored previously by comparisons of the mouse, marsupial, and monotreme genomes (Duret et al 2006;Hore et al 2007b). Interspersed repeats have played a role in differentially shaping primate genomes (Liu 2003;Liu et al 2009), and analysis of total repeat content across this region is in agreement with this conclusion (Table 1). Comparisons of specific classes of repeats in the lemurs and the inferred ancestral primate XIC region indicate that the lemurs and ancestral primate have a lower Alu, MIR, and LINE content relative to the rest of the primates (Table 1), while some of the other repeats tend to fluctuate with lineage-specific trends.…”

Origin and evolution of SINEs in eukaryotic genomes

“…B1 and ID have become inactive in the genomes of rat and mouse, respectively (Rat Genome Sequencing Consortium, 2004). A similar pattern is observed in SINE subfamilies remaining active over different evolutionary periods (Ohshima et al, 2003;Liu et al, 2009). Little is known about the factors that determine their duration, but it can substantially vary.…”

Reading TE leaves: New approaches to the identification of transposable element insertions

“…Researchers familiar with Alu SINEs will be aware that distinct subfamilies of Alu exist in each primate lineage Hedges et al 2004;Otieno et al 2004;Garber et al 2005;Ray and Batzer 2005;Ray et al 2005b;Salem et al 2005b;Han et al 2007;Liu et al 2009;Locke et al 2011). Each of the methods described relies on sequence characteristics unique to particular subfamilies of elements.…”