Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

Abstract

BackgroundAlu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet.ResultsHere we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage. We analyzed 233 Alu insertions in the genome of the olive baboon using locus specific polymerase chain reaction assays, covering 113 of the 129 subfamilies. The allele frequency data from these insertions show that none of the nine groups of subfamilies are nearing fixation in the lineage.ConclusionsMany subfamilies of Alu elements are actively mobilizing throughout the baboon lineage, with most being specific to the baboon lineage.Electronic supplementary materialThe online version of this article (10.1186/s13100-018-0115-6) contains supplementary material, which is available to authorized users.

Comparative genomics analysis reveals high levels of differential DNA transposition among primates

“…The number of SS-SINEs and most recent SS-SINEs in this genome is more than 4 times higher than the genome average (Table S5), reflecting SINEs being extremely successful in this genome. This confirms the previous observation that SINEs are quite active in the baboon genome (Steely, et al 2018). By the average numbers of both SS-MEs and most recent SS-MEs, SINEs are more successful in the Cercopithecidae group than in the Hominidae group, while LINEs showed an opposite trend (Table S5).…”

“…So far, only very limited comparative analyses involving a small number of genomes have been reported. Among these, the work by Mills et al (Mills, et al 2006) compared the ME profile between human and chimpanzee, and a recent study has focused on lineage-specific Alu subfamilies in the baboon genome (Steely, et al 2018). Due to the challenges described above, a large scale systematic comparative analysis of mobile elements in primate genomes still represents a gap in the field.…”

“…Despite more and more non-human primate genomes have been sequenced and assembled in the recent years, prior studies on DNA transposition have mostly focused on the analysis of ME profiles for individual genomes separately (Battilana, et al 2006;Ewing and Kazazian 2011;Jha, et al 2009;Jordan, et al 2018;Mills, et al 2006;Ray, et al 2005;Steely, et al 2018;Stewart, et al 2011;Tang, et al 2018;Wang, et al 2006). So far, only very limited comparative analyses involving a small number of genomes have been reported.…”

“…Other studies focused on species-specific MEs target on either one particular ME type and/or a few primate genomes. For example, Steely and colleague have recently ascertained 28,114 baboon-specific Alu elements by comparing the genomic sequences of baboon to both rhesus macaque and human genomes (Steely, et al 2018).…”

The comparative genomics and complex population history ofPapiobaboons

“…A computational analysis was performed to identify full-length lineage specific Alu Y sequences in the olive baboon (Panu_3.0), rhesus macaque (Mmul_8.0.1), African green monkey (chlSab2), orangutan (P_pygmaeus 2.0.2), chimpanzee (Pan_tro3), and human (GRCH38/hg38) reference genomes, as previously described by Steely et al ( 53 ).…”