Comparative analysis of Alu repeats in primate genomes

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.Alu repeats are primate-specific short interspersed sequence elements (SINEs), ∼300 nt in length, propagating within a genome through retrotransposition (Schmid 1996). They are the most abundant repeat sequences found in humans, with more than 1.1 million copies accounting for ∼10% of the human genome sequence (Lander et al. 2001). Recent work increasingly recognizes that Alu elements have a greater impact than expected on phenotypic change, diseases, and evolution. Alu elements were demonstrated to mediate insertion mutagenesis, “exonization” by alternative splicing, genomic rearrangements, segmental duplication, and expression regulation causing disorders like Hunter syndrome, hemophilia A, and Sly syndrome (Batzer and Deininger 2002). The oldest Alu elements were estimated to emerge either coincident with or immediately after the radiation of primates. Based on Alu subfamily sequence diversity, a major burst in Alu amplification was estimated to have occurred 25–50 million years ago (Mya) (Shen et al. 1991). Younger Alu repeat elements have emerged in the hominoid, although the rate of more recent retrotransposition events has declined (Batzer and Deininger 2002). Owing to their unidirectional mode of evolution, SINE insertions have been used as largely homoplasy-free character states in cladistic analyses of primates (Schmitz et al. 2001; Roos et al. 2004). Alu insertion loci have also been used to clarify relationships among New World monkeys (NWM), Old World monkeys (OWM), and the human–chimpanzee–gorilla trichotomy (Salem et al. 2003; Ray and Batzer 2005; Ray et al. 2005; Xing et al. 2005).Alu elements in human lineage have been extensively characterized (Batzer and Deininger 2002). They are divided into subfamilies based on the extent of sequence diversity and diagnostic mutations (Britten et al. 1988; Jurka and Smith 1988). The monomeric repeats (such as FAM, FRAM, and FLAM) are the oldest Alu-related elements derived from the 7SL RNA gene. The more recent dimeric Alu elements consist of two similar but not identical monomers with a short adenine-rich linker between the two monomers and a longer and more variable A-rich region at the 3′-end. The various dimeric Alu subfamilies have been identified in different evolutionary ages with overlap. AluJo and AluJb are the most ancient Alu dimeric subfamilies. AluS represents the major burst of Alu elements, which contains subfamilies such as Sx, Sp, Sq, Sg, and Sc, with Sx being the most common. AluY is the youngest subfamily in the hominoid lineage, which continues to retrotranspose, and is subsequently polymorphic in the population. Pevzner and colleagues identified 213 human Alu subfamilies at a much finer resolution using a novel method (Alucode) (Price et al. 2004). This method first split Alu subfamilies based on “biprofiles,” that is, linkage of pairs of nucleotide values, and then used the calibration of Alu mutation rates to split subfamilies containing overrepresented individual mutations. These observations generally support the master-gene hypothesis for Alu amplifications, i.e., Alu subfamilies originated through successive waves of fixation from sequential small subsets of master elements (Batzer and Deininger 2002).To date, genome-wide characterization of Alu repeats in nonhuman primates has been limited to chimpanzee and macaque (The Chimpanzee Sequencing and Analysis Consortium 2005; Gibbs et al. 2007). Most chimpanzee-specific elements belong to a subfamily (AluYc1) that is very similar to the source gene in the human–chimpanzee last common ancestor. In macaque, Alu elements have evolved into four currently active lineages: AluYRa1-4, AluYRb1-4, AluYRc1-2, and AluYRd1-4 (Han et al. 2007). Currently, there are three macaque consensus sequences: AluMacYa3, AluMacYb2, and AluMAcYb4 in Repbase (Version 13.5). For other primate genomes, most studies have been based on PCR cross-amplification among diverse primate taxa and, therefore, are potentially biased to either conserved regions or limited to closely related species. Ray and Batzer (2005) recovered 48 NWM-specific Alu elements using a combination of PCR and computational approaches and reported three NWM-specific subfamilies: AluTa7, AluTa10, and AluTa1. In another publication, Herke et al. (2007) reported a few loci (such as {"type":"entrez-nucleotide","attrs":{"text":"DQ822065","term_id":"112418420","term_text":"DQ822065"}}DQ822065) from the lemur derived from PCR display. Initial comparative analysis based on small samples of primate genomic sequences demonstrated that the fixation rates of retroelements (especially SINE/Alu) vary radically in different primate lineages (Liu et al. 2003; Hedges et al. 2004). In this study, we analyze Alu elements in randomly sampled BAC end sequences (BES) and finished genomic sequence alignments (ALN) from five nonhuman primates—lemur, marmoset, macaque, baboon, and chimpanzee—using two distinct approaches combining mutation profile and insertion/deletion analysis. The five species, including great apes (chimpanzee), OWM (baboon and macaque), NWM (marmoset), and prosimians (lemur), are estimated to have diverged from humans at distant time points, ∼6, 25, 25, 35, and 55 Mya, respectively (Goodman 1999). Thus, this spectrum of the taxa provides a vista of Alu-element changes at different nodes during primate evolution.